Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 1.41262538386557e-05 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:55955444T>GN/A show variant in all transcripts   IGV
HGNC symbol PCDH15
Ensembl transcript ID ENST00000395438
Genbank transcript ID NM_001142770
UniProt peptide Q96QU1
alteration type single base exchange
alteration region CDS
DNA changes c.1304A>C
cDNA.1699A>C
g.1432259A>C
AA changes D435A Score: 126 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 435
frameshift 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  all identical  ENSMMUG00000009794  435LRIVALDKDIEDTKDPELHLFLN
Fcatus  not conserved  ENSFCAG00000010122  435XXXXXXXXXXXXTKDPELHLFLN
Mmusculus  all identical  ENSMUSG00000052613  440LRIVALDKDIEDTKDPELHLFLN
Ggallus  all conserved  ENSGALG00000002744  383LQITVLDNDVEETKDPQLHLFLN
Trubripes  all conserved  ENSTRUG00000010819  424ETKDPLVKISLD
Drerio  all conserved  ENSDARG00000008127  383LAIIVLDNDIEETKDPMVRISLD
Dmelanogaster  all identical  FBgn0039709  427ISFMTTDADLSDS-DPKPDYIYE
Celegans  not conserved  F15B9.7  415--VKATDEDFGT--
Xtropicalis  all conserved  ENSXETG00000018945  386LKFVALDNDIEETKDPQLYLYLN
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 4620 / 4620
position (AA) of stopcodon in wt / mu AA sequence 1540 / 1540
position of stopcodon in wt / mu cDNA 5015 / 5015
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 396 / 396
chromosome 10
strand -1
last intron/exon boundary 4949
theoretical NMD boundary in CDS 4503
length of CDS 4620
coding sequence (CDS) position 1304
cDNA position
(for ins/del: last normal base / first normal base)		 1699
gDNA position
(for ins/del: last normal base / first normal base)		 1432259
chromosomal position
(for ins/del: last normal base / first normal base)		 55955444
original gDNA sequence snippet TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT
altered gDNA sequence snippet TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT
original cDNA sequence snippet TCTGGACAAGGACATAGAAGATACAAAAGACCCAGAGCTTC
altered cDNA sequence snippet TCTGGACAAGGACATAGAAGCTACAAAAGACCCAGAGCTTC
wildtype AA sequence MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEDTKDPE LHLFLNDYTS VFTVTQTGIT RYLTLLQPVD REEQQTYTFS
ITAFDGVQES EPVIVNIQVM DANDNTPTFP EISYDVYVYT DMRPGDSVIQ LTAVDADEGS
NGEITYEILV GAQGDFIINK TTGLITIAPG VEMIVGRTYA LTVQAADNAP PAERRNSICT
VYIEVLPPNN QSPPRFPQLM YSLEISEAMR VGAVLLNLQA TDREGDSITY AIENGDPQRV
FNLSETTGIL TLGKALDRES TDRYILIITA SDGRPDGTST ATVNIVVTDV NDNAPVFDPY
LPRNLSVVEE EANAFVGQVK ATDPDAGING QVHYSLGNFN NLFRITSNGS IYTAVKLNRE
VRDYYELVVV ATDGAVHPRH STLTLAIKVL DIDDNSPVFT NSTYTVLVEE NLPAGTTILQ
IEAKDVDLGA NVSYRIRSPE VKHFFALHPF TGELSLLRSL DYEAFPDQEA SITFLVEAFD
IYGTMPPGIA TVTVIVKDMN DYPPVFSKRI YKGMVAPDAV KGTPITTVYA EDADPPGLPA
SRVRYRVDDV QFPYPASIFE VEEDSGRVIT RVNLNEEPTT IFKLVVVAFD DGEPVMSSSA
TVKILVLHPG EIPRFTQEEY RPPPVSELAT KGTMVGVISA AAINQSIVYS IVSGNEEDTF
GINNITGVIY VNGPLDYETR TSYVLRVQAD SLEVVLANLR VPSKSNTAKV YIEIQDENNH
PPVFQKKFYI GGVSEDARMF TSVLRVKATD KDTGNYSVMA YRLIIPPIKE GKEGFVVETY
TGLIKTAMLF HNMRRSYFKF QVIATDDYGK GLSGKADVLV SVVNQLDMQV IVSNVPPTLV
EKKIEDLTEI LDRYVQEQIP GAKVVVESIG ARRHGDAFSL EDYTKCDLTV YAIDPQTNRA
IDRNELFKFL DGKLLDINKD FQPYYGEGGR ILEIRTPEAV TSIKKRGESL GYTEGALLAL
AFIIILCCIP AILVVLVSYR QFKVRQAECT KTARIQAALP AAKPAVPAPA PVAAPPPPPP
PPPGAHLYEE LGDSSMHKNY PWSLELILAR NMDKIITVMS MGMKCLNMGV AVDCYHQLDR
RNMVRWLVKL RKNMRRKRKS QRKLKNQRLK LESLVRRKK*
mutated AA sequence MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEATKDPE LHLFLNDYTS VFTVTQTGIT RYLTLLQPVD REEQQTYTFS
ITAFDGVQES EPVIVNIQVM DANDNTPTFP EISYDVYVYT DMRPGDSVIQ LTAVDADEGS
NGEITYEILV GAQGDFIINK TTGLITIAPG VEMIVGRTYA LTVQAADNAP PAERRNSICT
VYIEVLPPNN QSPPRFPQLM YSLEISEAMR VGAVLLNLQA TDREGDSITY AIENGDPQRV
FNLSETTGIL TLGKALDRES TDRYILIITA SDGRPDGTST ATVNIVVTDV NDNAPVFDPY
LPRNLSVVEE EANAFVGQVK ATDPDAGING QVHYSLGNFN NLFRITSNGS IYTAVKLNRE
VRDYYELVVV ATDGAVHPRH STLTLAIKVL DIDDNSPVFT NSTYTVLVEE NLPAGTTILQ
IEAKDVDLGA NVSYRIRSPE VKHFFALHPF TGELSLLRSL DYEAFPDQEA SITFLVEAFD
IYGTMPPGIA TVTVIVKDMN DYPPVFSKRI YKGMVAPDAV KGTPITTVYA EDADPPGLPA
SRVRYRVDDV QFPYPASIFE VEEDSGRVIT RVNLNEEPTT IFKLVVVAFD DGEPVMSSSA
TVKILVLHPG EIPRFTQEEY RPPPVSELAT KGTMVGVISA AAINQSIVYS IVSGNEEDTF
GINNITGVIY VNGPLDYETR TSYVLRVQAD SLEVVLANLR VPSKSNTAKV YIEIQDENNH
PPVFQKKFYI GGVSEDARMF TSVLRVKATD KDTGNYSVMA YRLIIPPIKE GKEGFVVETY
TGLIKTAMLF HNMRRSYFKF QVIATDDYGK GLSGKADVLV SVVNQLDMQV IVSNVPPTLV
EKKIEDLTEI LDRYVQEQIP GAKVVVESIG ARRHGDAFSL EDYTKCDLTV YAIDPQTNRA
IDRNELFKFL DGKLLDINKD FQPYYGEGGR ILEIRTPEAV TSIKKRGESL GYTEGALLAL
AFIIILCCIP AILVVLVSYR QFKVRQAECT KTARIQAALP AAKPAVPAPA PVAAPPPPPP
PPPGAHLYEE LGDSSMHKNY PWSLELILAR NMDKIITVMS MGMKCLNMGV AVDCYHQLDR
RNMVRWLVKL RKNMRRKRKS QRKLKNQRLK LESLVRRKK*
speed 1.41 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