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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: ENST00000289746
MT speed 1.69 s - this script 7.082496 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CDH15disease_causing0.994302934818113simple_aaeR60Csingle base exchangers121434539show file

Taster files

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documentation

Prediction

disease causing

Model: simple_aae, prob: 0.994302934818113      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM086801)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:89245959C>TN/A show variant in all transcripts   IGV
HGNC symbol CDH15
Ensembl transcript ID ENST00000289746
Genbank transcript ID NM_004933
UniProt peptide P55291
alteration type single base exchange
alteration region CDS
DNA changes c.178C>T
cDNA.243C>T
g.7785C>T
AA changes R60C Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS
60
frameshift no
known variant Reference ID: rs121434539
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC01010

known disease mutation at this position, please check HGMD for details (HGMD ID CM086801)

known disease mutation at this position, please check HGMD for details (HGMD ID CM086801)
known disease mutation at this position, please check HGMD for details (HGMD ID CM086801)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.7181
0.6230.963
(flanking)1.480.839
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased7783wt: 0.2123 / mu: 0.2145 (marginal change - not scored)wt: CCACAAGCGTCTCCC
mu: CCACAAGTGTCTCCC
 ACAA|gcgt
Donor marginally increased7778wt: 0.9796 / mu: 0.9872 (marginal change - not scored)wt: GAGAACCACAAGCGT
mu: GAGAACCACAAGTGT
 GAAC|caca
distance from splice site 24
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      60IPPISVSENHKRLPYPLVQIKSDK
mutated  not conserved    60IPPISVSENHKCLPYPLVQIKSD
Ptroglodytes  all identical  ENSPTRG00000008473  46IPPISVSENHKRLPYPLVQIKSD
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000031962  60IPPISVSENHKRLPYPLVQIKSD
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000017254  34IPQIRVLENSKQVPEALVQIKSD
Drerio  not conserved  ENSDARG00000068191  61IPPIRVLENSKHLPEDLVQIKSD
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000011269  61RRLPMLLVQLKSD
protein features
start (aa)end (aa)featuredetails 
2260PROPEPPotential. /FTId=PRO_0000003805.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2445 / 2445
position (AA) of stopcodon in wt / mu AA sequence 815 / 815
position of stopcodon in wt / mu cDNA 2510 / 2510
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 66 / 66
chromosome 16
strand 1
last intron/exon boundary 2217
theoretical NMD boundary in CDS 2101
length of CDS 2445
coding sequence (CDS) position 178
cDNA position
(for ins/del: last normal base / first normal base)
243
gDNA position
(for ins/del: last normal base / first normal base)
7785
chromosomal position
(for ins/del: last normal base / first normal base)
89245959
original gDNA sequence snippet GCGTATCCGAGAACCACAAGCGTCTCCCCTACCCCCTGGTT
altered gDNA sequence snippet GCGTATCCGAGAACCACAAGTGTCTCCCCTACCCCCTGGTT
original cDNA sequence snippet GCGTATCCGAGAACCACAAGCGTCTCCCCTACCCCCTGGTT
altered cDNA sequence snippet GCGTATCCGAGAACCACAAGTGTCTCCCCTACCCCCTGGTT
wildtype AA sequence MDAAFLLVLG LLAQSLCLSL GVPGWRRPTT LYPWRRAPAL SRVRRAWVIP PISVSENHKR
LPYPLVQIKS DKQQLGSVIY SIQGPGVDEE PRGVFSIDKF TGKVFLNAML DREKTDRFRL
RAFALDLGGS TLEDPTDLEI VVVDQNDNRP AFLQEAFTGR VLEGAVPGTY VTRAEATDAD
DPETDNAALR FSILQQGSPE LFSIDELTGE IRTVQVGLDR EVVAVYNLTL QVADMSGDGL
TATASAIITL DDINDNAPEF TRDEFFMEAI EAVSGVDVGR LEVEDRDLPG SPNWVARFTI
LEGDPDGQFT IRTDPKTNEG VLSIVKALDY ESCEHYELKV SVQNEAPLQA AALRAERGQA
KVRVHVQDTN EPPVFQENPL RTSLAEGAPP GTLVATFSAR DPDTEQLQRL SYSKDYDPED
WLQVDAATGR IQTQHVLSPA SPFLKGGWYR AIVLAQDDAS QPRTATGTLS IEILEVNDHA
PVLAPPPPGS LCSEPHQGPG LLLGATDEDL PPHGAPFHFQ LSPRLPELGR NWSLSQVNVS
HARLRPRHQV PEGLHRLSLL LRDSGQPPQQ REQPLNVTVC RCGKDGVCLP GAAALLAGGT
GLSLGALVIV LASALLLLVL VLLVALRARF WKQSRGKGLL HGPQDDLRDN VLNYDEQGGG
EEDQDAYDIS QLRHPTALSL PLGPPPLRRD APQGRLHPQP PRVLPTSPLD IADFINDGLE
AADSDPSVPP YDTALIYDYE GDGSVAGTLS SILSSQGDED QDYDYLRDWG PRFARLADMY
GHPCGLEYGA RWDHQAREGL SPGALLPRHR GRTA*
mutated AA sequence MDAAFLLVLG LLAQSLCLSL GVPGWRRPTT LYPWRRAPAL SRVRRAWVIP PISVSENHKC
LPYPLVQIKS DKQQLGSVIY SIQGPGVDEE PRGVFSIDKF TGKVFLNAML DREKTDRFRL
RAFALDLGGS TLEDPTDLEI VVVDQNDNRP AFLQEAFTGR VLEGAVPGTY VTRAEATDAD
DPETDNAALR FSILQQGSPE LFSIDELTGE IRTVQVGLDR EVVAVYNLTL QVADMSGDGL
TATASAIITL DDINDNAPEF TRDEFFMEAI EAVSGVDVGR LEVEDRDLPG SPNWVARFTI
LEGDPDGQFT IRTDPKTNEG VLSIVKALDY ESCEHYELKV SVQNEAPLQA AALRAERGQA
KVRVHVQDTN EPPVFQENPL RTSLAEGAPP GTLVATFSAR DPDTEQLQRL SYSKDYDPED
WLQVDAATGR IQTQHVLSPA SPFLKGGWYR AIVLAQDDAS QPRTATGTLS IEILEVNDHA
PVLAPPPPGS LCSEPHQGPG LLLGATDEDL PPHGAPFHFQ LSPRLPELGR NWSLSQVNVS
HARLRPRHQV PEGLHRLSLL LRDSGQPPQQ REQPLNVTVC RCGKDGVCLP GAAALLAGGT
GLSLGALVIV LASALLLLVL VLLVALRARF WKQSRGKGLL HGPQDDLRDN VLNYDEQGGG
EEDQDAYDIS QLRHPTALSL PLGPPPLRRD APQGRLHPQP PRVLPTSPLD IADFINDGLE
AADSDPSVPP YDTALIYDYE GDGSVAGTLS SILSSQGDED QDYDYLRDWG PRFARLADMY
GHPCGLEYGA RWDHQAREGL SPGALLPRHR GRTA*
speed 1.69 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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