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 ENST00000395432
Genbank transcript ID NM_001142767
UniProt peptide Q96QU1
alteration type single base exchange
alteration region CDS
DNA changes c.1193A>C
cDNA.1588A>C
g.1432259A>C
AA changes D398A Score: 126 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 398
frameshift 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      398LRIVALDKDIEDTKDPELHLFLND
mutated  not conserved    398LRIVALDKDIEATKDPELHLFLN
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  302--LSVFARDLDSGENGEIEYSLG
Xtropicalis  all conserved  ENSXETG00000018945  386LKFVALDNDIEETKDPQLYLYLN
protein features
start (aa)end (aa)featuredetails 
271376TOPO_DOMExtracellular (Potential).lost
396509DOMAINCadherin 4.lost
419419CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
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 5748 / 5748
position (AA) of stopcodon in wt / mu AA sequence 1916 / 1916
position of stopcodon in wt / mu cDNA 6143 / 6143
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 396 / 396
chromosome 10
strand -1
last intron/exon boundary 4643
theoretical NMD boundary in CDS 4197
length of CDS 5748
coding sequence (CDS) position 1193
cDNA position
(for ins/del: last normal base / first normal base)		 1588
gDNA position
(for ins/del: last normal base / first normal base)		 1432259
chromosomal position
(for ins/del: last normal base / first normal base)		 55955444
original gDNA sequence snippet TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT
altered gDNA sequence snippet TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT
original cDNA sequence snippet TCTGGACAAGGACATAGAAGATACAAAAGACCCAGAGCTTC
altered cDNA sequence snippet TCTGGACAAGGACATAGAAGCTACAAAAGACCCAGAGCTTC
wildtype AA sequence MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPDR AQNLNERRTT TTTLTVDVLD GDDLGPMFLP CVLVPNTRDC
RPLTYQAAIP ELRTPEELNP IIVTPPIQAI DQDRNIQPPS DRPGILYSIL VGTPEDYPRF
FHMHPRTAEL SLLEPVNRDF HQKFDLVIKA EQDNGHPLPA FAGLHIEILD ENNQSPYFTM
PSYQGYILES APVGATISDS LNLTSPLRIV ALDKDIEDTK DPELHLFLND YTSVFTVTQT
GITRYLTLLQ PVDREEQQTY TFSITAFDGV QESEPVIVNI QVMDANDNTP TFPEISYDVY
VYTDMRPGDS VIQLTAVDAD EGSNGEITYE ILVGAQGDFI INKTTGLITI APGVEMIVGR
TYALTVQAAD NAPPAERRNS ICTVYIEVLP PNNQSPPRFP QLMYSLEISE AMRVGAVLLN
LQATDREGDS ITYAIENGDP QRVFNLSETT GILTLGKALD RESTDRYILI ITASDGRPDG
TSTATVNIVV TDVNDNAPVF DPYLPRNLSV VEEEANAFVG QVKATDPDAG INGQVHYSLG
NFNNLFRITS NGSIYTAVKL NREVRDYYEL VVVATDGAVH PRHSTLTLAI KVLDIDDNSP
VFTNSTYTVL VEENLPAGTT ILQIEAKDVD LGANVSYRIR SPEVKHFFAL HPFTGELSLL
RSLDYEAFPD QEASITFLVE AFDIYGTMPP GIATVTVIVK DMNDYPPVFS KRIYKGMVAP
DAVKGTPITT VYAEDADPPG LPASRVRYRV DDVQFPYPAS IFEVEEDSGR VITRVNLNEE
PTTIFKLVVV AFDDGEPVMS SSATVKILVL HPGEIPRFTQ EEYRPPPVSE LATKGTMVGV
ISAAAINQSI VYSIVSGNEE DTFGINNITG VIYVNGPLDY ETRTSYVLRV QADSLEVVLA
NLRVPSKSNT AKVYIEIQDE NNHPPVFQKK FYIGGVSEDA RMFTSVLRVK ATDKDTGNYS
VMAYRLIIPP IKEGKEGFVV ETYTGLIKTA MLFHNMRRSY FKFQVIATDD YGKGLSGKAD
VLVSVVNQLD MQVIVSNVPP TLVEKKIEDL TEILDRYVQE QIPGAKVVVE SIGARRHGDA
FSLEDYTKCD LTVYAIDPQT NRAIDRNELF KFLDGKLLDI NKDFQPYYGE GGRILEIRTP
EAVTSIKKRG ESLGYTEGAL LALAFIIILC CIPAILVVLV SYRQRQAECT KTARIQAALP
AAKPAVPAPA PVAAPPPPPP PPPGAHLYEE LGDSSILFLL YHFQQSRGNN SVSEDRKHQQ
VVMPFSSNTI EAHKSAHVDG SLKSNKLKSA RKFTFLSDED DLSAHNPLYK ENISQVSTNS
DISQRTDFVD PFSPKIQAKS KSLRGPREKI QRLWSQSVSL PRRLMRKVPN RPEIIDLQQW
QGTRQKAENE NTGICTNKRG SSNPLLTTEE ANLTEKEEIR QGETLMIEGT EQLKSLSSDS
SFCFPRPHFS FSTLPTVSRT VELKSEPNVI SSPAECSLEL SPSRPCVLHS SLSRRETPIC
MLPIETERNI FENFAHPPNI SPSACPLPPP PPISPPSPPP APAPLAPPPD ISPFSLFCPP
PSPPSIPLPL PPPTFFPLSV STSGPPTPPL LPPFPTPLPP PPPSIPCPPP PSASFLSTEC
VCITGVKCTT NLMPAEKIKS SMTQLSTTTV CKTDPQREPK GILRHVKNLA ELEKSVANMY
SQIEKNYLRT NVSELQTMCP SEVTNMEITS EQNKGSLNNI VEGTEKQSHS QSTSL*
mutated AA sequence MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPDR AQNLNERRTT TTTLTVDVLD GDDLGPMFLP CVLVPNTRDC
RPLTYQAAIP ELRTPEELNP IIVTPPIQAI DQDRNIQPPS DRPGILYSIL VGTPEDYPRF
FHMHPRTAEL SLLEPVNRDF HQKFDLVIKA EQDNGHPLPA FAGLHIEILD ENNQSPYFTM
PSYQGYILES APVGATISDS LNLTSPLRIV ALDKDIEATK DPELHLFLND YTSVFTVTQT
GITRYLTLLQ PVDREEQQTY TFSITAFDGV QESEPVIVNI QVMDANDNTP TFPEISYDVY
VYTDMRPGDS VIQLTAVDAD EGSNGEITYE ILVGAQGDFI INKTTGLITI APGVEMIVGR
TYALTVQAAD NAPPAERRNS ICTVYIEVLP PNNQSPPRFP QLMYSLEISE AMRVGAVLLN
LQATDREGDS ITYAIENGDP QRVFNLSETT GILTLGKALD RESTDRYILI ITASDGRPDG
TSTATVNIVV TDVNDNAPVF DPYLPRNLSV VEEEANAFVG QVKATDPDAG INGQVHYSLG
NFNNLFRITS NGSIYTAVKL NREVRDYYEL VVVATDGAVH PRHSTLTLAI KVLDIDDNSP
VFTNSTYTVL VEENLPAGTT ILQIEAKDVD LGANVSYRIR SPEVKHFFAL HPFTGELSLL
RSLDYEAFPD QEASITFLVE AFDIYGTMPP GIATVTVIVK DMNDYPPVFS KRIYKGMVAP
DAVKGTPITT VYAEDADPPG LPASRVRYRV DDVQFPYPAS IFEVEEDSGR VITRVNLNEE
PTTIFKLVVV AFDDGEPVMS SSATVKILVL HPGEIPRFTQ EEYRPPPVSE LATKGTMVGV
ISAAAINQSI VYSIVSGNEE DTFGINNITG VIYVNGPLDY ETRTSYVLRV QADSLEVVLA
NLRVPSKSNT AKVYIEIQDE NNHPPVFQKK FYIGGVSEDA RMFTSVLRVK ATDKDTGNYS
VMAYRLIIPP IKEGKEGFVV ETYTGLIKTA MLFHNMRRSY FKFQVIATDD YGKGLSGKAD
VLVSVVNQLD MQVIVSNVPP TLVEKKIEDL TEILDRYVQE QIPGAKVVVE SIGARRHGDA
FSLEDYTKCD LTVYAIDPQT NRAIDRNELF KFLDGKLLDI NKDFQPYYGE GGRILEIRTP
EAVTSIKKRG ESLGYTEGAL LALAFIIILC CIPAILVVLV SYRQRQAECT KTARIQAALP
AAKPAVPAPA PVAAPPPPPP PPPGAHLYEE LGDSSILFLL YHFQQSRGNN SVSEDRKHQQ
VVMPFSSNTI EAHKSAHVDG SLKSNKLKSA RKFTFLSDED DLSAHNPLYK ENISQVSTNS
DISQRTDFVD PFSPKIQAKS KSLRGPREKI QRLWSQSVSL PRRLMRKVPN RPEIIDLQQW
QGTRQKAENE NTGICTNKRG SSNPLLTTEE ANLTEKEEIR QGETLMIEGT EQLKSLSSDS
SFCFPRPHFS FSTLPTVSRT VELKSEPNVI SSPAECSLEL SPSRPCVLHS SLSRRETPIC
MLPIETERNI FENFAHPPNI SPSACPLPPP PPISPPSPPP APAPLAPPPD ISPFSLFCPP
PSPPSIPLPL PPPTFFPLSV STSGPPTPPL LPPFPTPLPP PPPSIPCPPP PSASFLSTEC
VCITGVKCTT NLMPAEKIKS SMTQLSTTTV CKTDPQREPK GILRHVKNLA ELEKSVANMY
SQIEKNYLRT NVSELQTMCP SEVTNMEITS EQNKGSLNNI VEGTEKQSHS QSTSL*
speed 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