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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: ENST00000458276
MT speed 0 s - this script 2.346728 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ABHD5disease_causing_automatic4.66539183747041e-08simple_aaeaffected0E7Ksingle base exchangers104893676show file

Taster files

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 documentation

Prediction

disease causing

 Model: simple_aae, prob: 4.66539183747041e-08 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • heterozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM013304)
  • known disease mutation: rs5351 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:43732503G>AN/A show variant in all transcripts   IGV
HGNC symbol ABHD5
Ensembl transcript ID ENST00000458276
Genbank transcript ID NM_016006
UniProt peptide Q8WTS1
alteration type single base exchange
alteration region CDS
DNA changes c.19G>A
cDNA.142G>A
g.899G>A
AA changes E7K Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 7
frameshift no
known variant Reference ID: rs104893676
databasehomozygous (A/A)heterozygousallele carriers
1000G077
ExAC01818

known disease mutation: rs5351 (pathogenic for Triglyceride storage disease with ichthyosis) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM013304)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013304)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013304)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
CBP, Transcription Factor, CBP Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
CTCFL, Transcription Factor, CTCFL Transcription Factor Binding
Cjun, Transcription Factor, Cjun TF binding
Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
GTF2B, Transcription Factor, GTF2B Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HDAC1, Transcription Factor, HDAC1 Transcription Factor Binding
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
Nrf1, Transcription Factor, Nrf1 Transcription Factor Binding
POU2F2, Transcription Factor, POU2F2 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
THAP1, Transcription Factor, THAP1 Transcription Factor Binding
Tcf12, Transcription Factor, Tcf12 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3220.009
0.0870.012
(flanking)-0.3380.019
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased901wt: 0.44 / mu: 0.85wt: GAGGAGGTGGACTCT
mu: GAGAAGGTGGACTCT		 GGAG|gtgg
Donor marginally increased892wt: 0.7941 / mu: 0.8590 (marginal change - not scored)wt: GCGGAGGAGGAGGAG
mu: GCGGAGGAGGAGAAG		 GGAG|gagg
Donor increased895wt: 0.85 / mu: 0.99wt: GAGGAGGAGGAGGTG
mu: GAGGAGGAGAAGGTG		 GGAG|gagg
distance from splice site 29
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      7 MAAEEEEVDSADTGERSGW
mutated  all conserved    7 MAAEEEKVDSADTGERSGWLTG
Ptroglodytes  all identical  ENSPTRG00000014812  7 MAAEEEEVDSADTGERSGWLTG
Mmulatta  all identical  ENSMMUG00000001031  7 MAAEEEEVDSADTEERSGWLTG
Fcatus  no alignment  ENSFCAG00000008874  n/a
Mmusculus  all identical  ENSMUSG00000032540  9 AAEEEVDSADAGGGSGWLTG
Ggallus  all identical  ENSGALG00000011510  5 EEEASS----ERLGWLFS
Trubripes  all conserved  ENSTRUG00000013439  4 DEQVITANEGWC--WIPS
Drerio  all identical  ENSDARG00000076874  4 EETVLADTG--SWWSAD
Dmelanogaster  not conserved  FBgn0033226  41 KSSMDLEDPRNNRFFLWK
Celegans  no alignment  C37H5.3  n/a
Xtropicalis  no alignment  ENSXETG00000022025  n/a
protein features
start (aa)end (aa)featuredetails 
263263CONFLICTF -> S (in Ref. 2; AAD34053).might get lost (downstream of altered splice site)
327332MOTIFHXXXXD motif.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1050 / 1050
position (AA) of stopcodon in wt / mu AA sequence 350 / 350
position of stopcodon in wt / mu cDNA 1173 / 1173
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 124 / 124
chromosome 3
strand 1
last intron/exon boundary 1084
theoretical NMD boundary in CDS 910
length of CDS 1050
coding sequence (CDS) position 19
cDNA position
(for ins/del: last normal base / first normal base)		 142
gDNA position
(for ins/del: last normal base / first normal base)		 899
chromosomal position
(for ins/del: last normal base / first normal base)		 43732503
original gDNA sequence snippet CTATGGCGGCGGAGGAGGAGGAGGTGGACTCTGCCGACACC
altered gDNA sequence snippet CTATGGCGGCGGAGGAGGAGAAGGTGGACTCTGCCGACACC
original cDNA sequence snippet CTATGGCGGCGGAGGAGGAGGAGGTGGACTCTGCCGACACC
altered cDNA sequence snippet CTATGGCGGCGGAGGAGGAGAAGGTGGACTCTGCCGACACC
wildtype AA sequence MAAEEEEVDS ADTGERSGWL TGWLPTWCPT SISHLKEAEE KMLKCVPCTY KKEPVRISNG
NKIWTLKFSH NISNKTPLVL LHGFGGGLGL WALNFGDLCT NRPVYAFDLL GFGRSSRPRF
DSDAEEVENQ FVESIEEWRC ALGLDKMILL GHNLGGFLAA AYSLKYPSRV NHLILVEPWG
FPERPDLADQ DRPIPVWIRA LGAALTPFNP LAGLRIAGPF GLSLVQRLRP DFKRKYSSMF
EDDTVTEYIY HCNVQTPSGE TAFKNMTIPY GWAKRPMLQR IGKMHPDIPV SVIFGARSCI
DGNSGTSIQS LRPHSYVKTI AILGAGHYVY ADQPEEFNQK VKEICDTVD*
mutated AA sequence MAAEEEKVDS ADTGERSGWL TGWLPTWCPT SISHLKEAEE KMLKCVPCTY KKEPVRISNG
NKIWTLKFSH NISNKTPLVL LHGFGGGLGL WALNFGDLCT NRPVYAFDLL GFGRSSRPRF
DSDAEEVENQ FVESIEEWRC ALGLDKMILL GHNLGGFLAA AYSLKYPSRV NHLILVEPWG
FPERPDLADQ DRPIPVWIRA LGAALTPFNP LAGLRIAGPF GLSLVQRLRP DFKRKYSSMF
EDDTVTEYIY HCNVQTPSGE TAFKNMTIPY GWAKRPMLQR IGKMHPDIPV SVIFGARSCI
DGNSGTSIQS LRPHSYVKTI AILGAGHYVY ADQPEEFNQK VKEICDTVD*
speed 0.29 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