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MutationTaster - study a chromosomal position

 MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000231484
MT speed 0 s - this script 2.871548 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
PCDH12polymorphism_automatic3.55067639734585e-08simple_aaeaffectedH385Nsingle base exchangers164075show file

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 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999964493236 (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) chr5:141336264G>TN/A show variant in all transcripts   IGV
HGNC symbol PCDH12
Ensembl transcript ID ENST00000231484
Genbank transcript ID NM_016580
UniProt peptide Q9NPG4
alteration type single base exchange
alteration region CDS
DNA changes c.1153C>A
cDNA.2364C>A
g.13041C>A
AA changes H385N Score: 68 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 385
frameshift no
known variant Reference ID: rs164075
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC25044-173217723
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0750.662
0.0320.663
(flanking)0.5440.798
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased13037wt: 0.26 / mu: 0.98wt: GATTCAGGACACAAT
mu: GATTCAGGAAACAAT		 TTCA|ggac
Donor gained130410.36mu: CAGGAAACAATGGTT GGAA|acaa
distance from splice site 1728
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      385ALVMADDLDSGHNGLVHCWLSQEL
mutated  all conserved    385ALVMADDLDSGNNGLVHCWLSQE
Ptroglodytes  all conserved  ENSPTRG00000017355  385ALVMADDLDSGNNGLVHCWLSQE
Mmulatta  all conserved  ENSMMUG00000006291  385ALVMADDLDSGNNGLVHCWLSQE
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000024440  385ALVSANDLDSGNNGLVHCWLNQE
Ggallus  all conserved  ENSGALG00000002544  384ASDPDSGNNGRVHCSLSPG
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000076594  385ALVMVSDADYGANGQVQVHILTG
Dmelanogaster  no homologue    
Celegans  not conserved  C45G7.5  1047AEFDVTDPDGSESYQVELE-GDG
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
25718TOPO_DOMExtracellular (Potential).lost
355460DOMAINCadherin 4.lost
385386CONFLICTHN -> KD (in Ref. 4; BAB55016).lost
389390CONFLICTVH -> LG (in Ref. 4; BAB55016).might get lost (downstream of altered splice site)
415415CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
442442CONFLICTA -> V (in Ref. 4; BAB14677).might get lost (downstream of altered splice site)
461565DOMAINCadherin 5.might get lost (downstream of altered splice site)
582582CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
600711DOMAINCadherin 6.might get lost (downstream of altered splice site)
659659CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
662662CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
719739TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
7401184TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
753753CONFLICTR -> W (in Ref. 4; BAB14677).might get lost (downstream of altered splice site)
814814CONFLICTA -> T (in Ref. 4; BAB14837).might get lost (downstream of altered splice site)
970970CONFLICTH -> Y (in Ref. 4; BAB14837).might get lost (downstream of altered splice site)
10511051CONFLICTS -> C (in Ref. 4; BAB14677).might get lost (downstream of altered splice site)
11771181COMPBIASPoly-Ser.might get lost (downstream of altered splice site)
11811181CONFLICTS -> SSSS (in Ref. 4; BAB14837).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3555 / 3555
position (AA) of stopcodon in wt / mu AA sequence 1185 / 1185
position of stopcodon in wt / mu cDNA 4766 / 4766
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 1212 / 1212
chromosome 5
strand -1
last intron/exon boundary 4342
theoretical NMD boundary in CDS 3080
length of CDS 3555
coding sequence (CDS) position 1153
cDNA position
(for ins/del: last normal base / first normal base)		 2364
gDNA position
(for ins/del: last normal base / first normal base)		 13041
chromosomal position
(for ins/del: last normal base / first normal base)		 141336264
original gDNA sequence snippet CAGATGACTTGGATTCAGGACACAATGGTTTGGTCCACTGC
altered gDNA sequence snippet CAGATGACTTGGATTCAGGAAACAATGGTTTGGTCCACTGC
original cDNA sequence snippet CAGATGACTTGGATTCAGGACACAATGGTTTGGTCCACTGC
altered cDNA sequence snippet CAGATGACTTGGATTCAGGAAACAATGGTTTGGTCCACTGC
wildtype AA sequence MMQLLQLLLG LLGPGGYLFL LGDCQEVTTL TVKYQVSEEV PSGTVIGKLS QELGREERRR
QAGAAFQVLQ LPQALPIQVD SEEGLLSTGR RLDREQLCRQ WDPCLVSFDV LATGDLALIH
VEIQVLDIND HQPRFPKGEQ ELEISESASL RTRIPLDRAL DPDTGPNTLH TYTLSPSEHF
ALDVIVGPDE TKHAELIVVK ELDREIHSFF DLVLTAYDNG NPPKSGTSLV KVNVLDSNDN
SPAFAESSLA LEIQEDAAPG TLLIKLTATD PDQGPNGEVE FFLSKHMPPE VLDTFSIDAK
TGQVILRRPL DYEKNPAYEV DVQARDLGPN PIPAHCKVLI KVLDVNDNIP SIHVTWASQP
SLVSEALPKD SFIALVMADD LDSGHNGLVH CWLSQELGHF RLKRTNGNTY MLLTNATLDR
EQWPKYTLTL LAQDQGLQPL SAKKQLSIQI SDINDNAPVF EKSRYEVSTR ENNLPSLHLI
TIKAHDADLG INGKVSYRIQ DSPVAHLVAI DSNTGEVTAQ RSLNYEEMAG FEFQVIAEDS
GQPMLASSVS VWVSLLDAND NAPEVVQPVL SDGKASLSVL VNASTGHLLV PIETPNGLGP
AGTDTPPLAT HSSRPFLLTT IVARDADSGA NGEPLYSIRS GNEAHLFILN PHTGQLFVNV
TNASSLIGSE WELEIVVEDQ GSPPLQTRAL LRVMFVTSVD HLRDSARKPG ALSMSMLTVI
CLAVLLGIFG LILALFMSIC RTEKKDNRAY NCREAESTYR QQPKRPQKHI QKADIHLVPV
LRGQAGEPCE VGQSHKDVDK EAMMEAGWDP CLQAPFHLTP TLYRTLRNQG NQGAPAESRE
VLQDTVNLLF NHPRQRNASR ENLNLPEPQP ATGQPRSRPL KVAGSPTGRL AGDQGSEEAP
QRPPASSATL RRQRHLNGKV SPEKESGPRQ ILRSLVRLSV AAFAERNPVE ELTVDSPPVQ
QISQLLSLLH QGQFQPKPNH RGNKYLAKPG GSRSAIPDTD GPSARAGGQT DPEQEEGPLD
PEEDLSVKQL LEEELSSLLD PSTGLALDRL SAPDPAWMAR LSLPLTTNYR DNVISPDAAA
TEEPRTFQTF GKAEAPELSP TGTRLASTFV SEMSSLLEML LEQRSSMPVE AASEALRRLS
VCGRTLSLDL ATSAASGMKV QGDPGGKTGT EGKSRGSSSS SRCL*
mutated AA sequence MMQLLQLLLG LLGPGGYLFL LGDCQEVTTL TVKYQVSEEV PSGTVIGKLS QELGREERRR
QAGAAFQVLQ LPQALPIQVD SEEGLLSTGR RLDREQLCRQ WDPCLVSFDV LATGDLALIH
VEIQVLDIND HQPRFPKGEQ ELEISESASL RTRIPLDRAL DPDTGPNTLH TYTLSPSEHF
ALDVIVGPDE TKHAELIVVK ELDREIHSFF DLVLTAYDNG NPPKSGTSLV KVNVLDSNDN
SPAFAESSLA LEIQEDAAPG TLLIKLTATD PDQGPNGEVE FFLSKHMPPE VLDTFSIDAK
TGQVILRRPL DYEKNPAYEV DVQARDLGPN PIPAHCKVLI KVLDVNDNIP SIHVTWASQP
SLVSEALPKD SFIALVMADD LDSGNNGLVH CWLSQELGHF RLKRTNGNTY MLLTNATLDR
EQWPKYTLTL LAQDQGLQPL SAKKQLSIQI SDINDNAPVF EKSRYEVSTR ENNLPSLHLI
TIKAHDADLG INGKVSYRIQ DSPVAHLVAI DSNTGEVTAQ RSLNYEEMAG FEFQVIAEDS
GQPMLASSVS VWVSLLDAND NAPEVVQPVL SDGKASLSVL VNASTGHLLV PIETPNGLGP
AGTDTPPLAT HSSRPFLLTT IVARDADSGA NGEPLYSIRS GNEAHLFILN PHTGQLFVNV
TNASSLIGSE WELEIVVEDQ GSPPLQTRAL LRVMFVTSVD HLRDSARKPG ALSMSMLTVI
CLAVLLGIFG LILALFMSIC RTEKKDNRAY NCREAESTYR QQPKRPQKHI QKADIHLVPV
LRGQAGEPCE VGQSHKDVDK EAMMEAGWDP CLQAPFHLTP TLYRTLRNQG NQGAPAESRE
VLQDTVNLLF NHPRQRNASR ENLNLPEPQP ATGQPRSRPL KVAGSPTGRL AGDQGSEEAP
QRPPASSATL RRQRHLNGKV SPEKESGPRQ ILRSLVRLSV AAFAERNPVE ELTVDSPPVQ
QISQLLSLLH QGQFQPKPNH RGNKYLAKPG GSRSAIPDTD GPSARAGGQT DPEQEEGPLD
PEEDLSVKQL LEEELSSLLD PSTGLALDRL SAPDPAWMAR LSLPLTTNYR DNVISPDAAA
TEEPRTFQTF GKAEAPELSP TGTRLASTFV SEMSSLLEML LEQRSSMPVE AASEALRRLS
VCGRTLSLDL ATSAASGMKV QGDPGGKTGT EGKSRGSSSS SRCL*
speed 0.81 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
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