MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 16 transcript(s)...
Querying Taster for transcript #1: ENST00000373965
Querying Taster for transcript #2: ENST00000395438
Querying Taster for transcript #3: ENST00000409834
Querying Taster for transcript #4: ENST00000395445
Querying Taster for transcript #5: ENST00000395446
Querying Taster for transcript #6: ENST00000395442
Querying Taster for transcript #7: ENST00000395440
Querying Taster for transcript #8: ENST00000361849
Querying Taster for transcript #9: ENST00000395433
Querying Taster for transcript #10: ENST00000373957
Querying Taster for transcript #11: ENST00000320301
Querying Taster for transcript #12: ENST00000395430
Querying Taster for transcript #13: ENST00000373955
Querying Taster for transcript #14: ENST00000414778
Querying Taster for transcript #15: ENST00000395432
Querying Taster for transcript #16: ENST00000437009
MT speed 0 s - this script 3.68936 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PCDH15	polymorphism_automatic	0.97384135263319	simple_aae		affected		D435A	single base exchange	rs4935502		show file
PCDH15	polymorphism_automatic	0.999985873746161	simple_aae		affected		D435A	single base exchange	rs4935502		show file
PCDH15	polymorphism_automatic	0.999985873746161	simple_aae		affected		D435A	single base exchange	rs4935502		show file
PCDH15	polymorphism_automatic	0.999985873746161	simple_aae		affected		D435A	single base exchange	rs4935502		show file
PCDH15	polymorphism_automatic	0.999985873746161	simple_aae		affected		D413A	single base exchange	rs4935502		show file
PCDH15	polymorphism_automatic	0.999985873746161	simple_aae		affected		D413A	single base exchange	rs4935502		show file
PCDH15	polymorphism_automatic	0.999985873746161	simple_aae		affected		D435A	single base exchange	rs4935502		show file
PCDH15	polymorphism_automatic	0.999985873746161	simple_aae		affected		D435A	single base exchange	rs4935502		show file
PCDH15	polymorphism_automatic	0.999985873746161	simple_aae		affected		D435A	single base exchange	rs4935502		show file
PCDH15	polymorphism_automatic	0.999985873746161	simple_aae		affected		D440A	single base exchange	rs4935502		show file
PCDH15	polymorphism_automatic	0.999985873746161	simple_aae		affected		D398A	single base exchange	rs4935502		show file
PCDH15	polymorphism_automatic	0.99999834599429	simple_aae		affected		D435A	single base exchange	rs4935502		show file
PCDH15	polymorphism_automatic	0.99999834599429	simple_aae		affected		D435A	single base exchange	rs4935502		show file
PCDH15	polymorphism_automatic	0.99999911106933	simple_aae		affected		D39A	single base exchange	rs4935502		show file
PCDH15	polymorphism_automatic	0.999999464692363	simple_aae		affected		D435A	single base exchange	rs4935502		show file
PCDH15	polymorphism_automatic	1	without_aae					single base exchange	rs4935502		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0261586473668097 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:55955444T>GN/A show variant in all transcripts IGV

HGNC symbol

PCDH15

Ensembl transcript ID

ENST00000437009

Genbank transcript ID

NM_001142765

UniProt peptide

Q96QU1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1304A>C
cDNA.1699A>C
g.1432259A>C

AA changes

D435A Score: 126 explain score(s)

position(s) of altered AA
if AA alteration in CDS

435

frameshift

known variant

Reference ID: rs4935502

database	homozygous (G/G)	heterozygous	allele carriers
1000G	481	767	1248
ExAC	5615	17649	23264

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.245	1
	4.774	1
(flanking)	5.784	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	1432260	sequence motif lost	-	wt: AGAT\|gtaa mu: AGCT.gtaa
Donor marginally increased	1432252	wt: 0.9798 / mu: 0.9914 (marginal change - not scored)	wt: AGGACATAGAAGATG mu: AGGACATAGAAGCTG	GACA\|taga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

435

mutated

not conserved

435

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000009794

549

Fcatus

not conserved

ENSFCAG00000010122

435

Mmusculus

not conserved

ENSMUSG00000052613

554

Ggallus

all conserved

ENSGALG00000002744

383

Trubripes

all conserved

ENSTRUG00000010819

424

Drerio

not conserved

ENSDARG00000008127

497

DDGPNGLVS

Dmelanogaster

all identical

FBgn0039709

427

Celegans

not conserved

F15B9.7

302

Xtropicalis

not conserved

ENSXETG00000018945

500

protein features

start (aa)	end (aa)	feature	details
27	1376	TOPO_DOM	Extracellular (Potential).	lost
396	509	DOMAIN	Cadherin 4.	lost
467	467	CONFLICT	Q -> L (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
510	616	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
559	559	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
617	717	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
662	662	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
719	819	DOMAIN	Cadherin 7.	might get lost (downstream of altered splice site)
724	724	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
768	768	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
820	926	DOMAIN	Cadherin 8.	might get lost (downstream of altered splice site)
821	821	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
851	851	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
927	1035	DOMAIN	Cadherin 9.	might get lost (downstream of altered splice site)
1037	1144	DOMAIN	Cadherin 10.	might get lost (downstream of altered splice site)
1064	1064	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1084	1084	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1145	1259	DOMAIN	Cadherin 11.	might get lost (downstream of altered splice site)
1175	1175	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1276	1276	CONFLICT	Q -> R (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
1377	1397	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1398	1955	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1435	1443	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1746	1752	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1815	1823	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1826	1831	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5661 / 5661

position (AA) of stopcodon in wt / mu AA sequence

1887 / 1887

position of stopcodon in wt / mu cDNA

6056 / 6056

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

396 / 396

chromosome

strand

-1

last intron/exon boundary

4555

theoretical NMD boundary in CDS

4109

length of CDS

5661

coding sequence (CDS) position

1304

cDNA position
(for ins/del: last normal base / first normal base)

1699

gDNA position
(for ins/del: last normal base / first normal base)

1432259

chromosomal position
(for ins/del: last normal base / first normal base)

55955444

original gDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT

altered gDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT

original cDNA sequence snippet

TCTGGACAAGGACATAGAAGATACAAAAGACCCAGAGCTTC

altered cDNA sequence snippet

TCTGGACAAGGACATAGAAGCTACAAAAGACCCAGAGCTTC

wildtype AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEDTKDPE LHLFLNDYTS VFTVTQTGIT RYLTLLQPVD REEQQTYTFS
ITAFDGVQES EPVIVNIQVM DANDNTPTFP EISYDVYVYT DMRPGDSVIQ LTAVDADEGS
NGEITYEILV GAQGDFIINK TTGLITIAPG VEMIVGRTYA LTVQAADNAP PAERSTGILT
LGKALDREST DRYILIITAS DGRPDGTSTA TVNIVVTDVN DNAPVFDPYL PRNLSVVEEE
ANAFVGQVKA TDPDAGINGQ VHYSLGNFNN LFRITSNGSI YTAVKLNREV RDYYELVVVA
TDGAVHPRHS TLTLAIKVLD IDDNSPVFTN STYTVLVEEN LPAGTTILQI EAKDVDLGAN
VSYRIRSPEV KHFFALHPFT GELSLLRSLD YEAFPDQEAS ITFLVEAFDI YGTMPPGIAT
VTVIVKDMND YPPVFSKRIY KGMVAPDAVK GTPITTVYAE DADPPGLPAS RVRYRVDDVQ
FPYPASIFEV EEDSGRVITR VNLNEEPTTI FKLVVVAFDD GEPVMSSSAT VKILVLHPGE
IPRFTQEEYR PPPVSELATK GTMVGVISAA AINQSIVYSI VSGNEEDTFG INNITGVIYV
NGPLDYETRT SYVLRVQADS LEVVLANLRV PSKSNTAKVY IEIQDENNHP PVFQKKFYIG
GVSEDARMFT SVLRVKATDK DTGNYSVMAY RLIIPPIKEG KEGFVVETYT GLIKTAMLFH
NMRRSYFKFQ VIATDDYGKG LSGKADVLVS VVNQLDMQVI VSNVPPTLVE KKIEDLTEIL
DRYVQEQIPG AKVVVESIGA RRHGDAFSLE DYTKCDLTVY AIDPQTNRAI DRNELFKFLD
GKLLDINKDF QPYYGEGGRI LEIRTPEAVT SIKKRGESLG YTEGALLALA FIIILCCIPA
ILVVLVSYRH FKRRQAECTK TARIQAALPA AKPAVPAPAP VAAPPPPPPP PPGAHLYEEL
GDSSMKGLFL LYHFQQSRGN NSVSEDRKHQ QVVMPFSSNT IEAHKSAHVD GSLKSNKLKS
ARKFTFLSDE DDLSAHNPLY KENISQVSTN SDISQRTDFV DPFSPKIQAK SKSLRGPREK
IQRLWSQSVS LPRRLMRKVP NRPEIIDLQQ WQGTRQKAEN ENTGICTNKR GSSNPLLTTE
EANLTEKEEI RQGETLMIEG TEQLKSLSSD SSFCFPRPHF SFSTLPTVSR TVELKSEPNV
ISSPAECSLE LSPSRPCVLH SSLSRRETPI CMLPIETERN IFENFAHPPN ISPSACPLPP
PPPISPPSPP PAPAPLAPPP DISPFSLFCP PPSPPSIPLP LPPPTFFPLS VSTSGPPTPP
LLPPFPTPLP PPPPSIPCPP PPSASFLSTE CVCITGVKCT TNLMPAEKIK SSMTQLSTTT
VCKTDPQREP KGILRHVKNL AELEKSVANM YSQIEKNYLR TNVSELQTMC PSEVTNMEIT
SEQNKGSLNN IVEGTEKQSH SQSTSL*

mutated AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEATKDPE LHLFLNDYTS VFTVTQTGIT RYLTLLQPVD REEQQTYTFS
ITAFDGVQES EPVIVNIQVM DANDNTPTFP EISYDVYVYT DMRPGDSVIQ LTAVDADEGS
NGEITYEILV GAQGDFIINK TTGLITIAPG VEMIVGRTYA LTVQAADNAP PAERSTGILT
LGKALDREST DRYILIITAS DGRPDGTSTA TVNIVVTDVN DNAPVFDPYL PRNLSVVEEE
ANAFVGQVKA TDPDAGINGQ VHYSLGNFNN LFRITSNGSI YTAVKLNREV RDYYELVVVA
TDGAVHPRHS TLTLAIKVLD IDDNSPVFTN STYTVLVEEN LPAGTTILQI EAKDVDLGAN
VSYRIRSPEV KHFFALHPFT GELSLLRSLD YEAFPDQEAS ITFLVEAFDI YGTMPPGIAT
VTVIVKDMND YPPVFSKRIY KGMVAPDAVK GTPITTVYAE DADPPGLPAS RVRYRVDDVQ
FPYPASIFEV EEDSGRVITR VNLNEEPTTI FKLVVVAFDD GEPVMSSSAT VKILVLHPGE
IPRFTQEEYR PPPVSELATK GTMVGVISAA AINQSIVYSI VSGNEEDTFG INNITGVIYV
NGPLDYETRT SYVLRVQADS LEVVLANLRV PSKSNTAKVY IEIQDENNHP PVFQKKFYIG
GVSEDARMFT SVLRVKATDK DTGNYSVMAY RLIIPPIKEG KEGFVVETYT GLIKTAMLFH
NMRRSYFKFQ VIATDDYGKG LSGKADVLVS VVNQLDMQVI VSNVPPTLVE KKIEDLTEIL
DRYVQEQIPG AKVVVESIGA RRHGDAFSLE DYTKCDLTVY AIDPQTNRAI DRNELFKFLD
GKLLDINKDF QPYYGEGGRI LEIRTPEAVT SIKKRGESLG YTEGALLALA FIIILCCIPA
ILVVLVSYRH FKRRQAECTK TARIQAALPA AKPAVPAPAP VAAPPPPPPP PPGAHLYEEL
GDSSMKGLFL LYHFQQSRGN NSVSEDRKHQ QVVMPFSSNT IEAHKSAHVD GSLKSNKLKS
ARKFTFLSDE DDLSAHNPLY KENISQVSTN SDISQRTDFV DPFSPKIQAK SKSLRGPREK
IQRLWSQSVS LPRRLMRKVP NRPEIIDLQQ WQGTRQKAEN ENTGICTNKR GSSNPLLTTE
EANLTEKEEI RQGETLMIEG TEQLKSLSSD SSFCFPRPHF SFSTLPTVSR TVELKSEPNV
ISSPAECSLE LSPSRPCVLH SSLSRRETPI CMLPIETERN IFENFAHPPN ISPSACPLPP
PPPISPPSPP PAPAPLAPPP DISPFSLFCP PPSPPSIPLP LPPPTFFPLS VSTSGPPTPP
LLPPFPTPLP PPPPSIPCPP PPSASFLSTE CVCITGVKCT TNLMPAEKIK SSMTQLSTTT
VCKTDPQREP KGILRHVKNL AELEKSVANM YSQIEKNYLR TNVSELQTMC PSEVTNMEIT
SEQNKGSLNN IVEGTEKQSH SQSTSL*

speed

0.13 s

All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1.41262538386557e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:55955444T>GN/A show variant in all transcripts IGV

HGNC symbol

PCDH15

Ensembl transcript ID

ENST00000395438

Genbank transcript ID

NM_001142770

UniProt peptide

Q96QU1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1304A>C
cDNA.1699A>C
g.1432259A>C

AA changes

D435A Score: 126 explain score(s)

position(s) of altered AA
if AA alteration in CDS

435

frameshift

known variant

Reference ID: rs4935502

database	homozygous (G/G)	heterozygous	allele carriers
1000G	481	767	1248
ExAC	5615	17649	23264

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.245	1
	4.774	1
(flanking)	5.784	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	1432260	sequence motif lost	-	wt: AGAT\|gtaa mu: AGCT.gtaa
Donor marginally increased	1432252	wt: 0.9798 / mu: 0.9914 (marginal change - not scored)	wt: AGGACATAGAAGATG mu: AGGACATAGAAGCTG	GACA\|taga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

435

mutated

not conserved

435

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000009794

435

Fcatus

not conserved

ENSFCAG00000010122

435

Mmusculus

all identical

ENSMUSG00000052613

440

Ggallus

all conserved

ENSGALG00000002744

383

Trubripes

all conserved

ENSTRUG00000010819

424

Drerio

all conserved

ENSDARG00000008127

383

Dmelanogaster

all identical

FBgn0039709

427

Celegans

not conserved

F15B9.7

415

Xtropicalis

all conserved

ENSXETG00000018945

386

protein features

start (aa)	end (aa)	feature	details
27	1376	TOPO_DOM	Extracellular (Potential).	lost
396	509	DOMAIN	Cadherin 4.	lost
467	467	CONFLICT	Q -> L (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
510	616	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
559	559	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
617	717	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
662	662	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
719	819	DOMAIN	Cadherin 7.	might get lost (downstream of altered splice site)
724	724	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
768	768	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
820	926	DOMAIN	Cadherin 8.	might get lost (downstream of altered splice site)
821	821	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
851	851	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
927	1035	DOMAIN	Cadherin 9.	might get lost (downstream of altered splice site)
1037	1144	DOMAIN	Cadherin 10.	might get lost (downstream of altered splice site)
1064	1064	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1084	1084	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1145	1259	DOMAIN	Cadherin 11.	might get lost (downstream of altered splice site)
1175	1175	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1276	1276	CONFLICT	Q -> R (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
1377	1397	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1398	1955	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1435	1443	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1746	1752	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1815	1823	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1826	1831	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4620 / 4620

position (AA) of stopcodon in wt / mu AA sequence

1540 / 1540

position of stopcodon in wt / mu cDNA

5015 / 5015

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

396 / 396

chromosome

strand

-1

last intron/exon boundary

4949

theoretical NMD boundary in CDS

4503

length of CDS

4620

coding sequence (CDS) position

1304

cDNA position
(for ins/del: last normal base / first normal base)

1699

gDNA position
(for ins/del: last normal base / first normal base)

1432259

chromosomal position
(for ins/del: last normal base / first normal base)

55955444

original gDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT

altered gDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT

original cDNA sequence snippet

TCTGGACAAGGACATAGAAGATACAAAAGACCCAGAGCTTC

altered cDNA sequence snippet

TCTGGACAAGGACATAGAAGCTACAAAAGACCCAGAGCTTC

wildtype AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEDTKDPE LHLFLNDYTS VFTVTQTGIT RYLTLLQPVD REEQQTYTFS
ITAFDGVQES EPVIVNIQVM DANDNTPTFP EISYDVYVYT DMRPGDSVIQ LTAVDADEGS
NGEITYEILV GAQGDFIINK TTGLITIAPG VEMIVGRTYA LTVQAADNAP PAERRNSICT
VYIEVLPPNN QSPPRFPQLM YSLEISEAMR VGAVLLNLQA TDREGDSITY AIENGDPQRV
FNLSETTGIL TLGKALDRES TDRYILIITA SDGRPDGTST ATVNIVVTDV NDNAPVFDPY
LPRNLSVVEE EANAFVGQVK ATDPDAGING QVHYSLGNFN NLFRITSNGS IYTAVKLNRE
VRDYYELVVV ATDGAVHPRH STLTLAIKVL DIDDNSPVFT NSTYTVLVEE NLPAGTTILQ
IEAKDVDLGA NVSYRIRSPE VKHFFALHPF TGELSLLRSL DYEAFPDQEA SITFLVEAFD
IYGTMPPGIA TVTVIVKDMN DYPPVFSKRI YKGMVAPDAV KGTPITTVYA EDADPPGLPA
SRVRYRVDDV QFPYPASIFE VEEDSGRVIT RVNLNEEPTT IFKLVVVAFD DGEPVMSSSA
TVKILVLHPG EIPRFTQEEY RPPPVSELAT KGTMVGVISA AAINQSIVYS IVSGNEEDTF
GINNITGVIY VNGPLDYETR TSYVLRVQAD SLEVVLANLR VPSKSNTAKV YIEIQDENNH
PPVFQKKFYI GGVSEDARMF TSVLRVKATD KDTGNYSVMA YRLIIPPIKE GKEGFVVETY
TGLIKTAMLF HNMRRSYFKF QVIATDDYGK GLSGKADVLV SVVNQLDMQV IVSNVPPTLV
EKKIEDLTEI LDRYVQEQIP GAKVVVESIG ARRHGDAFSL EDYTKCDLTV YAIDPQTNRA
IDRNELFKFL DGKLLDINKD FQPYYGEGGR ILEIRTPEAV TSIKKRGESL GYTEGALLAL
AFIIILCCIP AILVVLVSYR QFKVRQAECT KTARIQAALP AAKPAVPAPA PVAAPPPPPP
PPPGAHLYEE LGDSSMHKNY PWSLELILAR NMDKIITVMS MGMKCLNMGV AVDCYHQLDR
RNMVRWLVKL RKNMRRKRKS QRKLKNQRLK LESLVRRKK*

mutated AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEATKDPE LHLFLNDYTS VFTVTQTGIT RYLTLLQPVD REEQQTYTFS
ITAFDGVQES EPVIVNIQVM DANDNTPTFP EISYDVYVYT DMRPGDSVIQ LTAVDADEGS
NGEITYEILV GAQGDFIINK TTGLITIAPG VEMIVGRTYA LTVQAADNAP PAERRNSICT
VYIEVLPPNN QSPPRFPQLM YSLEISEAMR VGAVLLNLQA TDREGDSITY AIENGDPQRV
FNLSETTGIL TLGKALDRES TDRYILIITA SDGRPDGTST ATVNIVVTDV NDNAPVFDPY
LPRNLSVVEE EANAFVGQVK ATDPDAGING QVHYSLGNFN NLFRITSNGS IYTAVKLNRE
VRDYYELVVV ATDGAVHPRH STLTLAIKVL DIDDNSPVFT NSTYTVLVEE NLPAGTTILQ
IEAKDVDLGA NVSYRIRSPE VKHFFALHPF TGELSLLRSL DYEAFPDQEA SITFLVEAFD
IYGTMPPGIA TVTVIVKDMN DYPPVFSKRI YKGMVAPDAV KGTPITTVYA EDADPPGLPA
SRVRYRVDDV QFPYPASIFE VEEDSGRVIT RVNLNEEPTT IFKLVVVAFD DGEPVMSSSA
TVKILVLHPG EIPRFTQEEY RPPPVSELAT KGTMVGVISA AAINQSIVYS IVSGNEEDTF
GINNITGVIY VNGPLDYETR TSYVLRVQAD SLEVVLANLR VPSKSNTAKV YIEIQDENNH
PPVFQKKFYI GGVSEDARMF TSVLRVKATD KDTGNYSVMA YRLIIPPIKE GKEGFVVETY
TGLIKTAMLF HNMRRSYFKF QVIATDDYGK GLSGKADVLV SVVNQLDMQV IVSNVPPTLV
EKKIEDLTEI LDRYVQEQIP GAKVVVESIG ARRHGDAFSL EDYTKCDLTV YAIDPQTNRA
IDRNELFKFL DGKLLDINKD FQPYYGEGGR ILEIRTPEAV TSIKKRGESL GYTEGALLAL
AFIIILCCIP AILVVLVSYR QFKVRQAECT KTARIQAALP AAKPAVPAPA PVAAPPPPPP
PPPGAHLYEE LGDSSMHKNY PWSLELILAR NMDKIITVMS MGMKCLNMGV AVDCYHQLDR
RNMVRWLVKL RKNMRRKRKS QRKLKNQRLK LESLVRRKK*

speed

0.14 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1.41262538386557e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:55955444T>GN/A show variant in all transcripts IGV

HGNC symbol

PCDH15

Ensembl transcript ID

ENST00000395446

Genbank transcript ID

N/A

UniProt peptide

Q96QU1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1304A>C
cDNA.1699A>C
g.1432259A>C

AA changes

D435A Score: 126 explain score(s)

position(s) of altered AA
if AA alteration in CDS

435

frameshift

known variant

Reference ID: rs4935502

database	homozygous (G/G)	heterozygous	allele carriers
1000G	481	767	1248
ExAC	5615	17649	23264

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.245	1
	4.774	1
(flanking)	5.784	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	1432260	sequence motif lost	-	wt: AGAT\|gtaa mu: AGCT.gtaa
Donor marginally increased	1432252	wt: 0.9798 / mu: 0.9914 (marginal change - not scored)	wt: AGGACATAGAAGATG mu: AGGACATAGAAGCTG	GACA\|taga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

435

mutated

not conserved

435

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000009794

435

Fcatus

not conserved

ENSFCAG00000010122

435

Mmusculus

all identical

ENSMUSG00000052613

440

Ggallus

all conserved

ENSGALG00000002744

383

Trubripes

all conserved

ENSTRUG00000010819

424

Drerio

all conserved

ENSDARG00000008127

383

Dmelanogaster

all identical

FBgn0039709

427

Celegans

not conserved

F15B9.7

415

Xtropicalis

all conserved

ENSXETG00000018945

386

protein features

start (aa)	end (aa)	feature	details
27	1376	TOPO_DOM	Extracellular (Potential).	lost
396	509	DOMAIN	Cadherin 4.	lost
467	467	CONFLICT	Q -> L (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
510	616	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
559	559	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
617	717	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
662	662	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
719	819	DOMAIN	Cadherin 7.	might get lost (downstream of altered splice site)
724	724	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
768	768	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
820	926	DOMAIN	Cadherin 8.	might get lost (downstream of altered splice site)
821	821	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
851	851	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
927	1035	DOMAIN	Cadherin 9.	might get lost (downstream of altered splice site)
1037	1144	DOMAIN	Cadherin 10.	might get lost (downstream of altered splice site)
1064	1064	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1084	1084	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1145	1259	DOMAIN	Cadherin 11.	might get lost (downstream of altered splice site)
1175	1175	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1276	1276	CONFLICT	Q -> R (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
1377	1397	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1398	1955	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1435	1443	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1746	1752	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1815	1823	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1826	1831	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2946 / 2946

position (AA) of stopcodon in wt / mu AA sequence

982 / 982

position of stopcodon in wt / mu cDNA

3341 / 3341

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

396 / 396

chromosome

strand

-1

last intron/exon boundary

2487

theoretical NMD boundary in CDS

2041

length of CDS

2946

coding sequence (CDS) position

1304

cDNA position
(for ins/del: last normal base / first normal base)

1699

gDNA position
(for ins/del: last normal base / first normal base)

1432259

chromosomal position
(for ins/del: last normal base / first normal base)

55955444

original gDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT

altered gDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT

original cDNA sequence snippet

TCTGGACAAGGACATAGAAGATACAAAAGACCCAGAGCTTC

altered cDNA sequence snippet

TCTGGACAAGGACATAGAAGCTACAAAAGACCCAGAGCTTC

wildtype AA sequence

mutated AA sequence

speed

0.11 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1.41262538386557e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:55955444T>GN/A show variant in all transcripts IGV

HGNC symbol

PCDH15

Ensembl transcript ID

ENST00000361849

Genbank transcript ID

NM_001142763

UniProt peptide

Q96QU1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1304A>C
cDNA.1699A>C
g.1432259A>C

AA changes

D435A Score: 126 explain score(s)

position(s) of altered AA
if AA alteration in CDS

435

frameshift

known variant

Reference ID: rs4935502

database	homozygous (G/G)	heterozygous	allele carriers
1000G	481	767	1248
ExAC	5615	17649	23264

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.245	1
	4.774	1
(flanking)	5.784	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	1432260	sequence motif lost	-	wt: AGAT\|gtaa mu: AGCT.gtaa
Donor marginally increased	1432252	wt: 0.9798 / mu: 0.9914 (marginal change - not scored)	wt: AGGACATAGAAGATG mu: AGGACATAGAAGCTG	GACA\|taga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

435

mutated

not conserved

435

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000009794

435

Fcatus

not conserved

ENSFCAG00000010122

435

Mmusculus

all identical

ENSMUSG00000052613

440

Ggallus

all conserved

ENSGALG00000002744

383

Trubripes

all conserved

ENSTRUG00000010819

424

Drerio

all conserved

ENSDARG00000008127

383

Dmelanogaster

all identical

FBgn0039709

427

Celegans

not conserved

F15B9.7

415

Xtropicalis

all conserved

ENSXETG00000018945

386

protein features

start (aa)	end (aa)	feature	details
27	1376	TOPO_DOM	Extracellular (Potential).	lost
396	509	DOMAIN	Cadherin 4.	lost
467	467	CONFLICT	Q -> L (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
510	616	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
559	559	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
617	717	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
662	662	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
719	819	DOMAIN	Cadherin 7.	might get lost (downstream of altered splice site)
724	724	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
768	768	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
820	926	DOMAIN	Cadherin 8.	might get lost (downstream of altered splice site)
821	821	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
851	851	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
927	1035	DOMAIN	Cadherin 9.	might get lost (downstream of altered splice site)
1037	1144	DOMAIN	Cadherin 10.	might get lost (downstream of altered splice site)
1064	1064	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1084	1084	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1145	1259	DOMAIN	Cadherin 11.	might get lost (downstream of altered splice site)
1175	1175	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1276	1276	CONFLICT	Q -> R (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
1377	1397	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1398	1955	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1435	1443	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1746	1752	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1815	1823	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1826	1831	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5874 / 5874

position (AA) of stopcodon in wt / mu AA sequence

1958 / 1958

position of stopcodon in wt / mu cDNA

6269 / 6269

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

396 / 396

chromosome

strand

-1

last intron/exon boundary

4769

theoretical NMD boundary in CDS

4323

length of CDS

5874

coding sequence (CDS) position

1304

cDNA position
(for ins/del: last normal base / first normal base)

1699

gDNA position
(for ins/del: last normal base / first normal base)

1432259

chromosomal position
(for ins/del: last normal base / first normal base)

55955444

original gDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT

altered gDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT

original cDNA sequence snippet

TCTGGACAAGGACATAGAAGATACAAAAGACCCAGAGCTTC

altered cDNA sequence snippet

TCTGGACAAGGACATAGAAGCTACAAAAGACCCAGAGCTTC

wildtype AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEDTKDPE LHLFLNDYTS VFTVTQTGIT RYLTLLQPVD REEQQTYTFS
ITAFDGVQES EPVIVNIQVM DANDNTPTFP EISYDVYVYT DMRPGDSVIQ LTAVDADEGS
NGEITYEILV GAQGDFIINK TTGLITIAPG VEMIVGRTYA LTVQAADNAP PAERRNSICT
VYIEVLPPNN QSPPRFPQLM YSLEISEAMR VGAVLLNLQA TDREGDSITY AIENGDPQRV
FNLSETTGIL TLGKALDRES TDRYILIITA SDGRPDGTST ATVNIVVTDV NDNAPVFDPY
LPRNLSVVEE EANAFVGQVK ATDPDAGING QVHYSLGNFN NLFRITSNGS IYTAVKLNRE
VRDYYELVVV ATDGAVHPRH STLTLAIKVL DIDDNSPVFT NSTYTVLVEE NLPAGTTILQ
IEAKDVDLGA NVSYRIRSPE VKHFFALHPF TGELSLLRSL DYEAFPDQEA SITFLVEAFD
IYGTMPPGIA TVTVIVKDMN DYPPVFSKRI YKGMVAPDAV KGTPITTVYA EDADPPGLPA
SRVRYRVDDV QFPYPASIFE VEEDSGRVIT RVNLNEEPTT IFKLVVVAFD DGEPVMSSSA
TVKILVLHPG EIPRFTQEEY RPPPVSELAT KGTMVGVISA AAINQSIVYS IVSGNEEDTF
GINNITGVIY VNGPLDYETR TSYVLRVQAD SLEVVLANLR VPSKSNTAKV YIEIQDENNH
PPVFQKKFYI GGVSEDARMF TSVLRVKATD KDTGNYSVMA YRLIIPPIKE GKEGFVVETY
TGLIKTAMLF HNMRRSYFKF QVIATDDYGK GLSGKADVLV SVVNQLDMQV IVSNVPPTLV
EKKIEDLTEI LDRYVQEQIP GAKVVVESIG ARRHGDAFSL EDYTKCDLTV YAIDPQTNRA
IDRNELFKFL DGKLLDINKD FQPYYGEGGR ILEIRTPEAV TSIKKRGESL GYTEGALLAL
AFIIILCCIP AILVVLVSYR QFKVRQAECT KTARIQAALP AAKPAVPAPA PVAAPPPPPP
PPPGAHLYEE LGDSSMHNLF LLYHFQQSRG NNSVSEDRKH QQVVMPFSSN TIEAHKSAHV
DGSLKSNKLK SARKFTFLSD EDDLSAHNPL YKENISQVST NSDISQRTDF VDPFSPKIQA
KSKSLRGPRE KIQRLWSQSV SLPRRLMRKV PNRPEIIDLQ QWQGTRQKAE NENTGICTNK
RGSSNPLLTT EEANLTEKEE IRQGETLMIE GTEQLKSLSS DSSFCFPRPH FSFSTLPTVS
RTVELKSEPN VISSPAECSL ELSPSRPCVL HSSLSRRETP ICMLPIETER NIFENFAHPP
NISPSACPLP PPPPISPPSP PPAPAPLAPP PDISPFSLFC PPPSPPSIPL PLPPPTFFPL
SVSTSGPPTP PLLPPFPTPL PPPPPSIPCP PPPSASFLST ECVCITGVKC TTNLMPAEKI
KSSMTQLSTT TVCKTDPQRE PKGILRHVKN LAELEKSVAN MYSQIEKNYL RTNVSELQTM
CPSEVTNMEI TSEQNKGSLN NIVEGTEKQS HSQSTSL*

mutated AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEATKDPE LHLFLNDYTS VFTVTQTGIT RYLTLLQPVD REEQQTYTFS
ITAFDGVQES EPVIVNIQVM DANDNTPTFP EISYDVYVYT DMRPGDSVIQ LTAVDADEGS
NGEITYEILV GAQGDFIINK TTGLITIAPG VEMIVGRTYA LTVQAADNAP PAERRNSICT
VYIEVLPPNN QSPPRFPQLM YSLEISEAMR VGAVLLNLQA TDREGDSITY AIENGDPQRV
FNLSETTGIL TLGKALDRES TDRYILIITA SDGRPDGTST ATVNIVVTDV NDNAPVFDPY
LPRNLSVVEE EANAFVGQVK ATDPDAGING QVHYSLGNFN NLFRITSNGS IYTAVKLNRE
VRDYYELVVV ATDGAVHPRH STLTLAIKVL DIDDNSPVFT NSTYTVLVEE NLPAGTTILQ
IEAKDVDLGA NVSYRIRSPE VKHFFALHPF TGELSLLRSL DYEAFPDQEA SITFLVEAFD
IYGTMPPGIA TVTVIVKDMN DYPPVFSKRI YKGMVAPDAV KGTPITTVYA EDADPPGLPA
SRVRYRVDDV QFPYPASIFE VEEDSGRVIT RVNLNEEPTT IFKLVVVAFD DGEPVMSSSA
TVKILVLHPG EIPRFTQEEY RPPPVSELAT KGTMVGVISA AAINQSIVYS IVSGNEEDTF
GINNITGVIY VNGPLDYETR TSYVLRVQAD SLEVVLANLR VPSKSNTAKV YIEIQDENNH
PPVFQKKFYI GGVSEDARMF TSVLRVKATD KDTGNYSVMA YRLIIPPIKE GKEGFVVETY
TGLIKTAMLF HNMRRSYFKF QVIATDDYGK GLSGKADVLV SVVNQLDMQV IVSNVPPTLV
EKKIEDLTEI LDRYVQEQIP GAKVVVESIG ARRHGDAFSL EDYTKCDLTV YAIDPQTNRA
IDRNELFKFL DGKLLDINKD FQPYYGEGGR ILEIRTPEAV TSIKKRGESL GYTEGALLAL
AFIIILCCIP AILVVLVSYR QFKVRQAECT KTARIQAALP AAKPAVPAPA PVAAPPPPPP
PPPGAHLYEE LGDSSMHNLF LLYHFQQSRG NNSVSEDRKH QQVVMPFSSN TIEAHKSAHV
DGSLKSNKLK SARKFTFLSD EDDLSAHNPL YKENISQVST NSDISQRTDF VDPFSPKIQA
KSKSLRGPRE KIQRLWSQSV SLPRRLMRKV PNRPEIIDLQ QWQGTRQKAE NENTGICTNK
RGSSNPLLTT EEANLTEKEE IRQGETLMIE GTEQLKSLSS DSSFCFPRPH FSFSTLPTVS
RTVELKSEPN VISSPAECSL ELSPSRPCVL HSSLSRRETP ICMLPIETER NIFENFAHPP
NISPSACPLP PPPPISPPSP PPAPAPLAPP PDISPFSLFC PPPSPPSIPL PLPPPTFFPL
SVSTSGPPTP PLLPPFPTPL PPPPPSIPCP PPPSASFLST ECVCITGVKC TTNLMPAEKI
KSSMTQLSTT TVCKTDPQRE PKGILRHVKN LAELEKSVAN MYSQIEKNYL RTNVSELQTM
CPSEVTNMEI TSEQNKGSLN NIVEGTEKQS HSQSTSL*

speed

0.13 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1.41262538386557e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:55955444T>GN/A show variant in all transcripts IGV

HGNC symbol

PCDH15

Ensembl transcript ID

ENST00000395433

Genbank transcript ID

NM_001142768

UniProt peptide

Q96QU1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1238A>C
cDNA.1633A>C
g.1432259A>C

AA changes

D413A Score: 126 explain score(s)

position(s) of altered AA
if AA alteration in CDS

413

frameshift

known variant

Reference ID: rs4935502

database	homozygous (G/G)	heterozygous	allele carriers
1000G	481	767	1248
ExAC	5615	17649	23264

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.245	1
	4.774	1
(flanking)	5.784	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	1432260	sequence motif lost	-	wt: AGAT\|gtaa mu: AGCT.gtaa
Donor marginally increased	1432252	wt: 0.9798 / mu: 0.9914 (marginal change - not scored)	wt: AGGACATAGAAGATG mu: AGGACATAGAAGCTG	GACA\|taga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

413

mutated

not conserved

413

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000009794

435

Fcatus

not conserved

ENSFCAG00000010122

435

Mmusculus

all identical

ENSMUSG00000052613

440

Ggallus

all conserved

ENSGALG00000002744

383

Trubripes

all conserved

ENSTRUG00000010819

424

Drerio

all conserved

ENSDARG00000008127

383

Dmelanogaster

all identical

FBgn0039709

427

Celegans

not conserved

F15B9.7

415

Xtropicalis

all conserved

ENSXETG00000018945

386

protein features

start (aa)	end (aa)	feature	details
27	1376	TOPO_DOM	Extracellular (Potential).	lost
396	509	DOMAIN	Cadherin 4.	lost
419	419	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
467	467	CONFLICT	Q -> L (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
510	616	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
559	559	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
617	717	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
662	662	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
719	819	DOMAIN	Cadherin 7.	might get lost (downstream of altered splice site)
724	724	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
768	768	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
820	926	DOMAIN	Cadherin 8.	might get lost (downstream of altered splice site)
821	821	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
851	851	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
927	1035	DOMAIN	Cadherin 9.	might get lost (downstream of altered splice site)
1037	1144	DOMAIN	Cadherin 10.	might get lost (downstream of altered splice site)
1064	1064	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1084	1084	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1145	1259	DOMAIN	Cadherin 11.	might get lost (downstream of altered splice site)
1175	1175	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1276	1276	CONFLICT	Q -> R (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
1377	1397	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1398	1955	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1435	1443	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1746	1752	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1815	1823	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1826	1831	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5799 / 5799

position (AA) of stopcodon in wt / mu AA sequence

1933 / 1933

position of stopcodon in wt / mu cDNA

6194 / 6194

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

396 / 396

chromosome

strand

-1

last intron/exon boundary

4694

theoretical NMD boundary in CDS

4248

length of CDS

5799

coding sequence (CDS) position

1238

cDNA position
(for ins/del: last normal base / first normal base)

1633

gDNA position
(for ins/del: last normal base / first normal base)

1432259

chromosomal position
(for ins/del: last normal base / first normal base)

55955444

original gDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT

altered gDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT

original cDNA sequence snippet

TCTGGACAAGGACATAGAAGATACAAAAGACCCAGAGCTTC

altered cDNA sequence snippet

TCTGGACAAGGACATAGAAGCTACAAAAGACCCAGAGCTTC

wildtype AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD GTILVDNMLI KGTAGGPDPT IELSLKDNVD
YWVLMDPVKQ MLFLNSTGRV LDRDPPMNIH SIVVQVQCIN KKVGTIIYHE VRIVVRDRND
NSPTFKHESY YATVNELTPV GTTIFTGFSG DNGATDIDDG PNGQIEYVIQ YNPDDPTSND
TFEIPLMLTG NIVLRKRLNY EDKTRYFVII QANDRAQNLN ERRTTTTTLT VDVLDGDDLG
PMFLPCVLVP NTRDCRPLTY QAAIPELRTP EELNPIIVTP PIQAIDQDRN IQPPSDRPGI
LYSILVGTPE DYPRFFHMHP RTAELSLLEP VNRDFHQKFD LVIKAEQDNG HPLPAFAGLH
IEILDENNQS PYFTMPSYQG YILESAPVGA TISDSLNLTS PLRIVALDKD IEDTKDPELH
LFLNDYTSVF TVTQTGITRY LTLLQPVDRE EQQTYTFSIT AFDGVQESEP VIVNIQVMDA
NDNTPTFPEI SYDVYVYTDM RPGDSVIQLT AVDADEGSNG EITYEILVGA QGDFIINKTT
GLITIAPGVE MIVGRTYALT VQAADNAPPA ERRNSICTVY IEVLPPNNQS PPRFPQLMYS
LEISEAMRVG AVLLNLQATD REGDSITYAI ENGDPQRVFN LSETTGILTL GKALDRESTD
RYILIITASD GRPDGTSTAT VNIVVTDVND NAPVFDPYLP RNLSVVEEEA NAFVGQVKAT
DPDAGINGQV HYSLGNFNNL FRITSNGSIY TAVKLNREVR DYYELVVVAT DGAVHPRHST
LTLAIKVLDI DDNSPVFTNS TYTVLVEENL PAGTTILQIE AKDVDLGANV SYRIRSPEVK
HFFALHPFTG ELSLLRSLDY EAFPDQEASI TFLVEAFDIY GTMPPGIATV TVIVKDMNDY
PPVFSKRIYK GMVAPDAVKG TPITTVYAED ADPPGLPASR VRYRVDDVQF PYPASIFEVE
EDSGRVITRV NLNEEPTTIF KLVVVAFDDG EPVMSSSATV KILVLHPGEI PRFTQEEYRP
PPVSELATKG TMVGVISAAA INQSIVYSIV SGNEEDTFGI NNITGVIYVN GPLDYETRTS
YVLRVQADSL EVVLANLRVP SKSNTAKVYI EIQDENNHPP VFQKKFYIGG VSEDARMFTS
VLRVKATDKD TGNYSVMAYR LIIPPIKEGK EGFVVETYTG LIKTAMLFHN MRRSYFKFQV
IATDDYGKGL SGKADVLVSV VNQLDMQVIV SNVPPTLVEK KIEDLTEILD RYVQEQIPGA
KVVVESIGAR RHGDAFSLED YTKCDLTVYA IDPQTNRAID RNELFKFLDG KLLDINKDFQ
PYYGEGGRIL EIRTPEAVTS IKKRGESLGY TEGALLALAF IIILCCIPAI LVVLVSYRQR
QAECTKTARI QAALPAAKPA VPAPAPVAAP PPPPPPPPGA HLYEELGDSS MHNLFLLYHF
QQSRGNNSVS EDRKHQQVVM PFSSNTIEAH KSAHVDGSLK SNKLKSARKF TFLSDEDDLS
AHNPLYKENI SQVSTNSDIS QRTDFVDPFS PKIQAKSKSL RGPREKIQRL WSQSVSLPRR
LMRKVPNRPE IIDLQQWQGT RQKAENENTG ICTNKRGSSN PLLTTEEANL TEKEEIRQGE
TLMIEGTEQL KSLSSDSSFC FPRPHFSFST LPTVSRTVEL KSEPNVISSP AECSLELSPS
RPCVLHSSLS RRETPICMLP IETERNIFEN FAHPPNISPS ACPLPPPPPI SPPSPPPAPA
PLAPPPDISP FSLFCPPPSP PSIPLPLPPP TFFPLSVSTS GPPTPPLLPP FPTPLPPPPP
SIPCPPPPSA SFLSTECVCI TGVKCTTNLM PAEKIKSSMT QLSTTTVCKT DPQREPKGIL
RHVKNLAELE KSVANMYSQI EKNYLRTNVS ELQTMCPSEV TNMEITSEQN KGSLNNIVEG
TEKQSHSQST SL*

mutated AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD GTILVDNMLI KGTAGGPDPT IELSLKDNVD
YWVLMDPVKQ MLFLNSTGRV LDRDPPMNIH SIVVQVQCIN KKVGTIIYHE VRIVVRDRND
NSPTFKHESY YATVNELTPV GTTIFTGFSG DNGATDIDDG PNGQIEYVIQ YNPDDPTSND
TFEIPLMLTG NIVLRKRLNY EDKTRYFVII QANDRAQNLN ERRTTTTTLT VDVLDGDDLG
PMFLPCVLVP NTRDCRPLTY QAAIPELRTP EELNPIIVTP PIQAIDQDRN IQPPSDRPGI
LYSILVGTPE DYPRFFHMHP RTAELSLLEP VNRDFHQKFD LVIKAEQDNG HPLPAFAGLH
IEILDENNQS PYFTMPSYQG YILESAPVGA TISDSLNLTS PLRIVALDKD IEATKDPELH
LFLNDYTSVF TVTQTGITRY LTLLQPVDRE EQQTYTFSIT AFDGVQESEP VIVNIQVMDA
NDNTPTFPEI SYDVYVYTDM RPGDSVIQLT AVDADEGSNG EITYEILVGA QGDFIINKTT
GLITIAPGVE MIVGRTYALT VQAADNAPPA ERRNSICTVY IEVLPPNNQS PPRFPQLMYS
LEISEAMRVG AVLLNLQATD REGDSITYAI ENGDPQRVFN LSETTGILTL GKALDRESTD
RYILIITASD GRPDGTSTAT VNIVVTDVND NAPVFDPYLP RNLSVVEEEA NAFVGQVKAT
DPDAGINGQV HYSLGNFNNL FRITSNGSIY TAVKLNREVR DYYELVVVAT DGAVHPRHST
LTLAIKVLDI DDNSPVFTNS TYTVLVEENL PAGTTILQIE AKDVDLGANV SYRIRSPEVK
HFFALHPFTG ELSLLRSLDY EAFPDQEASI TFLVEAFDIY GTMPPGIATV TVIVKDMNDY
PPVFSKRIYK GMVAPDAVKG TPITTVYAED ADPPGLPASR VRYRVDDVQF PYPASIFEVE
EDSGRVITRV NLNEEPTTIF KLVVVAFDDG EPVMSSSATV KILVLHPGEI PRFTQEEYRP
PPVSELATKG TMVGVISAAA INQSIVYSIV SGNEEDTFGI NNITGVIYVN GPLDYETRTS
YVLRVQADSL EVVLANLRVP SKSNTAKVYI EIQDENNHPP VFQKKFYIGG VSEDARMFTS
VLRVKATDKD TGNYSVMAYR LIIPPIKEGK EGFVVETYTG LIKTAMLFHN MRRSYFKFQV
IATDDYGKGL SGKADVLVSV VNQLDMQVIV SNVPPTLVEK KIEDLTEILD RYVQEQIPGA
KVVVESIGAR RHGDAFSLED YTKCDLTVYA IDPQTNRAID RNELFKFLDG KLLDINKDFQ
PYYGEGGRIL EIRTPEAVTS IKKRGESLGY TEGALLALAF IIILCCIPAI LVVLVSYRQR
QAECTKTARI QAALPAAKPA VPAPAPVAAP PPPPPPPPGA HLYEELGDSS MHNLFLLYHF
QQSRGNNSVS EDRKHQQVVM PFSSNTIEAH KSAHVDGSLK SNKLKSARKF TFLSDEDDLS
AHNPLYKENI SQVSTNSDIS QRTDFVDPFS PKIQAKSKSL RGPREKIQRL WSQSVSLPRR
LMRKVPNRPE IIDLQQWQGT RQKAENENTG ICTNKRGSSN PLLTTEEANL TEKEEIRQGE
TLMIEGTEQL KSLSSDSSFC FPRPHFSFST LPTVSRTVEL KSEPNVISSP AECSLELSPS
RPCVLHSSLS RRETPICMLP IETERNIFEN FAHPPNISPS ACPLPPPPPI SPPSPPPAPA
PLAPPPDISP FSLFCPPPSP PSIPLPLPPP TFFPLSVSTS GPPTPPLLPP FPTPLPPPPP
SIPCPPPPSA SFLSTECVCI TGVKCTTNLM PAEKIKSSMT QLSTTTVCKT DPQREPKGIL
RHVKNLAELE KSVANMYSQI EKNYLRTNVS ELQTMCPSEV TNMEITSEQN KGSLNNIVEG
TEKQSHSQST SL*

speed

0.14 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1.41262538386557e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:55955444T>GN/A show variant in all transcripts IGV

HGNC symbol

PCDH15

Ensembl transcript ID

ENST00000373957

Genbank transcript ID

N/A

UniProt peptide

Q96QU1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1238A>C
cDNA.1600A>C
g.1432259A>C

AA changes

D413A Score: 126 explain score(s)

position(s) of altered AA
if AA alteration in CDS

413

frameshift

known variant

Reference ID: rs4935502

database	homozygous (G/G)	heterozygous	allele carriers
1000G	481	767	1248
ExAC	5615	17649	23264

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.245	1
	4.774	1
(flanking)	5.784	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	1432260	sequence motif lost	-	wt: AGAT\|gtaa mu: AGCT.gtaa
Donor marginally increased	1432252	wt: 0.9798 / mu: 0.9914 (marginal change - not scored)	wt: AGGACATAGAAGATG mu: AGGACATAGAAGCTG	GACA\|taga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

413

mutated

not conserved

413

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000009794

435

Fcatus

not conserved

ENSFCAG00000010122

435

Mmusculus

all identical

ENSMUSG00000052613

440

Ggallus

all conserved

ENSGALG00000002744

383

Trubripes

all conserved

ENSTRUG00000010819

424

Drerio

all conserved

ENSDARG00000008127

383

Dmelanogaster

all identical

FBgn0039709

427

Celegans

not conserved

F15B9.7

302

Xtropicalis

all conserved

ENSXETG00000018945

386

protein features

start (aa)	end (aa)	feature	details
27	1376	TOPO_DOM	Extracellular (Potential).	lost
396	509	DOMAIN	Cadherin 4.	lost
419	419	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
467	467	CONFLICT	Q -> L (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
510	616	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
559	559	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
617	717	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
662	662	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
719	819	DOMAIN	Cadherin 7.	might get lost (downstream of altered splice site)
724	724	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
768	768	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
820	926	DOMAIN	Cadherin 8.	might get lost (downstream of altered splice site)
821	821	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
851	851	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
927	1035	DOMAIN	Cadherin 9.	might get lost (downstream of altered splice site)
1037	1144	DOMAIN	Cadherin 10.	might get lost (downstream of altered splice site)
1064	1064	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1084	1084	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1145	1259	DOMAIN	Cadherin 11.	might get lost (downstream of altered splice site)
1175	1175	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1276	1276	CONFLICT	Q -> R (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
1377	1397	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1398	1955	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1435	1443	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1746	1752	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1815	1823	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1826	1831	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2430 / 2430

position (AA) of stopcodon in wt / mu AA sequence

810 / 810

position of stopcodon in wt / mu cDNA

2792 / 2792

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

363 / 363

chromosome

strand

-1

last intron/exon boundary

2517

theoretical NMD boundary in CDS

2104

length of CDS

2430

coding sequence (CDS) position

1238

cDNA position
(for ins/del: last normal base / first normal base)

1600

gDNA position
(for ins/del: last normal base / first normal base)

1432259

chromosomal position
(for ins/del: last normal base / first normal base)

55955444

original gDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT

altered gDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT

original cDNA sequence snippet

TCTGGACAAGGACATAGAAGATACAAAAGACCCAGAGCTTC

altered cDNA sequence snippet

TCTGGACAAGGACATAGAAGCTACAAAAGACCCAGAGCTTC

wildtype AA sequence

mutated AA sequence

speed

0.25 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1.41262538386557e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:55955444T>GN/A show variant in all transcripts IGV

HGNC symbol

PCDH15

Ensembl transcript ID

ENST00000320301

Genbank transcript ID

NM_033056

UniProt peptide

Q96QU1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1304A>C
cDNA.1699A>C
g.1432259A>C

AA changes

D435A Score: 126 explain score(s)

position(s) of altered AA
if AA alteration in CDS

435

frameshift

known variant

Reference ID: rs4935502

database	homozygous (G/G)	heterozygous	allele carriers
1000G	481	767	1248
ExAC	5615	17649	23264

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.245	1
	4.774	1
(flanking)	5.784	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	1432260	sequence motif lost	-	wt: AGAT\|gtaa mu: AGCT.gtaa
Donor marginally increased	1432252	wt: 0.9798 / mu: 0.9914 (marginal change - not scored)	wt: AGGACATAGAAGATG mu: AGGACATAGAAGCTG	GACA\|taga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

435

mutated

not conserved

435

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000009794

435

Fcatus

not conserved

ENSFCAG00000010122

435

Mmusculus

all identical

ENSMUSG00000052613

440

Ggallus

all conserved

ENSGALG00000002744

383

Trubripes

all conserved

ENSTRUG00000010819

424

Drerio

all conserved

ENSDARG00000008127

383

Dmelanogaster

all identical

FBgn0039709

427

Celegans

not conserved

F15B9.7

415

Xtropicalis

all conserved

ENSXETG00000018945

386

protein features

start (aa)	end (aa)	feature	details
27	1376	TOPO_DOM	Extracellular (Potential).	lost
396	509	DOMAIN	Cadherin 4.	lost
467	467	CONFLICT	Q -> L (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
510	616	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
559	559	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
617	717	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
662	662	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
719	819	DOMAIN	Cadherin 7.	might get lost (downstream of altered splice site)
724	724	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
768	768	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
820	926	DOMAIN	Cadherin 8.	might get lost (downstream of altered splice site)
821	821	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
851	851	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
927	1035	DOMAIN	Cadherin 9.	might get lost (downstream of altered splice site)
1037	1144	DOMAIN	Cadherin 10.	might get lost (downstream of altered splice site)
1064	1064	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1084	1084	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1145	1259	DOMAIN	Cadherin 11.	might get lost (downstream of altered splice site)
1175	1175	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1276	1276	CONFLICT	Q -> R (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
1377	1397	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1398	1955	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1435	1443	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1746	1752	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1815	1823	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1826	1831	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5868 / 5868

position (AA) of stopcodon in wt / mu AA sequence

1956 / 1956

position of stopcodon in wt / mu cDNA

6263 / 6263

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

396 / 396

chromosome

strand

-1

last intron/exon boundary

4763

theoretical NMD boundary in CDS

4317

length of CDS

5868

coding sequence (CDS) position

1304

cDNA position
(for ins/del: last normal base / first normal base)

1699

gDNA position
(for ins/del: last normal base / first normal base)

1432259

chromosomal position
(for ins/del: last normal base / first normal base)

55955444

original gDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT

altered gDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT

original cDNA sequence snippet

TCTGGACAAGGACATAGAAGATACAAAAGACCCAGAGCTTC

altered cDNA sequence snippet

TCTGGACAAGGACATAGAAGCTACAAAAGACCCAGAGCTTC

wildtype AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEDTKDPE LHLFLNDYTS VFTVTQTGIT RYLTLLQPVD REEQQTYTFS
ITAFDGVQES EPVIVNIQVM DANDNTPTFP EISYDVYVYT DMRPGDSVIQ LTAVDADEGS
NGEITYEILV GAQGDFIINK TTGLITIAPG VEMIVGRTYA LTVQAADNAP PAERRNSICT
VYIEVLPPNN QSPPRFPQLM YSLEISEAMR VGAVLLNLQA TDREGDSITY AIENGDPQRV
FNLSETTGIL TLGKALDRES TDRYILIITA SDGRPDGTST ATVNIVVTDV NDNAPVFDPY
LPRNLSVVEE EANAFVGQVK ATDPDAGING QVHYSLGNFN NLFRITSNGS IYTAVKLNRE
VRDYYELVVV ATDGAVHPRH STLTLAIKVL DIDDNSPVFT NSTYTVLVEE NLPAGTTILQ
IEAKDVDLGA NVSYRIRSPE VKHFFALHPF TGELSLLRSL DYEAFPDQEA SITFLVEAFD
IYGTMPPGIA TVTVIVKDMN DYPPVFSKRI YKGMVAPDAV KGTPITTVYA EDADPPGLPA
SRVRYRVDDV QFPYPASIFE VEEDSGRVIT RVNLNEEPTT IFKLVVVAFD DGEPVMSSSA
TVKILVLHPG EIPRFTQEEY RPPPVSELAT KGTMVGVISA AAINQSIVYS IVSGNEEDTF
GINNITGVIY VNGPLDYETR TSYVLRVQAD SLEVVLANLR VPSKSNTAKV YIEIQDENNH
PPVFQKKFYI GGVSEDARMF TSVLRVKATD KDTGNYSVMA YRLIIPPIKE GKEGFVVETY
TGLIKTAMLF HNMRRSYFKF QVIATDDYGK GLSGKADVLV SVVNQLDMQV IVSNVPPTLV
EKKIEDLTEI LDRYVQEQIP GAKVVVESIG ARRHGDAFSL EDYTKCDLTV YAIDPQTNRA
IDRNELFKFL DGKLLDINKD FQPYYGEGGR ILEIRTPEAV TSIKKRGESL GYTEGALLAL
AFIIILCCIP AILVVLVSYR QFKVRQAECT KTARIQAALP AAKPAVPAPA PVAAPPPPPP
PPPGAHLYEE LGDSSILFLL YHFQQSRGNN SVSEDRKHQQ VVMPFSSNTI EAHKSAHVDG
SLKSNKLKSA RKFTFLSDED DLSAHNPLYK ENISQVSTNS DISQRTDFVD PFSPKIQAKS
KSLRGPREKI QRLWSQSVSL PRRLMRKVPN RPEIIDLQQW QGTRQKAENE NTGICTNKRG
SSNPLLTTEE ANLTEKEEIR QGETLMIEGT EQLKSLSSDS SFCFPRPHFS FSTLPTVSRT
VELKSEPNVI SSPAECSLEL SPSRPCVLHS SLSRRETPIC MLPIETERNI FENFAHPPNI
SPSACPLPPP PPISPPSPPP APAPLAPPPD ISPFSLFCPP PSPPSIPLPL PPPTFFPLSV
STSGPPTPPL LPPFPTPLPP PPPSIPCPPP PSASFLSTEC VCITGVKCTT NLMPAEKIKS
SMTQLSTTTV CKTDPQREPK GILRHVKNLA ELEKSVANMY SQIEKNYLRT NVSELQTMCP
SEVTNMEITS EQNKGSLNNI VEGTEKQSHS QSTSL*

mutated AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEATKDPE LHLFLNDYTS VFTVTQTGIT RYLTLLQPVD REEQQTYTFS
ITAFDGVQES EPVIVNIQVM DANDNTPTFP EISYDVYVYT DMRPGDSVIQ LTAVDADEGS
NGEITYEILV GAQGDFIINK TTGLITIAPG VEMIVGRTYA LTVQAADNAP PAERRNSICT
VYIEVLPPNN QSPPRFPQLM YSLEISEAMR VGAVLLNLQA TDREGDSITY AIENGDPQRV
FNLSETTGIL TLGKALDRES TDRYILIITA SDGRPDGTST ATVNIVVTDV NDNAPVFDPY
LPRNLSVVEE EANAFVGQVK ATDPDAGING QVHYSLGNFN NLFRITSNGS IYTAVKLNRE
VRDYYELVVV ATDGAVHPRH STLTLAIKVL DIDDNSPVFT NSTYTVLVEE NLPAGTTILQ
IEAKDVDLGA NVSYRIRSPE VKHFFALHPF TGELSLLRSL DYEAFPDQEA SITFLVEAFD
IYGTMPPGIA TVTVIVKDMN DYPPVFSKRI YKGMVAPDAV KGTPITTVYA EDADPPGLPA
SRVRYRVDDV QFPYPASIFE VEEDSGRVIT RVNLNEEPTT IFKLVVVAFD DGEPVMSSSA
TVKILVLHPG EIPRFTQEEY RPPPVSELAT KGTMVGVISA AAINQSIVYS IVSGNEEDTF
GINNITGVIY VNGPLDYETR TSYVLRVQAD SLEVVLANLR VPSKSNTAKV YIEIQDENNH
PPVFQKKFYI GGVSEDARMF TSVLRVKATD KDTGNYSVMA YRLIIPPIKE GKEGFVVETY
TGLIKTAMLF HNMRRSYFKF QVIATDDYGK GLSGKADVLV SVVNQLDMQV IVSNVPPTLV
EKKIEDLTEI LDRYVQEQIP GAKVVVESIG ARRHGDAFSL EDYTKCDLTV YAIDPQTNRA
IDRNELFKFL DGKLLDINKD FQPYYGEGGR ILEIRTPEAV TSIKKRGESL GYTEGALLAL
AFIIILCCIP AILVVLVSYR QFKVRQAECT KTARIQAALP AAKPAVPAPA PVAAPPPPPP
PPPGAHLYEE LGDSSILFLL YHFQQSRGNN SVSEDRKHQQ VVMPFSSNTI EAHKSAHVDG
SLKSNKLKSA RKFTFLSDED DLSAHNPLYK ENISQVSTNS DISQRTDFVD PFSPKIQAKS
KSLRGPREKI QRLWSQSVSL PRRLMRKVPN RPEIIDLQQW QGTRQKAENE NTGICTNKRG
SSNPLLTTEE ANLTEKEEIR QGETLMIEGT EQLKSLSSDS SFCFPRPHFS FSTLPTVSRT
VELKSEPNVI SSPAECSLEL SPSRPCVLHS SLSRRETPIC MLPIETERNI FENFAHPPNI
SPSACPLPPP PPISPPSPPP APAPLAPPPD ISPFSLFCPP PSPPSIPLPL PPPTFFPLSV
STSGPPTPPL LPPFPTPLPP PPPSIPCPPP PSASFLSTEC VCITGVKCTT NLMPAEKIKS
SMTQLSTTTV CKTDPQREPK GILRHVKNLA ELEKSVANMY SQIEKNYLRT NVSELQTMCP
SEVTNMEITS EQNKGSLNNI VEGTEKQSHS QSTSL*

speed

0.31 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1.41262538386557e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:55955444T>GN/A show variant in all transcripts IGV

HGNC symbol

PCDH15

Ensembl transcript ID

ENST00000395430

Genbank transcript ID

NM_001142766

UniProt peptide

Q96QU1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1304A>C
cDNA.1699A>C
g.1432259A>C

AA changes

D435A Score: 126 explain score(s)

position(s) of altered AA
if AA alteration in CDS

435

frameshift

known variant

Reference ID: rs4935502

database	homozygous (G/G)	heterozygous	allele carriers
1000G	481	767	1248
ExAC	5615	17649	23264

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.245	1
	4.774	1
(flanking)	5.784	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	1432260	sequence motif lost	-	wt: AGAT\|gtaa mu: AGCT.gtaa
Donor marginally increased	1432252	wt: 0.9798 / mu: 0.9914 (marginal change - not scored)	wt: AGGACATAGAAGATG mu: AGGACATAGAAGCTG	GACA\|taga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

435

mutated

not conserved

435

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000009794

435

Fcatus

not conserved

ENSFCAG00000010122

435

Mmusculus

all identical

ENSMUSG00000052613

440

Ggallus

all conserved

ENSGALG00000002744

383

Trubripes

all conserved

ENSTRUG00000010819

424

Drerio

all conserved

ENSDARG00000008127

383

Dmelanogaster

all identical

FBgn0039709

427

Celegans

not conserved

F15B9.7

415

Xtropicalis

all conserved

ENSXETG00000018945

386

protein features

start (aa)	end (aa)	feature	details
27	1376	TOPO_DOM	Extracellular (Potential).	lost
396	509	DOMAIN	Cadherin 4.	lost
467	467	CONFLICT	Q -> L (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
510	616	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
559	559	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
617	717	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
662	662	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
719	819	DOMAIN	Cadherin 7.	might get lost (downstream of altered splice site)
724	724	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
768	768	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
820	926	DOMAIN	Cadherin 8.	might get lost (downstream of altered splice site)
821	821	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
851	851	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
927	1035	DOMAIN	Cadherin 9.	might get lost (downstream of altered splice site)
1037	1144	DOMAIN	Cadherin 10.	might get lost (downstream of altered splice site)
1064	1064	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1084	1084	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1145	1259	DOMAIN	Cadherin 11.	might get lost (downstream of altered splice site)
1175	1175	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1276	1276	CONFLICT	Q -> R (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
1377	1397	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1398	1955	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1435	1443	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1746	1752	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1815	1823	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1826	1831	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5859 / 5859

position (AA) of stopcodon in wt / mu AA sequence

1953 / 1953

position of stopcodon in wt / mu cDNA

6254 / 6254

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

396 / 396

chromosome

strand

-1

last intron/exon boundary

4754

theoretical NMD boundary in CDS

4308

length of CDS

5859

coding sequence (CDS) position

1304

cDNA position
(for ins/del: last normal base / first normal base)

1699

gDNA position
(for ins/del: last normal base / first normal base)

1432259

chromosomal position
(for ins/del: last normal base / first normal base)

55955444

original gDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT

altered gDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT

original cDNA sequence snippet

TCTGGACAAGGACATAGAAGATACAAAAGACCCAGAGCTTC

altered cDNA sequence snippet

TCTGGACAAGGACATAGAAGCTACAAAAGACCCAGAGCTTC

wildtype AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEDTKDPE LHLFLNDYTS VFTVTQTGIT RYLTLLQPVD REEQQTYTFS
ITAFDGVQES EPVIVNIQVM DANDNTPTFP EISYDVYVYT DMRPGDSVIQ LTAVDADEGS
NGEITYEILV GAQGDFIINK TTGLITIAPG VEMIVGRTYA LTVQAADNAP PAERRNSICT
VYIEVLPPNN QSPPRFPQLM YSLEISEAMR VGAVLLNLQA TDREGDSITY AIENGDPQRV
FNLSETTGIL TLGKALDRES TDRYILIITA SDGRPDGTST ATVNIVVTDV NDNAPVFDPY
LPRNLSVVEE EANAFVGQVK ATDPDAGING QVHYSLGNFN NLFRITSNGS IYTAVKLNRE
VRDYYELVVV ATDGAVHPRH STLTLAIKVL DIDDNSPVFT NSTYTVLVEE NLPAGTTILQ
IEAKDVDLGA NVSYRIRSPE VKHFFALHPF TGELSLLRSL DYEAFPDQEA SITFLVEAFD
IYGTMPPGIA TVTVIVKDMN DYPPVFSKRI YKGMVAPDAV KGTPITTVYA EDADPPGLPA
SRVRYRVDDV QFPYPASIFE VEEDSGRVIT RVNLNEEPTT IFKLVVVAFD DGEPVMSSSA
TVKILVLHPG EIPRFTQEEY RPPPVSELAT KGTMVGVISA AAINQSIVYS IVSGNEEDTF
GINNITGVIY VNGPLDYETR TSYVLRVQAD SLEVVLANLR VPSKSNTAKV YIEIQDENNH
PPVFQKKFYI GGVSEDARMF TSVLRVKATD KDTGNYSVMA YRLIIPPIKE GKEGFVVETY
TGLIKTAMLF HNMRRSYFKF QVIATDDYGK GLSGKADVLV SVVNQLDMQV IVSNVPPTLV
EKKIEDLTEI LDRYVQEQIP GAKVVVESIG ARRHGDAFSL EDYTKCDLTV YAIDPQTNRA
IDRNELFKFL DGKLLDINKD FQPYYGEGGR ILEIRTPEAV TSIKKRGESL GYTEGALLAL
AFIIILCCIP AILVVLVSYR QRQAECTKTA RIQAALPAAK PAVPAPAPVA APPPPPPPPP
GAHLYEELGD SSILFLLYHF QQSRGNNSVS EDRKHQQVVM PFSSNTIEAH KSAHVDGSLK
SNKLKSARKF TFLSDEDDLS AHNPLYKENI SQVSTNSDIS QRTDFVDPFS PKIQAKSKSL
RGPREKIQRL WSQSVSLPRR LMRKVPNRPE IIDLQQWQGT RQKAENENTG ICTNKRGSSN
PLLTTEEANL TEKEEIRQGE TLMIEGTEQL KSLSSDSSFC FPRPHFSFST LPTVSRTVEL
KSEPNVISSP AECSLELSPS RPCVLHSSLS RRETPICMLP IETERNIFEN FAHPPNISPS
ACPLPPPPPI SPPSPPPAPA PLAPPPDISP FSLFCPPPSP PSIPLPLPPP TFFPLSVSTS
GPPTPPLLPP FPTPLPPPPP SIPCPPPPSA SFLSTECVCI TGVKCTTNLM PAEKIKSSMT
QLSTTTVCKT DPQREPKGIL RHVKNLAELE KSVANMYSQI EKNYLRTNVS ELQTMCPSEV
TNMEITSEQN KGSLNNIVEG TEKQSHSQST SL*

mutated AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEATKDPE LHLFLNDYTS VFTVTQTGIT RYLTLLQPVD REEQQTYTFS
ITAFDGVQES EPVIVNIQVM DANDNTPTFP EISYDVYVYT DMRPGDSVIQ LTAVDADEGS
NGEITYEILV GAQGDFIINK TTGLITIAPG VEMIVGRTYA LTVQAADNAP PAERRNSICT
VYIEVLPPNN QSPPRFPQLM YSLEISEAMR VGAVLLNLQA TDREGDSITY AIENGDPQRV
FNLSETTGIL TLGKALDRES TDRYILIITA SDGRPDGTST ATVNIVVTDV NDNAPVFDPY
LPRNLSVVEE EANAFVGQVK ATDPDAGING QVHYSLGNFN NLFRITSNGS IYTAVKLNRE
VRDYYELVVV ATDGAVHPRH STLTLAIKVL DIDDNSPVFT NSTYTVLVEE NLPAGTTILQ
IEAKDVDLGA NVSYRIRSPE VKHFFALHPF TGELSLLRSL DYEAFPDQEA SITFLVEAFD
IYGTMPPGIA TVTVIVKDMN DYPPVFSKRI YKGMVAPDAV KGTPITTVYA EDADPPGLPA
SRVRYRVDDV QFPYPASIFE VEEDSGRVIT RVNLNEEPTT IFKLVVVAFD DGEPVMSSSA
TVKILVLHPG EIPRFTQEEY RPPPVSELAT KGTMVGVISA AAINQSIVYS IVSGNEEDTF
GINNITGVIY VNGPLDYETR TSYVLRVQAD SLEVVLANLR VPSKSNTAKV YIEIQDENNH
PPVFQKKFYI GGVSEDARMF TSVLRVKATD KDTGNYSVMA YRLIIPPIKE GKEGFVVETY
TGLIKTAMLF HNMRRSYFKF QVIATDDYGK GLSGKADVLV SVVNQLDMQV IVSNVPPTLV
EKKIEDLTEI LDRYVQEQIP GAKVVVESIG ARRHGDAFSL EDYTKCDLTV YAIDPQTNRA
IDRNELFKFL DGKLLDINKD FQPYYGEGGR ILEIRTPEAV TSIKKRGESL GYTEGALLAL
AFIIILCCIP AILVVLVSYR QRQAECTKTA RIQAALPAAK PAVPAPAPVA APPPPPPPPP
GAHLYEELGD SSILFLLYHF QQSRGNNSVS EDRKHQQVVM PFSSNTIEAH KSAHVDGSLK
SNKLKSARKF TFLSDEDDLS AHNPLYKENI SQVSTNSDIS QRTDFVDPFS PKIQAKSKSL
RGPREKIQRL WSQSVSLPRR LMRKVPNRPE IIDLQQWQGT RQKAENENTG ICTNKRGSSN
PLLTTEEANL TEKEEIRQGE TLMIEGTEQL KSLSSDSSFC FPRPHFSFST LPTVSRTVEL
KSEPNVISSP AECSLELSPS RPCVLHSSLS RRETPICMLP IETERNIFEN FAHPPNISPS
ACPLPPPPPI SPPSPPPAPA PLAPPPDISP FSLFCPPPSP PSIPLPLPPP TFFPLSVSTS
GPPTPPLLPP FPTPLPPPPP SIPCPPPPSA SFLSTECVCI TGVKCTTNLM PAEKIKSSMT
QLSTTTVCKT DPQREPKGIL RHVKNLAELE KSVANMYSQI EKNYLRTNVS ELQTMCPSEV
TNMEITSEQN KGSLNNIVEG TEKQSHSQST SL*

speed

0.22 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1.41262538386557e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:55955444T>GN/A show variant in all transcripts IGV

HGNC symbol

PCDH15

Ensembl transcript ID

ENST00000373955

Genbank transcript ID

N/A

UniProt peptide

Q96QU1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1304A>C
cDNA.1596A>C
g.1432259A>C

AA changes

D435A Score: 126 explain score(s)

position(s) of altered AA
if AA alteration in CDS

435

frameshift

known variant

Reference ID: rs4935502

database	homozygous (G/G)	heterozygous	allele carriers
1000G	481	767	1248
ExAC	5615	17649	23264

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.245	1
	4.774	1
(flanking)	5.784	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	1432260	sequence motif lost	-	wt: AGAT\|gtaa mu: AGCT.gtaa
Donor marginally increased	1432252	wt: 0.9798 / mu: 0.9914 (marginal change - not scored)	wt: AGGACATAGAAGATG mu: AGGACATAGAAGCTG	GACA\|taga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

435

mutated

not conserved

435

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000009794

435

Fcatus

not conserved

ENSFCAG00000010122

435

Mmusculus

all identical

ENSMUSG00000052613

440

Ggallus

all conserved

ENSGALG00000002744

383

Trubripes

all conserved

ENSTRUG00000010819

424

Drerio

all conserved

ENSDARG00000008127

383

Dmelanogaster

all identical

FBgn0039709

427

Celegans

not conserved

F15B9.7

415

Xtropicalis

all conserved

ENSXETG00000018945

386

protein features

start (aa)	end (aa)	feature	details
27	1376	TOPO_DOM	Extracellular (Potential).	lost
396	509	DOMAIN	Cadherin 4.	lost
467	467	CONFLICT	Q -> L (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
510	616	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
559	559	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
617	717	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
662	662	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
719	819	DOMAIN	Cadherin 7.	might get lost (downstream of altered splice site)
724	724	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
768	768	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
820	926	DOMAIN	Cadherin 8.	might get lost (downstream of altered splice site)
821	821	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
851	851	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
927	1035	DOMAIN	Cadherin 9.	might get lost (downstream of altered splice site)
1037	1144	DOMAIN	Cadherin 10.	might get lost (downstream of altered splice site)
1064	1064	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1084	1084	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1145	1259	DOMAIN	Cadherin 11.	might get lost (downstream of altered splice site)
1175	1175	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1276	1276	CONFLICT	Q -> R (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
1377	1397	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1398	1955	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1435	1443	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1746	1752	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1815	1823	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1826	1831	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2886 / 2886

position (AA) of stopcodon in wt / mu AA sequence

962 / 962

position of stopcodon in wt / mu cDNA

3178 / 3178

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

293 / 293

chromosome

strand

-1

last intron/exon boundary

3044

theoretical NMD boundary in CDS

2701

length of CDS

2886

coding sequence (CDS) position

1304

cDNA position
(for ins/del: last normal base / first normal base)

1596

gDNA position
(for ins/del: last normal base / first normal base)

1432259

chromosomal position
(for ins/del: last normal base / first normal base)

55955444

original gDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT

altered gDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT

original cDNA sequence snippet

TCTGGACAAGGACATAGAAGATACAAAAGACCCAGAGCTTC

altered cDNA sequence snippet

TCTGGACAAGGACATAGAAGCTACAAAAGACCCAGAGCTTC

wildtype AA sequence

mutated AA sequence

speed

0.14 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1.41262538386557e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:55955444T>GN/A show variant in all transcripts IGV

HGNC symbol

PCDH15

Ensembl transcript ID

ENST00000414778

Genbank transcript ID

NM_001142771

UniProt peptide

Q96QU1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1319A>C
cDNA.1714A>C
g.1432259A>C

AA changes

D440A Score: 126 explain score(s)

position(s) of altered AA
if AA alteration in CDS

440

frameshift

known variant

Reference ID: rs4935502

database	homozygous (G/G)	heterozygous	allele carriers
1000G	481	767	1248
ExAC	5615	17649	23264

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.245	1
	4.774	1
(flanking)	5.784	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	1432260	sequence motif lost	-	wt: AGAT\|gtaa mu: AGCT.gtaa
Donor marginally increased	1432252	wt: 0.9798 / mu: 0.9914 (marginal change - not scored)	wt: AGGACATAGAAGATG mu: AGGACATAGAAGCTG	GACA\|taga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

440

mutated

not conserved

440

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000009794

435

Fcatus

not conserved

ENSFCAG00000010122

435

Mmusculus

all identical

ENSMUSG00000052613

440

Ggallus

all conserved

ENSGALG00000002744

383

Trubripes

all conserved

ENSTRUG00000010819

424

Drerio

all conserved

ENSDARG00000008127

383

Dmelanogaster

all identical

FBgn0039709

427

Celegans

not conserved

F15B9.7

415

Xtropicalis

all conserved

ENSXETG00000018945

386

protein features

start (aa)	end (aa)	feature	details
27	1376	TOPO_DOM	Extracellular (Potential).	lost
396	509	DOMAIN	Cadherin 4.	lost
467	467	CONFLICT	Q -> L (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
510	616	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
559	559	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
617	717	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
662	662	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
719	819	DOMAIN	Cadherin 7.	might get lost (downstream of altered splice site)
724	724	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
768	768	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
820	926	DOMAIN	Cadherin 8.	might get lost (downstream of altered splice site)
821	821	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
851	851	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
927	1035	DOMAIN	Cadherin 9.	might get lost (downstream of altered splice site)
1037	1144	DOMAIN	Cadherin 10.	might get lost (downstream of altered splice site)
1064	1064	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1084	1084	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1145	1259	DOMAIN	Cadherin 11.	might get lost (downstream of altered splice site)
1175	1175	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1276	1276	CONFLICT	Q -> R (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
1377	1397	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1398	1955	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1435	1443	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1746	1752	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1815	1823	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1826	1831	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5046 / 5046

position (AA) of stopcodon in wt / mu AA sequence

1682 / 1682

position of stopcodon in wt / mu cDNA

5441 / 5441

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

396 / 396

chromosome

strand

-1

last intron/exon boundary

4890

theoretical NMD boundary in CDS

4444

length of CDS

5046

coding sequence (CDS) position

1319

cDNA position
(for ins/del: last normal base / first normal base)

1714

gDNA position
(for ins/del: last normal base / first normal base)

1432259

chromosomal position
(for ins/del: last normal base / first normal base)

55955444

original gDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT

altered gDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT

original cDNA sequence snippet

TCTGGACAAGGACATAGAAGATACAAAAGACCCAGAGCTTC

altered cDNA sequence snippet

TCTGGACAAGGACATAGAAGCTACAAAAGACCCAGAGCTTC

wildtype AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD GWRYMYCKLA RGGPPATIVA IDEESRNGTI
LVDNMLIKGT AGGPDPTIEL SLKDNVDYWV LMDPVKQMLF LNSTGRVLDR DPPMNIHSIV
VQVQCINKKV GTIIYHEVRI VVRDRNDNSP TFKHESYYAT VNELTPVGTT IFTGFSGDNG
ATDIDDGPNG QIEYVIQYNP DDPTSNDTFE IPLMLTGNIV LRKRLNYEDK TRYFVIIQAN
DRAQNLNERR TTTTTLTVDV LDGDDLGPMF LPCVLVPNTR DCRPLTYQAA IPELRTPEEL
NPIIVTPPIQ AIDQDRNIQP PSDRPGILYS ILVGTPEDYP RFFHMHPRTA ELSLLEPVNR
DFHQKFDLVI KAEQDNGHPL PAFAGLHIEI LDENNQSPYF TMPSYQGYIL ESAPVGATIS
DSLNLTSPLR IVALDKDIED TKDPELHLFL NDYTSVFTVT QTGITRYLTL LQPVDREEQQ
TYTFSITAFD GVQESEPVIV NIQVMDANDN TPTFPEISYD VYVYTDMRPG DSVIQLTAVD
ADEGSNGEIT YEILVGAQGD FIINKTTGLI TIAPGVEMIV GRTYALTVQA ADNAPPAERR
NSICTVYIEV LPPNNQSPPR FPQLMYSLEI SEAMRVGAVL LNLQATDREG DSITYAIENG
DPQRVFNLSE TTGILTLGKA LDRESTDRYI LIITASDGRP DGTSTATVNI VVTDVNDNAP
VFDPYLPRNL SVVEEEANAF VGQVKATDPD AGINGQVHYS LGNFNNLFRI TSNGSIYTAV
KLNREVRDYY ELVVVATDGA VHPRHSTLTL AIKVLDIDDN SPVFTNSTYT VLVEENLPAG
TTILQIEAKD VDLGANVSYR IRSPEVKHFF ALHPFTGELS LLRSLDYEAF PDQEASITFL
VEAFDIYGTM PPGIATVTVI VKDMNDYPPV FSKRIYKGMV APDAVKGTPI TTVYAEDADP
PGLPASRVRY RVDDVQFPYP ASIFEVEEDS GRVITRVNLN EEPTTIFKLV VVAFDDGEPV
MSSSATVKIL VLHPGEIPRF TQEEYRPPPV SELATKGTMV GVISAAAINQ SIVYSIVSGN
EEDTFGINNI TGVIYVNGPL DYETRTSYVL RVQADSLEVV LANLRVPSKS NTAKVYIEIQ
DENNHPPVFQ KKFYIGGVSE DARMFTSVLR VKATDKDTGN YSVMAYRLII PPIKEGKEGF
VVETYTGLIK TAMLFHNMRR SYFKFQVIAT DDYGKGLSGK ADVLVSVVNQ LDMQVIVSNV
PPTLVEKKIE DLTEILDRYV QEQIPGAKVV VESIGARRHG DAFSLEDYTK CDLTVYAIDP
QTNRAIDRNE LFKFLDGKLL DINKDFQPYY GEGGRILEIR TPEAVTSIKK RGESLGYTEG
ALLALAFIII LCCIPAILVV LVSYRQRQAE CTKTARIQAA LPAAKPAVPA PAPVAAPPPP
PPPPPGAHLY EELGDSSILY YRYEMPQYGS RRRLLPPAGQ EEYGEVVGEA EEEYEEEEWA
RKRMIKLVVD REYETSSTGE DSAPECQRNR LHHPSIHSNI NGNIYIAQNG SVVRTRRACL
TDNLKVASPV RLGGPFKKLD KLAVTHEENV PLNTLSKGPF STEKMNARPT LVTFAPCPVG
TDNTAVKPLR NRLKSTVEQE SMIDSKNIKE ALEFHSDHTQ SDDEELWMGP WNNLHIPMTK
L*

mutated AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD GWRYMYCKLA RGGPPATIVA IDEESRNGTI
LVDNMLIKGT AGGPDPTIEL SLKDNVDYWV LMDPVKQMLF LNSTGRVLDR DPPMNIHSIV
VQVQCINKKV GTIIYHEVRI VVRDRNDNSP TFKHESYYAT VNELTPVGTT IFTGFSGDNG
ATDIDDGPNG QIEYVIQYNP DDPTSNDTFE IPLMLTGNIV LRKRLNYEDK TRYFVIIQAN
DRAQNLNERR TTTTTLTVDV LDGDDLGPMF LPCVLVPNTR DCRPLTYQAA IPELRTPEEL
NPIIVTPPIQ AIDQDRNIQP PSDRPGILYS ILVGTPEDYP RFFHMHPRTA ELSLLEPVNR
DFHQKFDLVI KAEQDNGHPL PAFAGLHIEI LDENNQSPYF TMPSYQGYIL ESAPVGATIS
DSLNLTSPLR IVALDKDIEA TKDPELHLFL NDYTSVFTVT QTGITRYLTL LQPVDREEQQ
TYTFSITAFD GVQESEPVIV NIQVMDANDN TPTFPEISYD VYVYTDMRPG DSVIQLTAVD
ADEGSNGEIT YEILVGAQGD FIINKTTGLI TIAPGVEMIV GRTYALTVQA ADNAPPAERR
NSICTVYIEV LPPNNQSPPR FPQLMYSLEI SEAMRVGAVL LNLQATDREG DSITYAIENG
DPQRVFNLSE TTGILTLGKA LDRESTDRYI LIITASDGRP DGTSTATVNI VVTDVNDNAP
VFDPYLPRNL SVVEEEANAF VGQVKATDPD AGINGQVHYS LGNFNNLFRI TSNGSIYTAV
KLNREVRDYY ELVVVATDGA VHPRHSTLTL AIKVLDIDDN SPVFTNSTYT VLVEENLPAG
TTILQIEAKD VDLGANVSYR IRSPEVKHFF ALHPFTGELS LLRSLDYEAF PDQEASITFL
VEAFDIYGTM PPGIATVTVI VKDMNDYPPV FSKRIYKGMV APDAVKGTPI TTVYAEDADP
PGLPASRVRY RVDDVQFPYP ASIFEVEEDS GRVITRVNLN EEPTTIFKLV VVAFDDGEPV
MSSSATVKIL VLHPGEIPRF TQEEYRPPPV SELATKGTMV GVISAAAINQ SIVYSIVSGN
EEDTFGINNI TGVIYVNGPL DYETRTSYVL RVQADSLEVV LANLRVPSKS NTAKVYIEIQ
DENNHPPVFQ KKFYIGGVSE DARMFTSVLR VKATDKDTGN YSVMAYRLII PPIKEGKEGF
VVETYTGLIK TAMLFHNMRR SYFKFQVIAT DDYGKGLSGK ADVLVSVVNQ LDMQVIVSNV
PPTLVEKKIE DLTEILDRYV QEQIPGAKVV VESIGARRHG DAFSLEDYTK CDLTVYAIDP
QTNRAIDRNE LFKFLDGKLL DINKDFQPYY GEGGRILEIR TPEAVTSIKK RGESLGYTEG
ALLALAFIII LCCIPAILVV LVSYRQRQAE CTKTARIQAA LPAAKPAVPA PAPVAAPPPP
PPPPPGAHLY EELGDSSILY YRYEMPQYGS RRRLLPPAGQ EEYGEVVGEA EEEYEEEEWA
RKRMIKLVVD REYETSSTGE DSAPECQRNR LHHPSIHSNI NGNIYIAQNG SVVRTRRACL
TDNLKVASPV RLGGPFKKLD KLAVTHEENV PLNTLSKGPF STEKMNARPT LVTFAPCPVG
TDNTAVKPLR NRLKSTVEQE SMIDSKNIKE ALEFHSDHTQ SDDEELWMGP WNNLHIPMTK
L*

speed

0.13 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1.41262538386557e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:55955444T>GN/A show variant in all transcripts IGV

HGNC symbol

PCDH15

Ensembl transcript ID

ENST00000395432

Genbank transcript ID

NM_001142767

UniProt peptide

Q96QU1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1193A>C
cDNA.1588A>C
g.1432259A>C

AA changes

D398A Score: 126 explain score(s)

position(s) of altered AA
if AA alteration in CDS

398

frameshift

known variant

Reference ID: rs4935502

database	homozygous (G/G)	heterozygous	allele carriers
1000G	481	767	1248
ExAC	5615	17649	23264

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.245	1
	4.774	1
(flanking)	5.784	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	1432260	sequence motif lost	-	wt: AGAT\|gtaa mu: AGCT.gtaa
Donor marginally increased	1432252	wt: 0.9798 / mu: 0.9914 (marginal change - not scored)	wt: AGGACATAGAAGATG mu: AGGACATAGAAGCTG	GACA\|taga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

398

mutated

not conserved

398

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000009794

435

Fcatus

not conserved

ENSFCAG00000010122

435

Mmusculus

all identical

ENSMUSG00000052613

440

Ggallus

all conserved

ENSGALG00000002744

383

Trubripes

all conserved

ENSTRUG00000010819

424

Drerio

all conserved

ENSDARG00000008127

383

Dmelanogaster

all identical

FBgn0039709

427

Celegans

not conserved

F15B9.7

302

Xtropicalis

all conserved

ENSXETG00000018945

386

protein features

start (aa)	end (aa)	feature	details
27	1376	TOPO_DOM	Extracellular (Potential).	lost
396	509	DOMAIN	Cadherin 4.	lost
419	419	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
467	467	CONFLICT	Q -> L (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
510	616	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
559	559	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
617	717	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
662	662	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
719	819	DOMAIN	Cadherin 7.	might get lost (downstream of altered splice site)
724	724	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
768	768	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
820	926	DOMAIN	Cadherin 8.	might get lost (downstream of altered splice site)
821	821	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
851	851	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
927	1035	DOMAIN	Cadherin 9.	might get lost (downstream of altered splice site)
1037	1144	DOMAIN	Cadherin 10.	might get lost (downstream of altered splice site)
1064	1064	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1084	1084	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1145	1259	DOMAIN	Cadherin 11.	might get lost (downstream of altered splice site)
1175	1175	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1276	1276	CONFLICT	Q -> R (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
1377	1397	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1398	1955	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1435	1443	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1746	1752	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1815	1823	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1826	1831	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5748 / 5748

position (AA) of stopcodon in wt / mu AA sequence

1916 / 1916

position of stopcodon in wt / mu cDNA

6143 / 6143

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

396 / 396

chromosome

strand

-1

last intron/exon boundary

4643

theoretical NMD boundary in CDS

4197

length of CDS

5748

coding sequence (CDS) position

1193

cDNA position
(for ins/del: last normal base / first normal base)

1588

gDNA position
(for ins/del: last normal base / first normal base)

1432259

chromosomal position
(for ins/del: last normal base / first normal base)

55955444

original gDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT

altered gDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT

original cDNA sequence snippet

TCTGGACAAGGACATAGAAGATACAAAAGACCCAGAGCTTC

altered cDNA sequence snippet

TCTGGACAAGGACATAGAAGCTACAAAAGACCCAGAGCTTC

wildtype AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPDR AQNLNERRTT TTTLTVDVLD GDDLGPMFLP CVLVPNTRDC
RPLTYQAAIP ELRTPEELNP IIVTPPIQAI DQDRNIQPPS DRPGILYSIL VGTPEDYPRF
FHMHPRTAEL SLLEPVNRDF HQKFDLVIKA EQDNGHPLPA FAGLHIEILD ENNQSPYFTM
PSYQGYILES APVGATISDS LNLTSPLRIV ALDKDIEDTK DPELHLFLND YTSVFTVTQT
GITRYLTLLQ PVDREEQQTY TFSITAFDGV QESEPVIVNI QVMDANDNTP TFPEISYDVY
VYTDMRPGDS VIQLTAVDAD EGSNGEITYE ILVGAQGDFI INKTTGLITI APGVEMIVGR
TYALTVQAAD NAPPAERRNS ICTVYIEVLP PNNQSPPRFP QLMYSLEISE AMRVGAVLLN
LQATDREGDS ITYAIENGDP QRVFNLSETT GILTLGKALD RESTDRYILI ITASDGRPDG
TSTATVNIVV TDVNDNAPVF DPYLPRNLSV VEEEANAFVG QVKATDPDAG INGQVHYSLG
NFNNLFRITS NGSIYTAVKL NREVRDYYEL VVVATDGAVH PRHSTLTLAI KVLDIDDNSP
VFTNSTYTVL VEENLPAGTT ILQIEAKDVD LGANVSYRIR SPEVKHFFAL HPFTGELSLL
RSLDYEAFPD QEASITFLVE AFDIYGTMPP GIATVTVIVK DMNDYPPVFS KRIYKGMVAP
DAVKGTPITT VYAEDADPPG LPASRVRYRV DDVQFPYPAS IFEVEEDSGR VITRVNLNEE
PTTIFKLVVV AFDDGEPVMS SSATVKILVL HPGEIPRFTQ EEYRPPPVSE LATKGTMVGV
ISAAAINQSI VYSIVSGNEE DTFGINNITG VIYVNGPLDY ETRTSYVLRV QADSLEVVLA
NLRVPSKSNT AKVYIEIQDE NNHPPVFQKK FYIGGVSEDA RMFTSVLRVK ATDKDTGNYS
VMAYRLIIPP IKEGKEGFVV ETYTGLIKTA MLFHNMRRSY FKFQVIATDD YGKGLSGKAD
VLVSVVNQLD MQVIVSNVPP TLVEKKIEDL TEILDRYVQE QIPGAKVVVE SIGARRHGDA
FSLEDYTKCD LTVYAIDPQT NRAIDRNELF KFLDGKLLDI NKDFQPYYGE GGRILEIRTP
EAVTSIKKRG ESLGYTEGAL LALAFIIILC CIPAILVVLV SYRQRQAECT KTARIQAALP
AAKPAVPAPA PVAAPPPPPP PPPGAHLYEE LGDSSILFLL YHFQQSRGNN SVSEDRKHQQ
VVMPFSSNTI EAHKSAHVDG SLKSNKLKSA RKFTFLSDED DLSAHNPLYK ENISQVSTNS
DISQRTDFVD PFSPKIQAKS KSLRGPREKI QRLWSQSVSL PRRLMRKVPN RPEIIDLQQW
QGTRQKAENE NTGICTNKRG SSNPLLTTEE ANLTEKEEIR QGETLMIEGT EQLKSLSSDS
SFCFPRPHFS FSTLPTVSRT VELKSEPNVI SSPAECSLEL SPSRPCVLHS SLSRRETPIC
MLPIETERNI FENFAHPPNI SPSACPLPPP PPISPPSPPP APAPLAPPPD ISPFSLFCPP
PSPPSIPLPL PPPTFFPLSV STSGPPTPPL LPPFPTPLPP PPPSIPCPPP PSASFLSTEC
VCITGVKCTT NLMPAEKIKS SMTQLSTTTV CKTDPQREPK GILRHVKNLA ELEKSVANMY
SQIEKNYLRT NVSELQTMCP SEVTNMEITS EQNKGSLNNI VEGTEKQSHS QSTSL*

mutated AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPDR AQNLNERRTT TTTLTVDVLD GDDLGPMFLP CVLVPNTRDC
RPLTYQAAIP ELRTPEELNP IIVTPPIQAI DQDRNIQPPS DRPGILYSIL VGTPEDYPRF
FHMHPRTAEL SLLEPVNRDF HQKFDLVIKA EQDNGHPLPA FAGLHIEILD ENNQSPYFTM
PSYQGYILES APVGATISDS LNLTSPLRIV ALDKDIEATK DPELHLFLND YTSVFTVTQT
GITRYLTLLQ PVDREEQQTY TFSITAFDGV QESEPVIVNI QVMDANDNTP TFPEISYDVY
VYTDMRPGDS VIQLTAVDAD EGSNGEITYE ILVGAQGDFI INKTTGLITI APGVEMIVGR
TYALTVQAAD NAPPAERRNS ICTVYIEVLP PNNQSPPRFP QLMYSLEISE AMRVGAVLLN
LQATDREGDS ITYAIENGDP QRVFNLSETT GILTLGKALD RESTDRYILI ITASDGRPDG
TSTATVNIVV TDVNDNAPVF DPYLPRNLSV VEEEANAFVG QVKATDPDAG INGQVHYSLG
NFNNLFRITS NGSIYTAVKL NREVRDYYEL VVVATDGAVH PRHSTLTLAI KVLDIDDNSP
VFTNSTYTVL VEENLPAGTT ILQIEAKDVD LGANVSYRIR SPEVKHFFAL HPFTGELSLL
RSLDYEAFPD QEASITFLVE AFDIYGTMPP GIATVTVIVK DMNDYPPVFS KRIYKGMVAP
DAVKGTPITT VYAEDADPPG LPASRVRYRV DDVQFPYPAS IFEVEEDSGR VITRVNLNEE
PTTIFKLVVV AFDDGEPVMS SSATVKILVL HPGEIPRFTQ EEYRPPPVSE LATKGTMVGV
ISAAAINQSI VYSIVSGNEE DTFGINNITG VIYVNGPLDY ETRTSYVLRV QADSLEVVLA
NLRVPSKSNT AKVYIEIQDE NNHPPVFQKK FYIGGVSEDA RMFTSVLRVK ATDKDTGNYS
VMAYRLIIPP IKEGKEGFVV ETYTGLIKTA MLFHNMRRSY FKFQVIATDD YGKGLSGKAD
VLVSVVNQLD MQVIVSNVPP TLVEKKIEDL TEILDRYVQE QIPGAKVVVE SIGARRHGDA
FSLEDYTKCD LTVYAIDPQT NRAIDRNELF KFLDGKLLDI NKDFQPYYGE GGRILEIRTP
EAVTSIKKRG ESLGYTEGAL LALAFIIILC CIPAILVVLV SYRQRQAECT KTARIQAALP
AAKPAVPAPA PVAAPPPPPP PPPGAHLYEE LGDSSILFLL YHFQQSRGNN SVSEDRKHQQ
VVMPFSSNTI EAHKSAHVDG SLKSNKLKSA RKFTFLSDED DLSAHNPLYK ENISQVSTNS
DISQRTDFVD PFSPKIQAKS KSLRGPREKI QRLWSQSVSL PRRLMRKVPN RPEIIDLQQW
QGTRQKAENE NTGICTNKRG SSNPLLTTEE ANLTEKEEIR QGETLMIEGT EQLKSLSSDS
SFCFPRPHFS FSTLPTVSRT VELKSEPNVI SSPAECSLEL SPSRPCVLHS SLSRRETPIC
MLPIETERNI FENFAHPPNI SPSACPLPPP PPISPPSPPP APAPLAPPPD ISPFSLFCPP
PSPPSIPLPL PPPTFFPLSV STSGPPTPPL LPPFPTPLPP PPPSIPCPPP PSASFLSTEC
VCITGVKCTT NLMPAEKIKS SMTQLSTTTV CKTDPQREPK GILRHVKNLA ELEKSVANMY
SQIEKNYLRT NVSELQTMCP SEVTNMEITS EQNKGSLNNI VEGTEKQSHS QSTSL*

speed

0.13 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1.65400571018668e-06 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:55955444T>GN/A show variant in all transcripts IGV

HGNC symbol

PCDH15

Ensembl transcript ID

ENST00000373965

Genbank transcript ID

NM_001142772

UniProt peptide

Q96QU1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1304A>C
cDNA.1699A>C
g.1432259A>C

AA changes

D435A Score: 126 explain score(s)

position(s) of altered AA
if AA alteration in CDS

435

frameshift

known variant

Reference ID: rs4935502

database	homozygous (G/G)	heterozygous	allele carriers
1000G	481	767	1248
ExAC	5615	17649	23264

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.245	1
	4.774	1
(flanking)	5.784	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	1432260	sequence motif lost	-	wt: AGAT\|gtaa mu: AGCT.gtaa
Donor marginally increased	1432252	wt: 0.9798 / mu: 0.9914 (marginal change - not scored)	wt: AGGACATAGAAGATG mu: AGGACATAGAAGCTG	GACA\|taga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

435

mutated

not conserved

435

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000009794

435

Fcatus

not conserved

ENSFCAG00000010122

435

Mmusculus

all identical

ENSMUSG00000052613

440

Ggallus

all conserved

ENSGALG00000002744

383

Trubripes

all conserved

ENSTRUG00000010819

424

Drerio

all conserved

ENSDARG00000008127

383

Dmelanogaster

all identical

FBgn0039709

427

Celegans

all identical

F15B9.7

415

Xtropicalis

all conserved

ENSXETG00000018945

386

protein features

start (aa)	end (aa)	feature	details
27	1376	TOPO_DOM	Extracellular (Potential).	lost
396	509	DOMAIN	Cadherin 4.	lost
467	467	CONFLICT	Q -> L (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
510	616	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
559	559	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
617	717	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
662	662	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
719	819	DOMAIN	Cadherin 7.	might get lost (downstream of altered splice site)
724	724	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
768	768	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
820	926	DOMAIN	Cadherin 8.	might get lost (downstream of altered splice site)
821	821	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
851	851	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
927	1035	DOMAIN	Cadherin 9.	might get lost (downstream of altered splice site)
1037	1144	DOMAIN	Cadherin 10.	might get lost (downstream of altered splice site)
1064	1064	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1084	1084	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1145	1259	DOMAIN	Cadherin 11.	might get lost (downstream of altered splice site)
1175	1175	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1276	1276	CONFLICT	Q -> R (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
1377	1397	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1398	1955	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1435	1443	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1746	1752	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1815	1823	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1826	1831	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5055 / 5055

position (AA) of stopcodon in wt / mu AA sequence

1685 / 1685

position of stopcodon in wt / mu cDNA

5450 / 5450

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

396 / 396

chromosome

strand

-1

last intron/exon boundary

4899

theoretical NMD boundary in CDS

4453

length of CDS

5055

coding sequence (CDS) position

1304

cDNA position
(for ins/del: last normal base / first normal base)

1699

gDNA position
(for ins/del: last normal base / first normal base)

1432259

chromosomal position
(for ins/del: last normal base / first normal base)

55955444

original gDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT

altered gDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT

original cDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTTCCACCCAGTGGAGTTC

altered cDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTTCCACCCAGTGGAGTTC

wildtype AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEDVPPSG VPTKDPELHL FLNDYTSVFT VTQTGITRYL TLLQPVDREE
QQTYTFSITA FDGVQESEPV IVNIQVMDAN DNTPTFPEIS YDVYVYTDMR PGDSVIQLTA
VDADEGSNGE ITYEILVGAQ GDFIINKTTG LITIAPGVEM IVGRTYALTV QAADNAPPAE
RRNSICTVYI EVLPPNNQSP PRFPQLMYSL EISEAMRVGA VLLNLQATDR EGDSITYAIE
NGDPQRVFNL SETTGILTLG KALDRESTDR YILIITASDG RPDGTSTATV NIVVTDVNDN
APVFDPYLPR NLSVVEEEAN AFVGQVKATD PDAGINGQVH YSLGNFNNLF RITSNGSIYT
AVKLNREVRD YYELVVVATD GAVHPRHSTL TLAIKVLDID DNSPVFTNST YTVLVEENLP
AGTTILQIEA KDVDLGANVS YRIRSPEVKH FFALHPFTGE LSLLRSLDYE AFPDQEASIT
FLVEAFDIYG TMPPGIATVT VIVKDMNDYP PVFSKRIYKG MVAPDAVKGT PITTVYAEDA
DPPGLPASRV RYRVDDVQFP YPASIFEVEE DSGRVITRVN LNEEPTTIFK LVVVAFDDGE
PVMSSSATVK ILVLHPGEIP RFTQEEYRPP PVSELATKGT MVGVISAAAI NQSIVYSIVS
GNEEDTFGIN NITGVIYVNG PLDYETRTSY VLRVQADSLE VVLANLRVPS KSNTAKVYIE
IQDENNHPPV FQKKFYIGGV SEDARMFTSV LRVKATDKDT GNYSVMAYRL IIPPIKEGKE
GFVVETYTGL IKTAMLFHNM RRSYFKFQVI ATDDYGKGLS GKADVLVSVV NQLDMQVIVS
NVPPTLVEKK IEDLTEILDR YVQEQIPGAK VVVESIGARR HGDAFSLEDY TKCDLTVYAI
DPQTNRAIDR NELFKFLDGK LLDINKDFQP YYGEGGRILE IRTPEAVTSI KKRGESLGYT
EGALLALAFI IILCCIPAIL VVLVSYRQFK VRQAECTKTA RIQAALPAAK PAVPAPAPVA
APPPPPPPPP GAHLYEELGD SSMHKYEMPQ YGSRRRLLPP AGQEEYGEVV GEAEEEYEEE
EWARKRMIKL VVDREYETSS TGEDSAPECQ RNRLHHPSIH SNINGNIYIA QNGSVVRTRR
ACLTDNLKVA SPVRLGGPFK KLDKLAVTHE ENVPLNTLSK GPFSTEKMNA RPTLVTFAPC
PVGTDNTAVK PLRNRLKSTV EQESMIDSKN IKEALEFHSD HTQSDDEELW MGPWNNLHIP
MTKL*

mutated AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEAVPPSG VPTKDPELHL FLNDYTSVFT VTQTGITRYL TLLQPVDREE
QQTYTFSITA FDGVQESEPV IVNIQVMDAN DNTPTFPEIS YDVYVYTDMR PGDSVIQLTA
VDADEGSNGE ITYEILVGAQ GDFIINKTTG LITIAPGVEM IVGRTYALTV QAADNAPPAE
RRNSICTVYI EVLPPNNQSP PRFPQLMYSL EISEAMRVGA VLLNLQATDR EGDSITYAIE
NGDPQRVFNL SETTGILTLG KALDRESTDR YILIITASDG RPDGTSTATV NIVVTDVNDN
APVFDPYLPR NLSVVEEEAN AFVGQVKATD PDAGINGQVH YSLGNFNNLF RITSNGSIYT
AVKLNREVRD YYELVVVATD GAVHPRHSTL TLAIKVLDID DNSPVFTNST YTVLVEENLP
AGTTILQIEA KDVDLGANVS YRIRSPEVKH FFALHPFTGE LSLLRSLDYE AFPDQEASIT
FLVEAFDIYG TMPPGIATVT VIVKDMNDYP PVFSKRIYKG MVAPDAVKGT PITTVYAEDA
DPPGLPASRV RYRVDDVQFP YPASIFEVEE DSGRVITRVN LNEEPTTIFK LVVVAFDDGE
PVMSSSATVK ILVLHPGEIP RFTQEEYRPP PVSELATKGT MVGVISAAAI NQSIVYSIVS
GNEEDTFGIN NITGVIYVNG PLDYETRTSY VLRVQADSLE VVLANLRVPS KSNTAKVYIE
IQDENNHPPV FQKKFYIGGV SEDARMFTSV LRVKATDKDT GNYSVMAYRL IIPPIKEGKE
GFVVETYTGL IKTAMLFHNM RRSYFKFQVI ATDDYGKGLS GKADVLVSVV NQLDMQVIVS
NVPPTLVEKK IEDLTEILDR YVQEQIPGAK VVVESIGARR HGDAFSLEDY TKCDLTVYAI
DPQTNRAIDR NELFKFLDGK LLDINKDFQP YYGEGGRILE IRTPEAVTSI KKRGESLGYT
EGALLALAFI IILCCIPAIL VVLVSYRQFK VRQAECTKTA RIQAALPAAK PAVPAPAPVA
APPPPPPPPP GAHLYEELGD SSMHKYEMPQ YGSRRRLLPP AGQEEYGEVV GEAEEEYEEE
EWARKRMIKL VVDREYETSS TGEDSAPECQ RNRLHHPSIH SNINGNIYIA QNGSVVRTRR
ACLTDNLKVA SPVRLGGPFK KLDKLAVTHE ENVPLNTLSK GPFSTEKMNA RPTLVTFAPC
PVGTDNTAVK PLRNRLKSTV EQESMIDSKN IKEALEFHSD HTQSDDEELW MGPWNNLHIP
MTKL*

speed

0.22 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1.65400571018668e-06 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:55955444T>GN/A show variant in all transcripts IGV

HGNC symbol

PCDH15

Ensembl transcript ID

ENST00000395445

Genbank transcript ID

NM_001142769

UniProt peptide

Q96QU1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1304A>C
cDNA.1699A>C
g.1432259A>C

AA changes

D435A Score: 126 explain score(s)

position(s) of altered AA
if AA alteration in CDS

435

frameshift

known variant

Reference ID: rs4935502

database	homozygous (G/G)	heterozygous	allele carriers
1000G	481	767	1248
ExAC	5615	17649	23264

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.245	1
	4.774	1
(flanking)	5.784	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	1432260	sequence motif lost	-	wt: AGAT\|gtaa mu: AGCT.gtaa
Donor marginally increased	1432252	wt: 0.9798 / mu: 0.9914 (marginal change - not scored)	wt: AGGACATAGAAGATG mu: AGGACATAGAAGCTG	GACA\|taga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

435

mutated

not conserved

435

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000009794

435

Fcatus

not conserved

ENSFCAG00000010122

435

Mmusculus

all identical

ENSMUSG00000052613

440

Ggallus

all conserved

ENSGALG00000002744

383

Trubripes

all conserved

ENSTRUG00000010819

424

Drerio

all conserved

ENSDARG00000008127

383

Dmelanogaster

all identical

FBgn0039709

427

Celegans

all identical

F15B9.7

415

Xtropicalis

all conserved

ENSXETG00000018945

386

protein features

start (aa)	end (aa)	feature	details
27	1376	TOPO_DOM	Extracellular (Potential).	lost
396	509	DOMAIN	Cadherin 4.	lost
467	467	CONFLICT	Q -> L (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
510	616	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
559	559	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
617	717	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
662	662	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
719	819	DOMAIN	Cadherin 7.	might get lost (downstream of altered splice site)
724	724	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
768	768	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
820	926	DOMAIN	Cadherin 8.	might get lost (downstream of altered splice site)
821	821	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
851	851	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
927	1035	DOMAIN	Cadherin 9.	might get lost (downstream of altered splice site)
1037	1144	DOMAIN	Cadherin 10.	might get lost (downstream of altered splice site)
1064	1064	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1084	1084	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1145	1259	DOMAIN	Cadherin 11.	might get lost (downstream of altered splice site)
1175	1175	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1276	1276	CONFLICT	Q -> R (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
1377	1397	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1398	1955	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1435	1443	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1746	1752	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1815	1823	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1826	1831	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5358 / 5358

position (AA) of stopcodon in wt / mu AA sequence

1786 / 1786

position of stopcodon in wt / mu cDNA

5753 / 5753

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

396 / 396

chromosome

strand

-1

last intron/exon boundary

4899

theoretical NMD boundary in CDS

4453

length of CDS

5358

coding sequence (CDS) position

1304

cDNA position
(for ins/del: last normal base / first normal base)

1699

gDNA position
(for ins/del: last normal base / first normal base)

1432259

chromosomal position
(for ins/del: last normal base / first normal base)

55955444

original gDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT

altered gDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT

original cDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTTCCACCCAGTGGAGTTC

altered cDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTTCCACCCAGTGGAGTTC

wildtype AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEDVPPSG VPTKDPELHL FLNDYTSVFT VTQTGITRYL TLLQPVDREE
QQTYTFSITA FDGVQESEPV IVNIQVMDAN DNTPTFPEIS YDVYVYTDMR PGDSVIQLTA
VDADEGSNGE ITYEILVGAQ GDFIINKTTG LITIAPGVEM IVGRTYALTV QAADNAPPAE
RRNSICTVYI EVLPPNNQSP PRFPQLMYSL EISEAMRVGA VLLNLQATDR EGDSITYAIE
NGDPQRVFNL SETTGILTLG KALDRESTDR YILIITASDG RPDGTSTATV NIVVTDVNDN
APVFDPYLPR NLSVVEEEAN AFVGQVKATD PDAGINGQVH YSLGNFNNLF RITSNGSIYT
AVKLNREVRD YYELVVVATD GAVHPRHSTL TLAIKVLDID DNSPVFTNST YTVLVEENLP
AGTTILQIEA KDVDLGANVS YRIRSPEVKH FFALHPFTGE LSLLRSLDYE AFPDQEASIT
FLVEAFDIYG TMPPGIATVT VIVKDMNDYP PVFSKRIYKG MVAPDAVKGT PITTVYAEDA
DPPGLPASRV RYRVDDVQFP YPASIFEVEE DSGRVITRVN LNEEPTTIFK LVVVAFDDGE
PVMSSSATVK ILVLHPGEIP RFTQEEYRPP PVSELATKGT MVGVISAAAI NQSIVYSIVS
GNEEDTFGIN NITGVIYVNG PLDYETRTSY VLRVQADSLE VVLANLRVPS KSNTAKVYIE
IQDENNHPPV FQKKFYIGGV SEDARMFTSV LRVKATDKDT GNYSVMAYRL IIPPIKEGKE
GFVVETYTGL IKTAMLFHNM RRSYFKFQVI ATDDYGKGLS GKADVLVSVV NQLDMQVIVS
NVPPTLVEKK IEDLTEILDR YVQEQIPGAK VVVESIGARR HGDAFSLEDY TKCDLTVYAI
DPQTNRAIDR NELFKFLDGK LLDINKDFQP YYGEGGRILE IRTPEAVTSI KKRGESLGYT
EGALLALAFI IILCCIPAIL VVLVSYRQFK VRQAECTKTA RIQAALPAAK PAVPAPAPVA
APPPPPPPPP GAHLYEELGD SSMHKYEMPQ YGSRRRLLPP AGQEEYGEVV GEAEEEYEEE
EEEPKKIKKP KVEIREPSEE EEVVVTIEKP PAAEPTYTTW KRARIFPMIF KKVRGLADKR
GIVDLEGEEW QRRLEEEDKD YLKLTLDQEE ATESTVESEE ESSSDYTEYS EEESEFSESE
TTEEESESET PSEEEESSTP ESEESESTES EGEKARKNIV LARRRPMVEE VKEVKGRKEE
PQEEQKEPKM EEEEHSEEEE SGPAPVEEST DPEAQDIPEE GSAESASVEG GVESEEESES
GSSSSSSESQ SGGPWGYQVP AYDRSKNANQ KKSPGANSEG YNTAL*

mutated AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEAVPPSG VPTKDPELHL FLNDYTSVFT VTQTGITRYL TLLQPVDREE
QQTYTFSITA FDGVQESEPV IVNIQVMDAN DNTPTFPEIS YDVYVYTDMR PGDSVIQLTA
VDADEGSNGE ITYEILVGAQ GDFIINKTTG LITIAPGVEM IVGRTYALTV QAADNAPPAE
RRNSICTVYI EVLPPNNQSP PRFPQLMYSL EISEAMRVGA VLLNLQATDR EGDSITYAIE
NGDPQRVFNL SETTGILTLG KALDRESTDR YILIITASDG RPDGTSTATV NIVVTDVNDN
APVFDPYLPR NLSVVEEEAN AFVGQVKATD PDAGINGQVH YSLGNFNNLF RITSNGSIYT
AVKLNREVRD YYELVVVATD GAVHPRHSTL TLAIKVLDID DNSPVFTNST YTVLVEENLP
AGTTILQIEA KDVDLGANVS YRIRSPEVKH FFALHPFTGE LSLLRSLDYE AFPDQEASIT
FLVEAFDIYG TMPPGIATVT VIVKDMNDYP PVFSKRIYKG MVAPDAVKGT PITTVYAEDA
DPPGLPASRV RYRVDDVQFP YPASIFEVEE DSGRVITRVN LNEEPTTIFK LVVVAFDDGE
PVMSSSATVK ILVLHPGEIP RFTQEEYRPP PVSELATKGT MVGVISAAAI NQSIVYSIVS
GNEEDTFGIN NITGVIYVNG PLDYETRTSY VLRVQADSLE VVLANLRVPS KSNTAKVYIE
IQDENNHPPV FQKKFYIGGV SEDARMFTSV LRVKATDKDT GNYSVMAYRL IIPPIKEGKE
GFVVETYTGL IKTAMLFHNM RRSYFKFQVI ATDDYGKGLS GKADVLVSVV NQLDMQVIVS
NVPPTLVEKK IEDLTEILDR YVQEQIPGAK VVVESIGARR HGDAFSLEDY TKCDLTVYAI
DPQTNRAIDR NELFKFLDGK LLDINKDFQP YYGEGGRILE IRTPEAVTSI KKRGESLGYT
EGALLALAFI IILCCIPAIL VVLVSYRQFK VRQAECTKTA RIQAALPAAK PAVPAPAPVA
APPPPPPPPP GAHLYEELGD SSMHKYEMPQ YGSRRRLLPP AGQEEYGEVV GEAEEEYEEE
EEEPKKIKKP KVEIREPSEE EEVVVTIEKP PAAEPTYTTW KRARIFPMIF KKVRGLADKR
GIVDLEGEEW QRRLEEEDKD YLKLTLDQEE ATESTVESEE ESSSDYTEYS EEESEFSESE
TTEEESESET PSEEEESSTP ESEESESTES EGEKARKNIV LARRRPMVEE VKEVKGRKEE
PQEEQKEPKM EEEEHSEEEE SGPAPVEEST DPEAQDIPEE GSAESASVEG GVESEEESES
GSSSSSSESQ SGGPWGYQVP AYDRSKNANQ KKSPGANSEG YNTAL*

speed

0.21 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 8.88930669819938e-07 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:55955444T>GN/A show variant in all transcripts IGV

HGNC symbol

PCDH15

Ensembl transcript ID

ENST00000409834

Genbank transcript ID

N/A

UniProt peptide

Q96QU1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.116A>C
cDNA.692A>C
g.1432259A>C

AA changes

D39A Score: 126 explain score(s)

position(s) of altered AA
if AA alteration in CDS

frameshift

known variant

Reference ID: rs4935502

database	homozygous (G/G)	heterozygous	allele carriers
1000G	481	767	1248
ExAC	5615	17649	23264

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.245	1
	4.774	1
(flanking)	5.784	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	1432260	sequence motif lost	-	wt: AGAT\|gtaa mu: AGCT.gtaa
Donor marginally increased	1432252	wt: 0.9798 / mu: 0.9914 (marginal change - not scored)	wt: AGGACATAGAAGATG mu: AGGACATAGAAGCTG	GACA\|taga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000009794

435

Fcatus

no alignment

ENSFCAG00000010122

n/a

Mmusculus

all identical

ENSMUSG00000052613

440

Ggallus

all conserved

ENSGALG00000002744

383

Trubripes

all conserved

ENSTRUG00000010819

424

Drerio

all conserved

ENSDARG00000008127

383

Dmelanogaster

all identical

FBgn0039709

427

Celegans

all identical

F15B9.7

399

Xtropicalis

all conserved

ENSXETG00000018945

386

protein features

start (aa)	end (aa)	feature	details
27	1376	TOPO_DOM	Extracellular (Potential).	lost
40	147	DOMAIN	Cadherin 1.	might get lost (downstream of altered splice site)
52	52	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
97	97	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
148	265	DOMAIN	Cadherin 2.	might get lost (downstream of altered splice site)
201	201	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
261	261	CONFLICT	L -> S (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
278	395	DOMAIN	Cadherin 3.	might get lost (downstream of altered splice site)
396	509	DOMAIN	Cadherin 4.	might get lost (downstream of altered splice site)
419	419	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
467	467	CONFLICT	Q -> L (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
510	616	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
559	559	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
617	717	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
662	662	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
719	819	DOMAIN	Cadherin 7.	might get lost (downstream of altered splice site)
724	724	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
768	768	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
820	926	DOMAIN	Cadherin 8.	might get lost (downstream of altered splice site)
821	821	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
851	851	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
927	1035	DOMAIN	Cadherin 9.	might get lost (downstream of altered splice site)
1037	1144	DOMAIN	Cadherin 10.	might get lost (downstream of altered splice site)
1064	1064	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1084	1084	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1145	1259	DOMAIN	Cadherin 11.	might get lost (downstream of altered splice site)
1175	1175	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1276	1276	CONFLICT	Q -> R (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
1377	1397	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1398	1955	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1435	1443	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1746	1752	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1815	1823	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1826	1831	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3453 / 3453

position (AA) of stopcodon in wt / mu AA sequence

1151 / 1151

position of stopcodon in wt / mu cDNA

4029 / 4029

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

577 / 577

chromosome

strand

-1

last intron/exon boundary

3963

theoretical NMD boundary in CDS

3336

length of CDS

3453

coding sequence (CDS) position

116

cDNA position
(for ins/del: last normal base / first normal base)

692

gDNA position
(for ins/del: last normal base / first normal base)

1432259

chromosomal position
(for ins/del: last normal base / first normal base)

55955444

original gDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT

altered gDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT

original cDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTTCCACCCAGTGGAGTTC

altered cDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTTCCACCCAGTGGAGTTC

wildtype AA sequence

MPSYQGYILE SAPVGATISD SLNLTSPLRI VALDKDIEDV PPSGVPTKDP ELHLFLNDYT
SVFTVTQTGI TRYLTLLQPV DREEQQTYTF SITAFDGVQE SEPVIVNIQV MDANDNTPTF
PEISYDVYVY TDMRPGDSVI QLTAVDADEG SNGEITYEIL VGAQGDFIIN KTTGLITIAP
GVEMIVGRTY ALTVQAADNA PPAERRNSIC TVYIEVLPPN NQSPPRFPQL MYSLEISEAM
RVGAVLLNLQ ATDREGDSIT YAIENGDPQR VFNLSETTGI LTLGKALDRE STDRYILIIT
ASDGRPDGTS TATVNIVVTD VNDNAPVFDP YLPRNLSVVE EEANAFVGQV KATDPDAGIN
GQVHYSLGNF NNLFRITSNG SIYTAVKLNR EVRDYYELVV VATDGAVHPR HSTLTLAIKV
LDIDDNSPVF TNSTYTVLVE ENLPAGTTIL QIEAKDVDLG ANVSYRIRSP EVKHFFALHP
FTGELSLLRS LDYEAFPDQE ASITFLVEAF DIYGTMPPGI ATVTVIVKDM NDYPPVFSKR
IYKGMVAPDA VKGTPITTVY AEDADPPGLP ASRVRYRVDD VQFPYPASIF EVEEDSGRVI
TRVNLNEEPT TIFKLVVVAF DDGEPVMSSS ATVKILVLHP GEIPRFTQEE YRPPPVSELA
TKGTMVGVIS AAAINQSIVY SIVSGNEEDT FGINNITGVI YVNGPLDYET RTSYVLRVQA
DSLEVVLANL RVPSKSNTAK VYIEIQDENN HPPVFQKKFY IGGVSEDARM FTSVLRVKAT
DKDTGNYSVM AYRLIIPPIK EGKEGFVVET YTGLIKTAML FHNMRRSYFK FQVIATDDYG
KGLSGKADVL VSVVNQLDMQ VIVSNVPPTL VEKKIEDLTE ILDRYVQEQI PGAKVVVESI
GARRHGDAFS LEDYTKCDLT VYAIDPQTNR AIDRNELFKF LDGKLLDINK DFQPYYGEGG
RILEIRTPEA VTSIKKRGES LGYTEGALLA LAFIIILCCI PAILVVLVSY RQFKVRQAEC
TKTARIQAAL PAAKPAVPAP APVAAPPPPP PPPPGAHLYE ELGDSSMHKN YPWSLELILA
RNMDKIITVM SMGMKCLNMG VAVDCYHQLD RRNMVRWLVK LRKNMRRKRK SQRKLKNQRL
KLESLVRRKK *

mutated AA sequence

MPSYQGYILE SAPVGATISD SLNLTSPLRI VALDKDIEAV PPSGVPTKDP ELHLFLNDYT
SVFTVTQTGI TRYLTLLQPV DREEQQTYTF SITAFDGVQE SEPVIVNIQV MDANDNTPTF
PEISYDVYVY TDMRPGDSVI QLTAVDADEG SNGEITYEIL VGAQGDFIIN KTTGLITIAP
GVEMIVGRTY ALTVQAADNA PPAERRNSIC TVYIEVLPPN NQSPPRFPQL MYSLEISEAM
RVGAVLLNLQ ATDREGDSIT YAIENGDPQR VFNLSETTGI LTLGKALDRE STDRYILIIT
ASDGRPDGTS TATVNIVVTD VNDNAPVFDP YLPRNLSVVE EEANAFVGQV KATDPDAGIN
GQVHYSLGNF NNLFRITSNG SIYTAVKLNR EVRDYYELVV VATDGAVHPR HSTLTLAIKV
LDIDDNSPVF TNSTYTVLVE ENLPAGTTIL QIEAKDVDLG ANVSYRIRSP EVKHFFALHP
FTGELSLLRS LDYEAFPDQE ASITFLVEAF DIYGTMPPGI ATVTVIVKDM NDYPPVFSKR
IYKGMVAPDA VKGTPITTVY AEDADPPGLP ASRVRYRVDD VQFPYPASIF EVEEDSGRVI
TRVNLNEEPT TIFKLVVVAF DDGEPVMSSS ATVKILVLHP GEIPRFTQEE YRPPPVSELA
TKGTMVGVIS AAAINQSIVY SIVSGNEEDT FGINNITGVI YVNGPLDYET RTSYVLRVQA
DSLEVVLANL RVPSKSNTAK VYIEIQDENN HPPVFQKKFY IGGVSEDARM FTSVLRVKAT
DKDTGNYSVM AYRLIIPPIK EGKEGFVVET YTGLIKTAML FHNMRRSYFK FQVIATDDYG
KGLSGKADVL VSVVNQLDMQ VIVSNVPPTL VEKKIEDLTE ILDRYVQEQI PGAKVVVESI
GARRHGDAFS LEDYTKCDLT VYAIDPQTNR AIDRNELFKF LDGKLLDINK DFQPYYGEGG
RILEIRTPEA VTSIKKRGES LGYTEGALLA LAFIIILCCI PAILVVLVSY RQFKVRQAEC
TKTARIQAAL PAAKPAVPAP APVAAPPPPP PPPPGAHLYE ELGDSSMHKN YPWSLELILA
RNMDKIITVM SMGMKCLNMG VAVDCYHQLD RRNMVRWLVK LRKNMRRKRK SQRKLKNQRL
KLESLVRRKK *

speed

0.12 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 5.35307636695428e-07 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:55955444T>GN/A show variant in all transcripts IGV

HGNC symbol

PCDH15

Ensembl transcript ID

ENST00000395440

Genbank transcript ID

N/A

UniProt peptide

Q96QU1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1304A>C
cDNA.1699A>C
g.1432259A>C

AA changes

D435A Score: 126 explain score(s)

position(s) of altered AA
if AA alteration in CDS

435

frameshift

known variant

Reference ID: rs4935502

database	homozygous (G/G)	heterozygous	allele carriers
1000G	481	767	1248
ExAC	5615	17649	23264

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.245	1
	4.774	1
(flanking)	5.784	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	1432260	sequence motif lost	-	wt: AGAT\|gtaa mu: AGCT.gtaa
Donor marginally increased	1432252	wt: 0.9798 / mu: 0.9914 (marginal change - not scored)	wt: AGGACATAGAAGATG mu: AGGACATAGAAGCTG	GACA\|taga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

435

mutated

not conserved

435

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000009794

435

Fcatus

no alignment

ENSFCAG00000010122

n/a

Mmusculus

all identical

ENSMUSG00000052613

440

Ggallus

all conserved

ENSGALG00000002744

383

Trubripes

all conserved

ENSTRUG00000010819

424

Drerio

all conserved

ENSDARG00000008127

383

Dmelanogaster

all identical

FBgn0039709

427

Celegans

all identical

F15B9.7

510

DSGPNGIIKYSMEGSEDF

Xtropicalis

all conserved

ENSXETG00000018945

386

protein features

start (aa)	end (aa)	feature	details
27	1376	TOPO_DOM	Extracellular (Potential).	lost
396	509	DOMAIN	Cadherin 4.	lost
467	467	CONFLICT	Q -> L (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
510	616	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
559	559	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
617	717	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
662	662	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
719	819	DOMAIN	Cadherin 7.	might get lost (downstream of altered splice site)
724	724	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
768	768	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
820	926	DOMAIN	Cadherin 8.	might get lost (downstream of altered splice site)
821	821	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
851	851	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
927	1035	DOMAIN	Cadherin 9.	might get lost (downstream of altered splice site)
1037	1144	DOMAIN	Cadherin 10.	might get lost (downstream of altered splice site)
1064	1064	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1084	1084	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1145	1259	DOMAIN	Cadherin 11.	might get lost (downstream of altered splice site)
1175	1175	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1276	1276	CONFLICT	Q -> R (in Ref. 1; AAK31581).	might get lost (downstream of altered splice site)
1377	1397	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1398	1955	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1435	1443	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1746	1752	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1815	1823	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1826	1831	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2160 / 2160

position (AA) of stopcodon in wt / mu AA sequence

720 / 720

position of stopcodon in wt / mu cDNA

2555 / 2555

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

396 / 396

chromosome

strand

-1

last intron/exon boundary

1701

theoretical NMD boundary in CDS

1255

length of CDS

2160

coding sequence (CDS) position

1304

cDNA position
(for ins/del: last normal base / first normal base)

1699

gDNA position
(for ins/del: last normal base / first normal base)

1432259

chromosomal position
(for ins/del: last normal base / first normal base)

55955444

original gDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT

altered gDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT

original cDNA sequence snippet

TCTGGACAAGGACATAGAAGATGAAGAGCCAAAGAAAATTA

altered cDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGAAGAGCCAAAGAAAATTA

wildtype AA sequence

mutated AA sequence

speed

0.19 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 5.18418779895271e-55 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:55955444T>GN/A show variant in all transcripts IGV

HGNC symbol

PCDH15

Ensembl transcript ID

ENST00000395442

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.1432259A>C

AA changes

N/A

position(s) of altered AA
if AA alteration in CDS

N/A

frameshift

N/A

known variant

Reference ID: rs4935502

database	homozygous (G/G)	heterozygous	allele carriers
1000G	481	767	1248
ExAC	5615	17649	23264

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.245	1
	4.774	1
(flanking)	5.784	1

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splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor marginally increased	1432252	wt: 0.9798 / mu: 0.9914 (marginal change - not scored)	wt: AGGACATAGAAGATG mu: AGGACATAGAAGCTG	GACA\|taga

distance from splice site

18252

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

position (AA) of stopcodon in wt / mu AA sequence

N/A

position of stopcodon in wt / mu cDNA

N/A

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

396 / 396

chromosome

strand

-1

last intron/exon boundary

1494

theoretical NMD boundary in CDS

1048

length of CDS

1953

coding sequence (CDS) position

N/A

cDNA position
(for ins/del: last normal base / first normal base)

N/A

gDNA position
(for ins/del: last normal base / first normal base)

1432259

chromosomal position
(for ins/del: last normal base / first normal base)

55955444

original gDNA sequence snippet

TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT

altered gDNA sequence snippet

TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

mutated AA sequence

N/A

speed

0.10 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems