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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: ENST00000265838
MT speed 0 s - this script 2.842042 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ACAT1disease_causing0.999999999989299simple_aaeaffectedG183Rsingle base exchangers120074141show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.999999999989299      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs2833 (probable pathogenic)
  • known disease mutation at this position (HGMD CM920004)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:108009736G>AN/A show variant in all transcripts   IGV
HGNC symbol ACAT1
Ensembl transcript ID ENST00000265838
Genbank transcript ID NM_000019
UniProt peptide P24752
alteration type single base exchange
alteration region CDS
DNA changes c.547G>A
cDNA.638G>A
g.17494G>A
AA changes G183R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 183
frameshift no
known variant Reference ID: rs120074141
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC011

known as potential disease variant: rs2833 (probable pathogenic for Deficiency of acetyl-CoA acetyltransferase) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920004)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920004)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920004)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9191
5.6511
(flanking)5.6511
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 increased17495wt: 0.9053 / mu: 0.9493 (marginal change - not scored)wt: AGACGGGCTAACTGA
mu: AGACAGGCTAACTGA		 ACGG|gcta
Donor increased17490wt: 0.87 / mu: 0.99wt: GTAAAAGACGGGCTA
mu: GTAAAAGACAGGCTA		 AAAA|gacg
distance from splice site 33
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      183GVKLEDLIVKDGLTDVYNKIHMGS
mutated  not conserved    183KDRLTDVYNKIHMG
Ptroglodytes  all identical  ENSPTRG00000004247  183KDGLTDVYNKIHMG
Mmulatta  all identical  ENSMMUG00000004161  183KDGLTDVYNKIHMG
Fcatus  all identical  ENSFCAG00000012428  183KDGLTDVYNKIHMG
Mmusculus  all identical  ENSMUSG00000032047  180GVKLEDLIVKDGLTDVYNKIHMG
Ggallus  all identical  ENSGALG00000017163  165GVNLEDLIVKDGLTDVYNHIHMG
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000045888  176GVKMEDLIVKDGLTDVYNKFHM
Dmelanogaster  all identical  FBgn0029969  166GVNLTDGIVFDGLWDVYNKFHMG
Celegans  all identical  T02G5.8  165GFQVIDGIVKDGLTDAYDKVHMG
Xtropicalis  all identical  ENSXETG00000014477  176GVKLEDIIVKDGLTDVYNKFHMG
protein features
start (aa)end (aa)featuredetails 
178182HELIXmight get lost (downstream of altered splice site)
181181MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
187190TURNmight get lost (downstream of altered splice site)
190190MOD_RESN6-acetyllysine (By similarity).might get lost (downstream of altered splice site)
193204HELIXmight get lost (downstream of altered splice site)
208227HELIXmight get lost (downstream of altered splice site)
219219METALPotassium.might get lost (downstream of altered splice site)
219219BINDINGCoenzyme A.might get lost (downstream of altered splice site)
228234TURNmight get lost (downstream of altered splice site)
230230MOD_RESN6-acetyllysine (By similarity).might get lost (downstream of altered splice site)
238240STRANDmight get lost (downstream of altered splice site)
248250STRANDmight get lost (downstream of altered splice site)
251251MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
255257HELIXmight get lost (downstream of altered splice site)
258260REGIONCoenzyme A binding.might get lost (downstream of altered splice site)
261263TURNmight get lost (downstream of altered splice site)
263263MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
263263BINDINGCoenzyme A.might get lost (downstream of altered splice site)
264266HELIXmight get lost (downstream of altered splice site)
273275STRANDmight get lost (downstream of altered splice site)
280280METALPotassium; via carbonyl oxygen.might get lost (downstream of altered splice site)
280282TURNmight get lost (downstream of altered splice site)
281281METALPotassium; via carbonyl oxygen.might get lost (downstream of altered splice site)
283283METALPotassium; via carbonyl oxygen.might get lost (downstream of altered splice site)
284284BINDINGCoenzyme A.might get lost (downstream of altered splice site)
287297STRANDmight get lost (downstream of altered splice site)
298303HELIXmight get lost (downstream of altered splice site)
310319STRANDmight get lost (downstream of altered splice site)
322327HELIXmight get lost (downstream of altered splice site)
328340HELIXmight get lost (downstream of altered splice site)
338338MOD_RESN6-acetyllysine (By similarity).might get lost (downstream of altered splice site)
340340CONFLICTV -> M (in Ref. 2; BAA01387).might get lost (downstream of altered splice site)
344346HELIXmight get lost (downstream of altered splice site)
346346CONFLICTD -> N (in Ref. 2; BAA01387).might get lost (downstream of altered splice site)
347352STRANDmight get lost (downstream of altered splice site)
357367HELIXmight get lost (downstream of altered splice site)
371373HELIXmight get lost (downstream of altered splice site)
380380CONFLICTA -> S (in Ref. 2; BAA01387).might get lost (downstream of altered splice site)
380383HELIXmight get lost (downstream of altered splice site)
381381METALPotassium; via carbonyl oxygen.might get lost (downstream of altered splice site)
385385ACT_SITEProton acceptor (Probable).might get lost (downstream of altered splice site)
387389TURNmight get lost (downstream of altered splice site)
390401HELIXmight get lost (downstream of altered splice site)
407414STRANDmight get lost (downstream of altered splice site)
412412CONFLICTI -> F (in Ref. 2; BAA01387).might get lost (downstream of altered splice site)
413413ACT_SITEProton acceptor (Probable).might get lost (downstream of altered splice site)
415417TURNmight get lost (downstream of altered splice site)
418426STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1284 / 1284
position (AA) of stopcodon in wt / mu AA sequence 428 / 428
position of stopcodon in wt / mu cDNA 1375 / 1375
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 92 / 92
chromosome 11
strand 1
last intron/exon boundary 1255
theoretical NMD boundary in CDS 1113
length of CDS 1284
coding sequence (CDS) position 547
cDNA position
(for ins/del: last normal base / first normal base)		 638
gDNA position
(for ins/del: last normal base / first normal base)		 17494
chromosomal position
(for ins/del: last normal base / first normal base)		 108009736
original gDNA sequence snippet AAGATTTGATTGTAAAAGACGGGCTAACTGATGTCTACAAT
altered gDNA sequence snippet AAGATTTGATTGTAAAAGACAGGCTAACTGATGTCTACAAT
original cDNA sequence snippet AAGATTTGATTGTAAAAGACGGGCTAACTGATGTCTACAAT
altered cDNA sequence snippet AAGATTTGATTGTAAAAGACAGGCTAACTGATGTCTACAAT
wildtype AA sequence MAVLAALLRS GARSRSPLLR RLVQEIRYVE RSYVSKPTLK EVVIVSATRT PIGSFLGSLS
LLPATKLGSI AIQGAIEKAG IPKEEVKEAY MGNVLQGGEG QAPTRQAVLG AGLPISTPCT
TINKVCASGM KAIMMASQSL MCGHQDVMVA GGMESMSNVP YVMNRGSTPY GGVKLEDLIV
KDGLTDVYNK IHMGSCAENT AKKLNIARNE QDAYAINSYT RSKAAWEAGK FGNEVIPVTV
TVKGQPDVVV KEDEEYKRVD FSKVPKLKTV FQKENGTVTA ANASTLNDGA AALVLMTADA
AKRLNVTPLA RIVAFADAAV EPIDFPIAPV YAASMVLKDV GLKKEDIAMW EVNEAFSLVV
LANIKMLEID PQKVNINGGA VSLGHPIGMS GARIVGHLTH ALKQGEYGLA SICNGGGGAS
AMLIQKL*
mutated AA sequence MAVLAALLRS GARSRSPLLR RLVQEIRYVE RSYVSKPTLK EVVIVSATRT PIGSFLGSLS
LLPATKLGSI AIQGAIEKAG IPKEEVKEAY MGNVLQGGEG QAPTRQAVLG AGLPISTPCT
TINKVCASGM KAIMMASQSL MCGHQDVMVA GGMESMSNVP YVMNRGSTPY GGVKLEDLIV
KDRLTDVYNK IHMGSCAENT AKKLNIARNE QDAYAINSYT RSKAAWEAGK FGNEVIPVTV
TVKGQPDVVV KEDEEYKRVD FSKVPKLKTV FQKENGTVTA ANASTLNDGA AALVLMTADA
AKRLNVTPLA RIVAFADAAV EPIDFPIAPV YAASMVLKDV GLKKEDIAMW EVNEAFSLVV
LANIKMLEID PQKVNINGGA VSLGHPIGMS GARIVGHLTH ALKQGEYGLA SICNGGGGAS
AMLIQKL*
speed 0.77 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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Problems