MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000644397
Querying Taster for transcript #2: ENST00000373965
Querying Taster for transcript #3: ENST00000395445
Querying Taster for transcript #4: ENST00000613657
Querying Taster for transcript #5: ENST00000395440
Querying Taster for transcript #6: ENST00000395442
Querying Taster for transcript #7: ENST00000373957
Querying Taster for transcript #8: ENST00000395433
Querying Taster for transcript #9: ENST00000437009
Querying Taster for transcript #10: ENST00000617271
Querying Taster for transcript #11: ENST00000395446
Querying Taster for transcript #12: ENST00000409834
Querying Taster for transcript #13: ENST00000320301
Querying Taster for transcript #14: ENST00000361849
Querying Taster for transcript #15: ENST00000616114
Querying Taster for transcript #16: ENST00000621708
Querying Taster for transcript #17: ENST00000495484
Querying Taster for transcript #18: ENST00000395430
MT speed 1.67 s - this script 4.294485 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000373965	PCDH15	Undetermined	50\|50	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD
ENST00000395445	PCDH15	Deleterious	51\|49	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected
ENST00000617271	PCDH15	Deleterious	51\|49	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD
ENST00000361849	PCDH15	Deleterious	51\|49	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD
ENST00000613657	PCDH15	Deleterious	52\|48	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD
ENST00000395433	PCDH15	Deleterious	53\|47	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD
ENST00000437009	PCDH15	Deleterious	53\|47	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD
ENST00000409834	PCDH15	Deleterious	53\|47	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD
ENST00000320301(MANE Select)	PCDH15	Deleterious	53\|47	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected
ENST00000395430	PCDH15	Deleterious	53\|47	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD
ENST00000373957	PCDH15	Deleterious	54\|46	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD
ENST00000395446	PCDH15	Benign	9\|191	without_aae	No	Single base exchange	N/A	Heterozygous in gnomAD
ENST00000395440	PCDH15	Benign	11\|189	without_aae	No	Single base exchange	N/A	Heterozygous in gnomAD
ENST00000395442	PCDH15	Benign	17\|183	without_aae	No	Single base exchange	N/A	Heterozygous in gnomAD
ENST00000495484	PCDH15	Benign	26\|174	without_aae	No	Single base exchange	N/A	Heterozygous in gnomAD
ENST00000644397(MANE Select)	PCDH15	Benign	45\|55	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD
ENST00000616114	PCDH15	Benign	49\|51	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected
ENST00000621708	PCDH15	Benign	49\|51	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD

MutationT@ster 2025

Variant:

10:53961876C>A_2_ENST00000373965

Back to summary table

Prediction:

UndeterminedPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD

Model: simple_aae
Tree vote: 50|50 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:53961876C>A (GRCh38)

Gene symbol

PCDH15

Gene constraints

LOEUF: 0.85, LOF (oe): 0.72, misssense (oe): 1.01, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000373965.6

Genbank transcript ID

NM_001142772 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2885G>T
g.1666067G>T

AA changes

AAE:	R962L	?
Score:	102

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45483395
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	11	4817	4828

Protein conservation

Species	Match	AA	Alignment
Human		962	E	D	A	D	P	P	G	L	P	A	S	R	V	R	Y	R	V	D	D	V	Q	F	P	Y
mutated	not conserved	962											S	L	V	R	Y	R	V	D	D	V	Q	F	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.006	0.815
	1.2	0.878
(flanking)	0.812	0.919

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TTAGGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered gDNA sequence snippet

TTAGGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Original cDNA sequence snippet

TCCTGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered cDNA sequence snippet

TCCTGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

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 LGDSSMHKYE MPQYGSRRRL LPPAGQEEYG EVVGEAEEEY EEEEWARKRM
IKLVVDREYE TSSTGEDSAP ECQRNRLHHP SIHSNINGNI YIAQNGSVVR TRRACLTDNL
KVASPVRLGG PFKKLDKLAV THEENVPLNT LSKGPFSTEK MNARPTLVTF APCPVGTDNT
AVKPLRNRLK STVEQESMID SKNIKEALEF HSDHTQSDDE ELWMGPWNNL HIPMTKL*

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 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
SLVRYRVDDV 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 LGDSSMHKYE MPQYGSRRRL LPPAGQEEYG EVVGEAEEEY EEEEWARKRM
IKLVVDREYE TSSTGEDSAP ECQRNRLHHP SIHSNINGNI YIAQNGSVVR TRRACLTDNL
KVASPVRLGG PFKKLDKLAV THEENVPLNT LSKGPFSTEK MNARPTLVTF APCPVGTDNT
AVKPLRNRLK STVEQESMID SKNIKEALEF HSDHTQSDDE ELWMGPWNNL HIPMTKL*

Position of stopcodon in wt / mu CDS

5034 / 5034

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

1678 / 1678

Position of stopcodon in wt / mu cDNA

5429 / 5429

Position of start ATG in wt / mu cDNA

396 / 396

Last intron/exon boundary

4877

Theoretical NMD boundary in CDS

4431

Length of CDS

5034

Coding sequence (CDS) position

2885

cDNA position

3280

gDNA position

1666067

Chromosomal position

53961876

Speed

0.10 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

10:53961876C>A_3_ENST00000395445

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 51|49 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:53961876C>A (GRCh38)

Gene symbol

PCDH15

Gene constraints

LOEUF: 0.83, LOF (oe): 0.70, misssense (oe): 1.02, synonymous (oe): 1.03 ? (gnomAD)

Ensembl transcript ID

ENST00000395445.6

Genbank transcript ID

NM_001354411 (by similarity)

UniProt / AlphaMissense peptide

PCD15_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2906G>T
g.1666067G>T

AA changes

AAE:	R969L	?
Score:	102

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45483395
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	11	4817	4828

Protein conservation

Species	Match	AA	Alignment
Human		969	E	D	A	D	P	P	G	L	P	A	S	R	V	R	Y	R	V	D	D	V	Q	F	P	Y
mutated	not conserved	969				D	P	P	G	L	P	A	S	L	V	R	Y	R	V	D	D	V	Q	F	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
27	1376	TOPO_DOM	Extracellular	lost
27	1955	CHAIN		lost
927	1035	DOMAIN	Cadherin	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.006	0.815
	1.2	0.878
(flanking)	0.812	0.919

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TTAGGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered gDNA sequence snippet

TTAGGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Original cDNA sequence snippet

TCCTGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered cDNA sequence snippet

TCCTGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

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 SSMYEMPQYG SRRRLLPPAG QEEYGEVVGE AEEEYEEEEE
EPKKIKKPKV EIREPSEEEE VVVTIEKPPA AEPTYTTWKR ARIFPMIFKK VRGLADKRGI
VDLEGEEWQR RLEEEDKDYL KLTLDQEEAT ESTVESEEES SSDYTEYSEE ESEFSESETT
EEESESETPS EEEESSTPES EESESTESEG EKARKNIVLA RRRPMVEEVK EVKGRKEEPQ
EEQKEPKMEE EEHSEEEESG PAPVEESTDP EAQDIPEEGS AESASVEGGV ESEEESESGS
SSSSSESQSG GPWGYQVPAY DRSKNANQKK SPGANSEGYN TAL*

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 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
DPPGLPASLV 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 SSMYEMPQYG SRRRLLPPAG QEEYGEVVGE AEEEYEEEEE
EPKKIKKPKV EIREPSEEEE VVVTIEKPPA AEPTYTTWKR ARIFPMIFKK VRGLADKRGI
VDLEGEEWQR RLEEEDKDYL KLTLDQEEAT ESTVESEEES SSDYTEYSEE ESEFSESETT
EEESESETPS EEEESSTPES EESESTESEG EKARKNIVLA RRRPMVEEVK EVKGRKEEPQ
EEQKEPKMEE EEHSEEEESG PAPVEESTDP EAQDIPEEGS AESASVEGGV ESEEESESGS
SSSSSESQSG GPWGYQVPAY DRSKNANQKK SPGANSEGYN TAL*

Position of stopcodon in wt / mu CDS

5352 / 5352

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

1784 / 1784

Position of stopcodon in wt / mu cDNA

5687 / 5687

Position of start ATG in wt / mu cDNA

336 / 336

Last intron/exon boundary

4832

Theoretical NMD boundary in CDS

4446

Length of CDS

5352

Coding sequence (CDS) position

2906

cDNA position

3241

gDNA position

1666067

Chromosomal position

53961876

Speed

0.10 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

10:53961876C>A_10_ENST00000617271

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD

Model: simple_aae
Tree vote: 51|49 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:53961876C>A (GRCh38)

Gene symbol

PCDH15

Gene constraints

LOEUF: 0.87, LOF (oe): 0.74, misssense (oe): 1.00, synonymous (oe): 1.04 ? (gnomAD)

Ensembl transcript ID

ENST00000617271.4

Genbank transcript ID

NM_001142770 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2885G>T
g.1666067G>T

AA changes

AAE:	R962L	?
Score:	102

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45483395
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	11	4817	4828

Protein conservation

Species	Match	AA	Alignment
Human		962	E	D	A	D	P	P	G	L	P	A	S	R	V	R	Y	R	V	D	D	V	Q	F	P	Y
mutated	not conserved	962											S	L	V	R	Y	R	V	D	D	V	Q	F	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.006	0.815
	1.2	0.878
(flanking)	0.812	0.919

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TTAGGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered gDNA sequence snippet

TTAGGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Original cDNA sequence snippet

TCCTGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered cDNA sequence snippet

TCCTGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

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 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
SLVRYRVDDV 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*

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

Position of start ATG in wt / mu cDNA

396 / 396

Last intron/exon boundary

4948

Theoretical NMD boundary in CDS

4502

Length of CDS

4620

Coding sequence (CDS) position

2885

cDNA position

3280

gDNA position

1666067

Chromosomal position

53961876

Speed

0.10 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

10:53961876C>A_14_ENST00000361849

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD

Model: simple_aae
Tree vote: 51|49 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:53961876C>A (GRCh38)

Gene symbol

PCDH15

Gene constraints

LOEUF: 0.87, LOF (oe): 0.74, misssense (oe): 1.03, synonymous (oe): 1.06 ? (gnomAD)

Ensembl transcript ID

ENST00000361849.7

Genbank transcript ID

NM_001142768 (by similarity), NM_001142764 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2885G>T
g.1666067G>T

AA changes

AAE:	R962L	?
Score:	102

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45483395
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	11	4817	4828

Protein conservation

Species	Match	AA	Alignment
Human		962	E	D	A	D	P	P	G	L	P	A	S	R	V	R	Y	R	V	D	D	V	Q	F	P	Y
mutated	not conserved	962											S	L	V	R	Y	R	V	D	D	V	Q	F	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.006	0.815
	1.2	0.878
(flanking)	0.812	0.919

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TTAGGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered gDNA sequence snippet

TTAGGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Original cDNA sequence snippet

TCCTGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered cDNA sequence snippet

TCCTGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

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 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
SLVRYRVDDV 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*

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

Position of start ATG in wt / mu cDNA

396 / 396

Last intron/exon boundary

4768

Theoretical NMD boundary in CDS

4322

Length of CDS

5874

Coding sequence (CDS) position

2885

cDNA position

3280

gDNA position

1666067

Chromosomal position

53961876

Speed

0.11 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

10:53961876C>A_4_ENST00000613657

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD

Model: simple_aae
Tree vote: 52|48 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:53961876C>A (GRCh38)

Gene symbol

PCDH15

Gene constraints

LOEUF: 0.88, LOF (oe): 0.75, misssense (oe): 1.03, synonymous (oe): 1.03 ? (gnomAD)

Ensembl transcript ID

ENST00000613657.6

Genbank transcript ID

NM_001142769 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2921G>T
g.1666067G>T

AA changes

AAE:	R974L	?
Score:	102

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45483395
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	11	4817	4828

Protein conservation

Species	Match	AA	Alignment
Human		974	E	D	A	D	P	P	G	L	P	A	S	R	V	R	Y	R	V	D	D	V	Q	F	P	Y
mutated	not conserved	974	E	D	A	D	P	P	G	L	P	A	S	L	V	R	Y	R	V	D	D	V	Q	F	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.006	0.815
	1.2	0.878
(flanking)	0.812	0.919

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TTAGGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered gDNA sequence snippet

TTAGGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Original cDNA sequence snippet

TCCTGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered cDNA sequence snippet

TCCTGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Wildtype AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DWQYEDCKLA 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 VPPSGVPTKD PELHLFLNDY TSVFTVTQTG ITRYLTLLQP
VDREEQQTYT FSITAFDGVQ ESEPVIVNIQ VMDANDNTPT FPEISYDVYV YTDMRPGDSV
IQLTAVDADE GSNGEITYEI LVGAQGDFII NKTTGLITIA PGVEMIVGRT YALTVQAADN
APPAERRNSI CTVYIEVLPP NNQSPPRFPQ LMYSLEISEA MRVGAVLLNL QATDREGDSI
TYAIENGDPQ RVFNLSETTG ILTLGKALDR ESTDRYILII TASDGRPDGT STATVNIVVT
DVNDNAPVFD PYLPRNLSVV EEEANAFVGQ VKATDPDAGI NGQVHYSLGN FNNLFRITSN
GSIYTAVKLN REVRDYYELV VVATDGAVHP RHSTLTLAIK VLDIDDNSPV FTNSTYTVLV
EENLPAGTTI LQIEAKDVDL GANVSYRIRS PEVKHFFALH PFTGELSLLR SLDYEAFPDQ
EASITFLVEA FDIYGTMPPG IATVTVIVKD MNDYPPVFSK RIYKGMVAPD AVKGTPITTV
YAEDADPPGL PASRVRYRVD DVQFPYPASI FEVEEDSGRV ITRVNLNEEP TTIFKLVVVA
FDDGEPVMSS SATVKILVLH PGEIPRFTQE EYRPPPVSEL ATKGTMVGVI SAAAINQSIV
YSIVSGNEED TFGINNITGV IYVNGPLDYE TRTSYVLRVQ ADSLEVVLAN LRVPSKSNTA
KVYIEIQDEN NHPPVFQKKF YIGGVSEDAR MFTSVLRVKA TDKDTGNYSV MAYRLIIPPI
KEGKEGFVVE TYTGLIKTAM LFHNMRRSYF KFQVIATDDY GKGLSGKADV LVSVVNQLDM
QVIVSNVPPT LVEKKIEDLT EILDRYVQEQ IPGAKVVVES IGARRHGDAF SLEDYTKCDL
TVYAIDPQTN RAIDRNELFK FLDGKLLDIN KDFQPYYGEG GRILEIRTPE AVTSIKKRGE
SLGYTEGALL ALAFIIILCC IPAILVVLVS YRQFKVRQAE CTKTARIQAA LPAAKPAVPA
PAPVAAPPPP PPPPPGAHLY EELGDSSMHK YEMPQYGSRR RLLPPAGQEE YGEVVGEAEE
EYEEEEEEPK KIKKPKVEIR EPSEEEEVVV TIEKPPAAEP TYTTWKRARI FPMIFKKVRG
LADKRGIVDL EGEEWQRRLE EEDKDYLKLT LDQEEATEST VESEEESSSD YTEYSEEESE
FSESETTEEE SESETPSEEE ESSTPESEES ESTESEGEKA RKNIVLARRR PMVEEVKEVK
GRKEEPQEEQ KEPKMEEEEH SEEEESGPAP VEESTDPEAQ DIPEEGSAES ASVEGGVESE
EESESGSSSS SSESQSGGPW GYQVPAYDRS KNANQKKSPG ANSEGYNTAL *

Mutated AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DWQYEDCKLA 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 VPPSGVPTKD PELHLFLNDY TSVFTVTQTG ITRYLTLLQP
VDREEQQTYT FSITAFDGVQ ESEPVIVNIQ VMDANDNTPT FPEISYDVYV YTDMRPGDSV
IQLTAVDADE GSNGEITYEI LVGAQGDFII NKTTGLITIA PGVEMIVGRT YALTVQAADN
APPAERRNSI CTVYIEVLPP NNQSPPRFPQ LMYSLEISEA MRVGAVLLNL QATDREGDSI
TYAIENGDPQ RVFNLSETTG ILTLGKALDR ESTDRYILII TASDGRPDGT STATVNIVVT
DVNDNAPVFD PYLPRNLSVV EEEANAFVGQ VKATDPDAGI NGQVHYSLGN FNNLFRITSN
GSIYTAVKLN REVRDYYELV VVATDGAVHP RHSTLTLAIK VLDIDDNSPV FTNSTYTVLV
EENLPAGTTI LQIEAKDVDL GANVSYRIRS PEVKHFFALH PFTGELSLLR SLDYEAFPDQ
EASITFLVEA FDIYGTMPPG IATVTVIVKD MNDYPPVFSK RIYKGMVAPD AVKGTPITTV
YAEDADPPGL PASLVRYRVD DVQFPYPASI FEVEEDSGRV ITRVNLNEEP TTIFKLVVVA
FDDGEPVMSS SATVKILVLH PGEIPRFTQE EYRPPPVSEL ATKGTMVGVI SAAAINQSIV
YSIVSGNEED TFGINNITGV IYVNGPLDYE TRTSYVLRVQ ADSLEVVLAN LRVPSKSNTA
KVYIEIQDEN NHPPVFQKKF YIGGVSEDAR MFTSVLRVKA TDKDTGNYSV MAYRLIIPPI
KEGKEGFVVE TYTGLIKTAM LFHNMRRSYF KFQVIATDDY GKGLSGKADV LVSVVNQLDM
QVIVSNVPPT LVEKKIEDLT EILDRYVQEQ IPGAKVVVES IGARRHGDAF SLEDYTKCDL
TVYAIDPQTN RAIDRNELFK FLDGKLLDIN KDFQPYYGEG GRILEIRTPE AVTSIKKRGE
SLGYTEGALL ALAFIIILCC IPAILVVLVS YRQFKVRQAE CTKTARIQAA LPAAKPAVPA
PAPVAAPPPP PPPPPGAHLY EELGDSSMHK YEMPQYGSRR RLLPPAGQEE YGEVVGEAEE
EYEEEEEEPK KIKKPKVEIR EPSEEEEVVV TIEKPPAAEP TYTTWKRARI FPMIFKKVRG
LADKRGIVDL EGEEWQRRLE EEDKDYLKLT LDQEEATEST VESEEESSSD YTEYSEEESE
FSESETTEEE SESETPSEEE ESSTPESEES ESTESEGEKA RKNIVLARRR PMVEEVKEVK
GRKEEPQEEQ KEPKMEEEEH SEEEESGPAP VEESTDPEAQ DIPEEGSAES ASVEGGVESE
EESESGSSSS SSESQSGGPW GYQVPAYDRS KNANQKKSPG ANSEGYNTAL *

Position of stopcodon in wt / mu CDS

5373 / 5373

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

1791 / 1791

Position of stopcodon in wt / mu cDNA

5708 / 5708

Position of start ATG in wt / mu cDNA

336 / 336

Last intron/exon boundary

4853

Theoretical NMD boundary in CDS

4467

Length of CDS

5373

Coding sequence (CDS) position

2921

cDNA position

3256

gDNA position

1666067

Chromosomal position

53961876

Speed

0.12 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

10:53961876C>A_8_ENST00000395433

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD

Model: simple_aae
Tree vote: 53|47 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:53961876C>A (GRCh38)

Gene symbol

PCDH15

Gene constraints

LOEUF: 0.88, LOF (oe): 0.74, misssense (oe): 1.02, synonymous (oe): 1.06 ? (gnomAD)

Ensembl transcript ID

ENST00000395433.5

Genbank transcript ID

NM_001142773 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2819G>T
g.1666067G>T

AA changes

AAE:	R940L	?
Score:	102

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45483395
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	11	4817	4828

Protein conservation

Species	Match	AA	Alignment
Human		940	E	D	A	D	P	P	G	L	P	A	S	R	V	R	Y	R	V	D	D	V	Q	F	P	Y
mutated	not conserved	940	E	D	A	D	P	P	G	L	P	A	S	L	V	R	Y	R	V	D	D	V	Q	F	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.006	0.815
	1.2	0.878
(flanking)	0.812	0.919

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TTAGGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered gDNA sequence snippet

TTAGGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Original cDNA sequence snippet

TCCTGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered cDNA sequence snippet

TCCTGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

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 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 ADPPGLPASL 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*

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

Position of start ATG in wt / mu cDNA

396 / 396

Last intron/exon boundary

4693

Theoretical NMD boundary in CDS

4247

Length of CDS

5799

Coding sequence (CDS) position

2819

cDNA position

3214

gDNA position

1666067

Chromosomal position

53961876

Speed

0.12 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

10:53961876C>A_9_ENST00000437009

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD

Model: simple_aae
Tree vote: 53|47 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:53961876C>A (GRCh38)

Gene symbol

PCDH15

Gene constraints

LOEUF: 0.86, LOF (oe): 0.72, misssense (oe): 1.03, synonymous (oe): 1.06 ? (gnomAD)

Ensembl transcript ID

ENST00000437009.5

Genbank transcript ID

NM_001142765 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2672G>T
g.1666067G>T

AA changes

AAE:	R891L	?
Score:	102

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45483395
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	11	4817	4828

Protein conservation

Species	Match	AA	Alignment
Human		891	E	D	A	D	P	P	G	L	P	A	S	R	V	R	Y	R	V	D	D	V	Q	F	P	Y
mutated	not conserved	891	E	D	A	D	P	P	G	L	P	A	S	L	V	R	Y	R	V	D	D	V	Q
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.006	0.815
	1.2	0.878
(flanking)	0.812	0.919

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TTAGGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered gDNA sequence snippet

TTAGGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Original cDNA sequence snippet

TCCTGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered cDNA sequence snippet

TCCTGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

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
ILVVLVSYRQ FKVRQAECTK TARIQAALPA AKPAVPAPAP VAAPPPPPPP PPGAHLYEEL
GDSSMHNLFL 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 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 LVRYRVDDVQ
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
ILVVLVSYRQ FKVRQAECTK TARIQAALPA AKPAVPAPAP VAAPPPPPPP PPGAHLYEEL
GDSSMHNLFL 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*

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

Position of start ATG in wt / mu cDNA

396 / 396

Last intron/exon boundary

4555

Theoretical NMD boundary in CDS

4109

Length of CDS

5661

Coding sequence (CDS) position

2672

cDNA position

3067

gDNA position

1666067

Chromosomal position

53961876

Speed

0.10 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

10:53961876C>A_12_ENST00000409834

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD

Model: simple_aae
Tree vote: 53|47 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:53961876C>A (GRCh38)

Gene symbol

PCDH15

Gene constraints

LOEUF: 0.94, LOF (oe): 0.77, misssense (oe): 0.99, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000409834.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1718G>T
g.1666067G>T

AA changes

AAE:	R573L	?
Score:	102

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45483395
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	11	4817	4828

Protein conservation

Species	Match	AA	Alignment
Human		573	E	D	A	D	P	P	G	L	P	A	S	R	V	R	Y	R	V	D	D	V	Q	F	P	Y
mutated	not conserved	573	E	D	A	D	P	P	G	L	P	A	S	L	V	R	Y	R	V	D	D	V	Q	F	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.006	0.815
	1.2	0.878
(flanking)	0.812	0.919

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TTAGGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered gDNA sequence snippet

TTAGGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Original cDNA sequence snippet

TCCTGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered cDNA sequence snippet

TCCTGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

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 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 ASLVRYRVDD 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 *

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

Position of start ATG in wt / mu cDNA

577 / 577

Last intron/exon boundary

3962

Theoretical NMD boundary in CDS

3335

Length of CDS

3453

Coding sequence (CDS) position

1718

cDNA position

2294

gDNA position

1666067

Chromosomal position

53961876

Speed

0.11 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

10:53961876C>A_13_ENST00000320301

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 53|47 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:53961876C>A (GRCh38)

Gene symbol

PCDH15

Gene constraints

LOEUF: 0.84, LOF (oe): 0.71, misssense (oe): 1.03, synonymous (oe): 1.06 ? (gnomAD)

Ensembl transcript ID

ENST00000320301.11

Genbank transcript ID

NM_033056 (exact from MANE), NM_001354404 (by similarity)

UniProt / AlphaMissense peptide

PCD15_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2885G>T
g.1666067G>T

AA changes

AAE:	R962L	?
Score:	102

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45483395
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	11	4817	4828

Protein conservation

Species	Match	AA	Alignment
Human		962	E	D	A	D	P	P	G	L	P	A	S	R	V	R	Y	R	V	D	D	V	Q	F	P	Y
mutated	not conserved	962											S	L	V	R	Y	R	V	D	D	V	Q	F	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
27	1376	TOPO_DOM	Extracellular	lost
27	1955	CHAIN		lost
927	1035	DOMAIN	Cadherin	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.006	0.815
	1.2	0.878
(flanking)	0.812	0.919

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TTAGGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered gDNA sequence snippet

TTAGGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Original cDNA sequence snippet

TCCTGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered cDNA sequence snippet

TCCTGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

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 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
SLVRYRVDDV 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*

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

6203 / 6203

Position of start ATG in wt / mu cDNA

336 / 336

Last intron/exon boundary

4702

Theoretical NMD boundary in CDS

4316

Length of CDS

5868

Coding sequence (CDS) position

2885

cDNA position

3220

gDNA position

1666067

Chromosomal position

53961876

Speed

0.12 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

10:53961876C>A_18_ENST00000395430

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD

Model: simple_aae
Tree vote: 53|47 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:53961876C>A (GRCh38)

Gene symbol

PCDH15

Gene constraints

LOEUF: 0.84, LOF (oe): 0.71, misssense (oe): 1.03, synonymous (oe): 1.06 ? (gnomAD)

Ensembl transcript ID

ENST00000395430.5

Genbank transcript ID

NM_001142767 (by similarity), NM_001142766 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2885G>T
g.1666067G>T

AA changes

AAE:	R962L	?
Score:	102

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45483395
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	11	4817	4828

Protein conservation

Species	Match	AA	Alignment
Human		962	E	D	A	D	P	P	G	L	P	A	S	R	V	R	Y	R	V	D	D	V	Q	F	P	Y
mutated	not conserved	962											S	L	V	R	Y	R	V	D	D	V	Q	F	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.006	0.815
	1.2	0.878
(flanking)	0.812	0.919

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TTAGGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered gDNA sequence snippet

TTAGGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Original cDNA sequence snippet

TCCTGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered cDNA sequence snippet

TCCTGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

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 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
SLVRYRVDDV 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*

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

Position of start ATG in wt / mu cDNA

396 / 396

Last intron/exon boundary

4753

Theoretical NMD boundary in CDS

4307

Length of CDS

5859

Coding sequence (CDS) position

2885

cDNA position

3280

gDNA position

1666067

Chromosomal position

53961876

Speed

0.15 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

10:53961876C>A_7_ENST00000373957

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD

Model: simple_aae
Tree vote: 54|46 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:53961876C>A (GRCh38)

Gene symbol

PCDH15

Gene constraints

LOEUF: 0.90, LOF (oe): 0.76, misssense (oe): 1.03, synonymous (oe): 1.06 ? (gnomAD)

Ensembl transcript ID

ENST00000373957.7

Genbank transcript ID

NM_001142763 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2900G>T
g.1666067G>T

AA changes

AAE:	R967L	?
Score:	102

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45483395
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	11	4817	4828

Protein conservation

Species	Match	AA	Alignment
Human		967	E	D	A	D	P	P	G	L	P	A	S	R	V	R	Y	R	V	D	D	V	Q	F	P	Y
mutated	not conserved	967						P	G	L	P	A	S	L	V	R	Y	R	V	D	D	V	Q	F	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.006	0.815
	1.2	0.878
(flanking)	0.812	0.919

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TTAGGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered gDNA sequence snippet

TTAGGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Original cDNA sequence snippet

TCCTGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered cDNA sequence snippet

TCCTGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Wildtype AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DWQYEDCKLA 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 LVSYRQFKVR 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 DWQYEDCKLA 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
PGLPASLVRY 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 LVSYRQFKVR 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*

Position of stopcodon in wt / mu CDS

5889 / 5889

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

1963 / 1963

Position of stopcodon in wt / mu cDNA

6284 / 6284

Position of start ATG in wt / mu cDNA

396 / 396

Last intron/exon boundary

4783

Theoretical NMD boundary in CDS

4337

Length of CDS

5889

Coding sequence (CDS) position

2900

cDNA position

3295

gDNA position

1666067

Chromosomal position

53961876

Speed

0.10 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

10:53961876C>A_11_ENST00000395446

Back to summary table

Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: without_aae
Tree vote: 9|191 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:53961876C>A (GRCh38)

Gene symbol

PCDH15

Gene constraints

LOEUF: 0.91, LOF (oe): 0.72, misssense (oe): 1.05, synonymous (oe): 1.07 ? (gnomAD)

Ensembl transcript ID

ENST00000395446.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2091+117455G>T
g.1666067G>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45483395
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	11	4817	4828

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.006	0.815
	1.2	0.878
(flanking)	0.812	0.919

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TTAGGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered gDNA sequence snippet

TTAGGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

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 SDGRPDGEEP KKIKKPKVEI REPSEEEEVV
VTIEKPPAAE PTYTTWKRAR IFPMIFKKVR GLADKRGIVD LEGEEWQRRL EEEDKDYLKL
TLDQEEATES TVESEEESSS DYTEYSEEES EFSESETTEE ESESETPSEE EESSTPESEE
SESTESEGEK ARKNIVLARR RPMVEEVKEV KGRKEEPQEE QKEPKMEEEE HSEEEESGPA
PVEESTDPEA QDIPEEGSAE SASVEGGVES EEESESGSSS SSSESQSGGP WGYQVPAYDR
SKNANQKKSP GANSEGYNTA L*

Mutated AA sequence

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

Position of start ATG in wt / mu cDNA

396 / 396

Last intron/exon boundary

2486

Theoretical NMD boundary in CDS

2040

Length of CDS

2946

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

1666067

Chromosomal position

53961876

Speed

0.03 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

10:53961876C>A_5_ENST00000395440

Back to summary table

Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: without_aae
Tree vote: 11|189 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:53961876C>A (GRCh38)

Gene symbol

PCDH15

Gene constraints

LOEUF: 0.94, LOF (oe): 0.69, misssense (oe): 1.06, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000395440.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1306-152330G>T
g.1666067G>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45483395
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	11	4817	4828

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.006	0.815
	1.2	0.878
(flanking)	0.812	0.919

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TTAGGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered gDNA sequence snippet

TTAGGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

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 KDIEDEEPKK IKKPKVEIRE PSEEEEVVVT IEKPPAAEPT YTTWKRARIF
PMIFKKVRGL ADKRGIVDLE GEEWQRRLEE EDKDYLKLTL DQEEATESTV ESEEESSSDY
TEYSEEESEF SESETTEEES ESETPSEEEE SSTPESEESE STESEGEKAR KNIVLARRRP
MVEEVKEVKG RKEEPQEEQK EPKMEEEEHS EEEESGPAPV EESTDPEAQD IPEEGSAESA
SVEGGVESEE ESESGSSSSS SESQSGGPWG YQVPAYDRSK NANQKKSPGA NSEGYNTAL*

Mutated AA sequence

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

Position of start ATG in wt / mu cDNA

396 / 396

Last intron/exon boundary

1700

Theoretical NMD boundary in CDS

1254

Length of CDS

2160

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

1666067

Chromosomal position

53961876

Speed

0.03 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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MutationT@ster 2025

Variant:

10:53961876C>A_6_ENST00000395442

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Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: without_aae
Tree vote: 17|183 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:53961876C>A (GRCh38)

Gene symbol

PCDH15

Gene constraints

LOEUF: 0.97, LOF (oe): 0.70, misssense (oe): 1.07, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000395442.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1099-152330G>T
g.1666067G>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45483395
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	11	4817	4828

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.006	0.815
	1.2	0.878
(flanking)	0.812	0.919

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TTAGGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered gDNA sequence snippet

TTAGGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

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
FDLVIKEEPK KIKKPKVEIR EPSEEEEVVV TIEKPPAAEP TYTTWKRARI FPMIFKKVRG
LADKRGIVDL EGEEWQRRLE EEDKDYLKLT LDQEEATEST VESEEESSSD YTEYSEEESE
FSESETTEEE SESETPSEEE ESSTPESEES ESTESEGEKA RKNIVLARRR PMVEEVKEVK
GRKEEPQEEQ KEPKMEEEEH SEEEESGPAP VEESTDPEAQ DIPEEGSAES ASVEGGVESE
EESESGSSSS SSESQSGGPW GYQVPAYDRS KNANQKKSPG ANSEGYNTAL *

Mutated AA sequence

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

Position of start ATG in wt / mu cDNA

396 / 396

Last intron/exon boundary

1493

Theoretical NMD boundary in CDS

1047

Length of CDS

1953

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

1666067

Chromosomal position

53961876

Speed

0.03 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

10:53961876C>A_17_ENST00000495484

Back to summary table

Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: without_aae
Tree vote: 26|174 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:53961876C>A (GRCh38)

Gene symbol

PCDH15

Gene constraints

LOEUF: 0.92, LOF (oe): 0.63, misssense (oe): 1.02, synonymous (oe): 1.04 ? (gnomAD)

Ensembl transcript ID

ENST00000495484.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-24-104613G>T
g.1666067G>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45483395
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	11	4817	4828

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.006	0.815
	1.2	0.878
(flanking)	0.812	0.919

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TTAGGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered gDNA sequence snippet

TTAGGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MQVIVSNVPP TLVEKKIEDL TEILDRYVQE QIPGAKVVVE SIGARRHGDA FSLEDYTKCD
LTVYAIDPQT NRAIDRNELF KFLDGKLLDI NKDFQPYYGE GGRILEIRTP EAVTSIKKRG
ESLGYTEGAL LALAFIIILC CIPAILVVLV SYRQRGYGSE QQQLLRPSLL KPEELSMESG
IDPGQEYGQD YYSYEHGYEM PQYGSRRRLL PPAGQEEYGE VVGEAEEEYE EEEWARKRMI
KLVVDREYET SSTGEDSAPE CQRNRLHHPS IHSNINGNIY IAQNGSVVRT RRACLTDNLK
VASPVRLGGP FKKLDKLAVT HEENVPLNTL SKGPFSTEKM NARPTLVTFA PCPVGTDNTA
VKPLRNRLKS TVEQESMIDS KNIKEALEFH SDHTQSDDEE LWMGPWNNLH IPMTKL*

Mutated AA sequence

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

Position of start ATG in wt / mu cDNA

392 / 392

Last intron/exon boundary

1090

Theoretical NMD boundary in CDS

648

Length of CDS

1251

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

1666067

Chromosomal position

53961876

Speed

0.03 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

10:53961876C>A_1_ENST00000644397

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD

Model: simple_aae
Tree vote: 45|55 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:53961876C>A (GRCh38)

Gene symbol

PCDH15

Gene constraints

LOEUF: 0.82, LOF (oe): 0.69, misssense (oe): 1.01, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000644397.2

Genbank transcript ID

NM_001384140 (exact from MANE), NM_001354429 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2885G>T
g.1666067G>T

AA changes

AAE:	R962L	?
Score:	102

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45483395
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	11	4817	4828

Protein conservation

Species	Match	AA	Alignment
Human		962	E	D	A	D	P	P	G	L	P	A	S	R	V	R	Y	R	V	D	D	V	Q	F	P	Y
mutated	not conserved	962											S	L	V	R	Y	R	V	D	D	V	Q	F	P
Ptroglodytes	all identical	967						P	G	L	P	A	S	R	V	R	Y	R	V	D	D	V	Q	F	P
Mmulatta	all identical	967						P	G	L	P	A	S	R	V	R	Y	R	V	D	D	V	Q	F	P
Fcatus	all identical	974	E	D	A	D	P	P	G	L	P	A	S	R	V	R	Y	R	V	D	D	V	Q	F	P
Mmusculus	all identical	967						P	G	M	P	A	S	R	V	R	Y	R	V	D	D	V	Q	F	P
Ggallus	all identical	962											S	R	V	R	Y	K	V	D	V	V	Q	F	P
Trubripes	not conserved	948	N	D	S	D	P	T	G	T	P	A	G	L	V	R	Y	K	V	D	P	E	A	Y	P
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all conserved	916	E	D	K	D	P	P	G	T	P	A	S	K	V	R	Y	K	V	D	V	V	Q	F	P

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.006	0.815
	1.2	0.878
(flanking)	0.812	0.919

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TTAGGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered gDNA sequence snippet

TTAGGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Original cDNA sequence snippet

TCCTGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered cDNA sequence snippet

TCCTGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

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 LGDSSIWSFC WQLVICMRTC AIWRTLTRRG YGSEQQQLLR PSLLKPEELS
MESGIDPGQE YGQDYYSYEH GYEMPQYGSR RRLLPPAGQE EYGEVVGEAE EEYEEEEWAR
KRMIKLVVDR EYETSSTGED SAPECQRNRL HHPSIHSNIN GNIYIAQNGS VVRTRRACLT
DNLKVASPVR LGGPFKKLDK LAVTHEENVP LNTLSKGPFS TEKMNARPTL VTFAPCPVGT
DNTAVKPLRN RLKSTVEQES MIDSKNIKEA LEFHSDHTQS DDEELWMGPW NNLHIPMTKL
*

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 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
SLVRYRVDDV 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 LGDSSIWSFC WQLVICMRTC AIWRTLTRRG YGSEQQQLLR PSLLKPEELS
MESGIDPGQE YGQDYYSYEH GYEMPQYGSR RRLLPPAGQE EYGEVVGEAE EEYEEEEWAR
KRMIKLVVDR EYETSSTGED SAPECQRNRL HHPSIHSNIN GNIYIAQNGS VVRTRRACLT
DNLKVASPVR LGGPFKKLDK LAVTHEENVP LNTLSKGPFS TEKMNARPTL VTFAPCPVGT
DNTAVKPLRN RLKSTVEQES MIDSKNIKEA LEFHSDHTQS DDEELWMGPW NNLHIPMTKL
*

Position of stopcodon in wt / mu CDS

5223 / 5223

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

1741 / 1741

Position of stopcodon in wt / mu cDNA

5558 / 5558

Position of start ATG in wt / mu cDNA

336 / 336

Last intron/exon boundary

5006

Theoretical NMD boundary in CDS

4620

Length of CDS

5223

Coding sequence (CDS) position

2885

cDNA position

3220

gDNA position

1666067

Chromosomal position

53961876

Speed

0.12 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

10:53961876C>A_15_ENST00000616114

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 49|51 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:53961876C>A (GRCh38)

Gene symbol

PCDH15

Gene constraints

LOEUF: 0.82, LOF (oe): 0.69, misssense (oe): 1.01, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000616114.4

Genbank transcript ID

NM_001354420 (by similarity)

UniProt / AlphaMissense peptide

PCD15_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2885G>T
g.1666067G>T

AA changes

AAE:	R962L	?
Score:	102

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45483395
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	11	4817	4828

Protein conservation

Species	Match	AA	Alignment
Human		962	E	D	A	D	P	P	G	L	P	A	S	R	V	R	Y	R	V	D	D	V	Q	F	P	Y
mutated	not conserved	962											S	L	V	R	Y	R	V	D	D	V	Q	F	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
27	1376	TOPO_DOM	Extracellular	lost
27	1955	CHAIN		lost
927	1035	DOMAIN	Cadherin	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.006	0.815
	1.2	0.878
(flanking)	0.812	0.919

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TTAGGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered gDNA sequence snippet

TTAGGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Original cDNA sequence snippet

TCCTGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered cDNA sequence snippet

TCCTGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

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 LGDSSMYEMP QYGSRRRLLP PAGQEEYGEV VGEAEEEYEE EEWARKRMIK
LVVDREYETS STGEDSAPEC QRNRLHHPSI HSNINGNIYI AQNGSVVRTR RACLTDNLKV
ASPVRLGGPF KKLDKLAVTH EENVPLNTLS KGPFSTEKMN ARPTLVTFAP CPVGTDNTAV
KPLRNRLKST VEQESMIDSK NIKEALEFHS DHTQSDDEEL WMGPWNNLHI PMTKL*

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 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
SLVRYRVDDV 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 LGDSSMYEMP QYGSRRRLLP PAGQEEYGEV VGEAEEEYEE EEWARKRMIK
LVVDREYETS STGEDSAPEC QRNRLHHPSI HSNINGNIYI AQNGSVVRTR RACLTDNLKV
ASPVRLGGPF KKLDKLAVTH EENVPLNTLS KGPFSTEKMN ARPTLVTFAP CPVGTDNTAV
KPLRNRLKST VEQESMIDSK NIKEALEFHS DHTQSDDEEL WMGPWNNLHI PMTKL*

Position of stopcodon in wt / mu CDS

5028 / 5028

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

1676 / 1676

Position of stopcodon in wt / mu cDNA

5423 / 5423

Position of start ATG in wt / mu cDNA

396 / 396

Last intron/exon boundary

4871

Theoretical NMD boundary in CDS

4425

Length of CDS

5028

Coding sequence (CDS) position

2885

cDNA position

3280

gDNA position

1666067

Chromosomal position

53961876

Speed

0.11 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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MutationT@ster 2025

Variant:

10:53961876C>A_16_ENST00000621708

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD

Model: simple_aae
Tree vote: 49|51 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:53961876C>A (GRCh38)

Gene symbol

PCDH15

Gene constraints

LOEUF: 0.86, LOF (oe): 0.74, misssense (oe): 1.01, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000621708.4

Genbank transcript ID

NM_001142771 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2900G>T
g.1666067G>T

AA changes

AAE:	R967L	?
Score:	102

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs45483395
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	11	4817	4828

Protein conservation

Species	Match	AA	Alignment
Human		967	E	D	A	D	P	P	G	L	P	A	S	R	V	R	Y	R	V	D	D	V	Q	F	P	Y
mutated	not conserved	967						P	G	L	P	A	S	L	V	R	Y	R	V	D	D	V	Q	F	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.006	0.815
	1.2	0.878
(flanking)	0.812	0.919

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TTAGGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered gDNA sequence snippet

TTAGGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Original cDNA sequence snippet

TCCTGGATTACCTGCAAGTCGTGTGAGGTATAGAGTAGATG

Altered cDNA sequence snippet

TCCTGGATTACCTGCAAGTCTTGTGAGGTATAGAGTAGATG

Wildtype AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DWQYEDCKLA 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 LVSYRQFKVR QAECTKTARI QAALPAAKPA VPAPAPVAAP
PPPPPPPPGA HLYEELGDSS MHKYEMPQYG SRRRLLPPAG QEEYGEVVGE AEEEYEEEEW
ARKRMIKLVV DREYETSSTG EDSAPECQRN RLHHPSIHSN INGNIYIAQN GSVVRTRRAC
LTDNLKVASP VRLGGPFKKL DKLAVTHEEN VPLNTLSKGP FSTEKMNARP TLVTFAPCPV
GTDNTAVKPL RNRLKSTVEQ ESMIDSKNIK EALEFHSDHT QSDDEELWMG PWNNLHIPMT
KL*

Mutated AA sequence

MFRQFYLWTC LASGIILGSL FEICLGQYDD DWQYEDCKLA 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
PGLPASLVRY 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 LVSYRQFKVR QAECTKTARI QAALPAAKPA VPAPAPVAAP
PPPPPPPPGA HLYEELGDSS MHKYEMPQYG SRRRLLPPAG QEEYGEVVGE AEEEYEEEEW
ARKRMIKLVV DREYETSSTG EDSAPECQRN RLHHPSIHSN INGNIYIAQN GSVVRTRRAC
LTDNLKVASP VRLGGPFKKL DKLAVTHEEN VPLNTLSKGP FSTEKMNARP TLVTFAPCPV
GTDNTAVKPL RNRLKSTVEQ ESMIDSKNIK EALEFHSDHT QSDDEELWMG PWNNLHIPMT
KL*

Position of stopcodon in wt / mu CDS

5049 / 5049

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

1683 / 1683

Position of stopcodon in wt / mu cDNA

5444 / 5444

Position of start ATG in wt / mu cDNA

396 / 396

Last intron/exon boundary

4892

Theoretical NMD boundary in CDS

4446

Length of CDS

5049

Coding sequence (CDS) position

2900

cDNA position

3295

gDNA position

1666067

Chromosomal position

53961876

Speed

0.09 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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