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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 2.207437 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ACAT1disease_causing_automatic0.419637078061658simple_aaeaffected0A333Psingle base exchangers120074147show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.419637078061658 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950009)
  • known disease mutation: rs2845 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:108014766G>CN/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.997G>C
cDNA.1088G>C
g.22524G>C
AA changes A333P Score: 27 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 333
frameshift no
known variant Reference ID: rs120074147
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs2845 (pathogenic for Deficiency of acetyl-CoA acetyltransferase) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950009)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950009)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950009)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4631
4.4181
(flanking)3.4740.997
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased22532wt: 0.27 / mu: 0.55wt: CCTGTATATGCTGCATCTATGGTGAGAACAAAGTGAGGGGC
mu: CCTGTATATGCTCCATCTATGGTGAGAACAAAGTGAGGGGC		 tatg|GTGA
Acc increased22529wt: 0.21 / mu: 0.80wt: GCTCCTGTATATGCTGCATCTATGGTGAGAACAAAGTGAGG
mu: GCTCCTGTATATGCTCCATCTATGGTGAGAACAAAGTGAGG		 atct|ATGG
Acc marginally increased22518wt: 0.3841 / mu: 0.3971 (marginal change - not scored)wt: ATTTTCCAATTGCTCCTGTATATGCTGCATCTATGGTGAGA
mu: ATTTTCCAATTGCTCCTGTATATGCTCCATCTATGGTGAGA		 gtat|ATGC
Acc marginally increased22525wt: 0.7618 / mu: 0.7850 (marginal change - not scored)wt: AATTGCTCCTGTATATGCTGCATCTATGGTGAGAACAAAGT
mu: AATTGCTCCTGTATATGCTCCATCTATGGTGAGAACAAAGT		 ctgc|ATCT
Acc marginally increased22522wt: 0.4875 / mu: 0.5415 (marginal change - not scored)wt: TCCAATTGCTCCTGTATATGCTGCATCTATGGTGAGAACAA
mu: TCCAATTGCTCCTGTATATGCTCCATCTATGGTGAGAACAA		 atgc|TGCA
Acc marginally increased22527wt: 0.7195 / mu: 0.7785 (marginal change - not scored)wt: TTGCTCCTGTATATGCTGCATCTATGGTGAGAACAAAGTGA
mu: TTGCTCCTGTATATGCTCCATCTATGGTGAGAACAAAGTGA		 gcat|CTAT
Acc gained225330.60mu: CTGTATATGCTCCATCTATGGTGAGAACAAAGTGAGGGGCG atgg|TGAG
Donor gained225260.42mu: GCTCCATCTATGGTG TCCA|tcta
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      333PIDFPIAPVYAASMVLKDVGLKKE
mutated  not conserved    333PIDFPIAPVYAPSMVLKDVGLKK
Ptroglodytes  all identical  ENSPTRG00000004247  333PIDFPIAPVYAASMVLKDVGLKK
Mmulatta  not conserved  ENSMMUG00000004161  333PIDFPIAPVHAVSMVLKDVGLKK
Fcatus  not conserved  ENSFCAG00000012428  333PIDFPVAPAYAVPKVLKDAGLKK
Mmusculus  not conserved  ENSMUSG00000032047  330PIDFPLAPAYAVPKVLKYAGLKK
Ggallus  not conserved  ENSGALG00000017163  315DFPIAPAHAVPKILSETGLKK
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000045888  326PIDFPIAPAFAVPKVLKAAGIKK
Dmelanogaster  not conserved  FBgn0029969  316PIDFPIAPALAIPKLLKRAGVRK
Celegans  not conserved  T02G5.8  313PLDFAVAPTLMFPKILER
Xtropicalis  not conserved  ENSXETG00000014477  326PIDFPIAPAYAVPKLLSEAGLKK
protein features
start (aa)end (aa)featuredetails 
328340HELIXlost
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 997
cDNA position
(for ins/del: last normal base / first normal base)		 1088
gDNA position
(for ins/del: last normal base / first normal base)		 22524
chromosomal position
(for ins/del: last normal base / first normal base)		 108014766
original gDNA sequence snippet CAATTGCTCCTGTATATGCTGCATCTATGGTGAGAACAAAG
altered gDNA sequence snippet CAATTGCTCCTGTATATGCTCCATCTATGGTGAGAACAAAG
original cDNA sequence snippet CAATTGCTCCTGTATATGCTGCATCTATGGTTCTTAAAGAT
altered cDNA sequence snippet CAATTGCTCCTGTATATGCTCCATCTATGGTTCTTAAAGAT
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
KDGLTDVYNK IHMGSCAENT AKKLNIARNE QDAYAINSYT RSKAAWEAGK FGNEVIPVTV
TVKGQPDVVV KEDEEYKRVD FSKVPKLKTV FQKENGTVTA ANASTLNDGA AALVLMTADA
AKRLNVTPLA RIVAFADAAV EPIDFPIAPV YAPSMVLKDV GLKKEDIAMW EVNEAFSLVV
LANIKMLEID PQKVNINGGA VSLGHPIGMS GARIVGHLTH ALKQGEYGLA SICNGGGGAS
AMLIQKL*
speed 0.14 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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