Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.0261586473668097 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:55955444T>GN/A show variant in all transcripts   IGV
HGNC symbol PCDH15
Ensembl transcript ID ENST00000437009
Genbank transcript ID NM_001142765
UniProt peptide Q96QU1
alteration type single base exchange
alteration region CDS
DNA changes c.1304A>C
cDNA.1699A>C
g.1432259A>C
AA changes D435A Score: 126 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 435
frameshift no
known variant Reference ID: rs4935502
databasehomozygous (G/G)heterozygousallele carriers
1000G4817671248
ExAC56151764923264
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)2.2451
4.7741
(flanking)5.7841
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost1432260sequence motif lost- wt: AGAT|gtaa
 mu: AGCT.gtaa
Donor marginally increased1432252wt: 0.9798 / mu: 0.9914 (marginal change - not scored)wt: AGGACATAGAAGATG
mu: AGGACATAGAAGCTG		 GACA|taga
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      435LRIVALDKDIEDTKDPELHLFLND
mutated  not conserved    435LRIVALDKDIEATKDPELHLFLN
Ptroglodytes  no homologue    
Mmulatta  not conserved  ENSMMUG00000009794  549IQLTAVDAD-EGSNGEITYE
Fcatus  not conserved  ENSFCAG00000010122  435XXXXXXXXXXXXTKDPELHLFLN
Mmusculus  not conserved  ENSMUSG00000052613  554IQLTAVDAD-EGSNGEISYEILV
Ggallus  all conserved  ENSGALG00000002744  383LQITVLDNDVEETKDPQLHLFLN
Trubripes  all conserved  ENSTRUG00000010819  424ETKDPLVKISLD
Drerio  not conserved  ENSDARG00000008127  497LQLTALDADDGPNGLVSYKILAGDQ
Dmelanogaster  all identical  FBgn0039709  427ISFMTTDADLSDS-DPKPDYIYE
Celegans  not conserved  F15B9.7  302--LSVFARDLDSGENGEIEYSLG
Xtropicalis  not conserved  ENSXETG00000018945  500IRLTALDAD-EGVNGQITYE
protein features
start (aa)end (aa)featuredetails 
271376TOPO_DOMExtracellular (Potential).lost
396509DOMAINCadherin 4.lost
467467CONFLICTQ -> L (in Ref. 1; AAK31581).might get lost (downstream of altered splice site)
510616DOMAINCadherin 5.might get lost (downstream of altered splice site)
559559CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
617717DOMAINCadherin 6.might get lost (downstream of altered splice site)
662662CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
719819DOMAINCadherin 7.might get lost (downstream of altered splice site)
724724CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
768768CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
820926DOMAINCadherin 8.might get lost (downstream of altered splice site)
821821CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
851851CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
9271035DOMAINCadherin 9.might get lost (downstream of altered splice site)
10371144DOMAINCadherin 10.might get lost (downstream of altered splice site)
10641064CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
10841084CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
11451259DOMAINCadherin 11.might get lost (downstream of altered splice site)
11751175CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
12761276CONFLICTQ -> R (in Ref. 1; AAK31581).might get lost (downstream of altered splice site)
13771397TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
13981955TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
14351443COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
17461752COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
18151823COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
18261831COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 5661 / 5661
position (AA) of stopcodon in wt / mu AA sequence 1887 / 1887
position of stopcodon in wt / mu cDNA 6056 / 6056
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 396 / 396
chromosome 10
strand -1
last intron/exon boundary 4555
theoretical NMD boundary in CDS 4109
length of CDS 5661
coding sequence (CDS) position 1304
cDNA position
(for ins/del: last normal base / first normal base)		 1699
gDNA position
(for ins/del: last normal base / first normal base)		 1432259
chromosomal position
(for ins/del: last normal base / first normal base)		 55955444
original gDNA sequence snippet TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT
altered gDNA sequence snippet TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT
original cDNA sequence snippet TCTGGACAAGGACATAGAAGATACAAAAGACCCAGAGCTTC
altered cDNA sequence snippet TCTGGACAAGGACATAGAAGCTACAAAAGACCCAGAGCTTC
wildtype AA sequence MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEDTKDPE LHLFLNDYTS VFTVTQTGIT RYLTLLQPVD REEQQTYTFS
ITAFDGVQES EPVIVNIQVM DANDNTPTFP EISYDVYVYT DMRPGDSVIQ LTAVDADEGS
NGEITYEILV GAQGDFIINK TTGLITIAPG VEMIVGRTYA LTVQAADNAP PAERSTGILT
LGKALDREST DRYILIITAS DGRPDGTSTA TVNIVVTDVN DNAPVFDPYL PRNLSVVEEE
ANAFVGQVKA TDPDAGINGQ VHYSLGNFNN LFRITSNGSI YTAVKLNREV RDYYELVVVA
TDGAVHPRHS TLTLAIKVLD IDDNSPVFTN STYTVLVEEN LPAGTTILQI EAKDVDLGAN
VSYRIRSPEV KHFFALHPFT GELSLLRSLD YEAFPDQEAS ITFLVEAFDI YGTMPPGIAT
VTVIVKDMND YPPVFSKRIY KGMVAPDAVK GTPITTVYAE DADPPGLPAS RVRYRVDDVQ
FPYPASIFEV EEDSGRVITR VNLNEEPTTI FKLVVVAFDD GEPVMSSSAT VKILVLHPGE
IPRFTQEEYR PPPVSELATK GTMVGVISAA AINQSIVYSI VSGNEEDTFG INNITGVIYV
NGPLDYETRT SYVLRVQADS LEVVLANLRV PSKSNTAKVY IEIQDENNHP PVFQKKFYIG
GVSEDARMFT SVLRVKATDK DTGNYSVMAY RLIIPPIKEG KEGFVVETYT GLIKTAMLFH
NMRRSYFKFQ VIATDDYGKG LSGKADVLVS VVNQLDMQVI VSNVPPTLVE KKIEDLTEIL
DRYVQEQIPG AKVVVESIGA RRHGDAFSLE DYTKCDLTVY AIDPQTNRAI DRNELFKFLD
GKLLDINKDF QPYYGEGGRI LEIRTPEAVT SIKKRGESLG YTEGALLALA FIIILCCIPA
ILVVLVSYRH FKRRQAECTK TARIQAALPA AKPAVPAPAP VAAPPPPPPP PPGAHLYEEL
GDSSMKGLFL LYHFQQSRGN NSVSEDRKHQ QVVMPFSSNT IEAHKSAHVD GSLKSNKLKS
ARKFTFLSDE DDLSAHNPLY KENISQVSTN SDISQRTDFV DPFSPKIQAK SKSLRGPREK
IQRLWSQSVS LPRRLMRKVP NRPEIIDLQQ WQGTRQKAEN ENTGICTNKR GSSNPLLTTE
EANLTEKEEI RQGETLMIEG TEQLKSLSSD SSFCFPRPHF SFSTLPTVSR TVELKSEPNV
ISSPAECSLE LSPSRPCVLH SSLSRRETPI CMLPIETERN IFENFAHPPN ISPSACPLPP
PPPISPPSPP PAPAPLAPPP DISPFSLFCP PPSPPSIPLP LPPPTFFPLS VSTSGPPTPP
LLPPFPTPLP PPPPSIPCPP PPSASFLSTE CVCITGVKCT TNLMPAEKIK SSMTQLSTTT
VCKTDPQREP KGILRHVKNL AELEKSVANM YSQIEKNYLR TNVSELQTMC PSEVTNMEIT
SEQNKGSLNN IVEGTEKQSH SQSTSL*
mutated AA sequence MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEATKDPE LHLFLNDYTS VFTVTQTGIT RYLTLLQPVD REEQQTYTFS
ITAFDGVQES EPVIVNIQVM DANDNTPTFP EISYDVYVYT DMRPGDSVIQ LTAVDADEGS
NGEITYEILV GAQGDFIINK TTGLITIAPG VEMIVGRTYA LTVQAADNAP PAERSTGILT
LGKALDREST DRYILIITAS DGRPDGTSTA TVNIVVTDVN DNAPVFDPYL PRNLSVVEEE
ANAFVGQVKA TDPDAGINGQ VHYSLGNFNN LFRITSNGSI YTAVKLNREV RDYYELVVVA
TDGAVHPRHS TLTLAIKVLD IDDNSPVFTN STYTVLVEEN LPAGTTILQI EAKDVDLGAN
VSYRIRSPEV KHFFALHPFT GELSLLRSLD YEAFPDQEAS ITFLVEAFDI YGTMPPGIAT
VTVIVKDMND YPPVFSKRIY KGMVAPDAVK GTPITTVYAE DADPPGLPAS RVRYRVDDVQ
FPYPASIFEV EEDSGRVITR VNLNEEPTTI FKLVVVAFDD GEPVMSSSAT VKILVLHPGE
IPRFTQEEYR PPPVSELATK GTMVGVISAA AINQSIVYSI VSGNEEDTFG INNITGVIYV
NGPLDYETRT SYVLRVQADS LEVVLANLRV PSKSNTAKVY IEIQDENNHP PVFQKKFYIG
GVSEDARMFT SVLRVKATDK DTGNYSVMAY RLIIPPIKEG KEGFVVETYT GLIKTAMLFH
NMRRSYFKFQ VIATDDYGKG LSGKADVLVS VVNQLDMQVI VSNVPPTLVE KKIEDLTEIL
DRYVQEQIPG AKVVVESIGA RRHGDAFSLE DYTKCDLTVY AIDPQTNRAI DRNELFKFLD
GKLLDINKDF QPYYGEGGRI LEIRTPEAVT SIKKRGESLG YTEGALLALA FIIILCCIPA
ILVVLVSYRH FKRRQAECTK TARIQAALPA AKPAVPAPAP VAAPPPPPPP PPGAHLYEEL
GDSSMKGLFL LYHFQQSRGN NSVSEDRKHQ QVVMPFSSNT IEAHKSAHVD GSLKSNKLKS
ARKFTFLSDE DDLSAHNPLY KENISQVSTN SDISQRTDFV DPFSPKIQAK SKSLRGPREK
IQRLWSQSVS LPRRLMRKVP NRPEIIDLQQ WQGTRQKAEN ENTGICTNKR GSSNPLLTTE
EANLTEKEEI RQGETLMIEG TEQLKSLSSD SSFCFPRPHF SFSTLPTVSR TVELKSEPNV
ISSPAECSLE LSPSRPCVLH SSLSRRETPI CMLPIETERN IFENFAHPPN ISPSACPLPP
PPPISPPSPP PAPAPLAPPP DISPFSLFCP PPSPPSIPLP LPPPTFFPLS VSTSGPPTPP
LLPPFPTPLP PPPPSIPCPP PPSASFLSTE CVCITGVKCT TNLMPAEKIK SSMTQLSTTT
VCKTDPQREP KGILRHVKNL AELEKSVANM YSQIEKNYLR TNVSELQTMC PSEVTNMEIT
SEQNKGSLNN IVEGTEKQSH SQSTSL*
speed 1.09 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project