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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: ENST00000377169
MT speed 0 s - this script 2.790777 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
OR2J3polymorphism_automatic3.49720252756924e-14simple_aaeaffectedR226Qsingle base exchangers3749977show file

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Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999965 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM1212921)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:29080344G>AN/A show variant in all transcripts   IGV
HGNC symbol OR2J3
Ensembl transcript ID ENST00000377169
Genbank transcript ID NM_001005216
UniProt peptide O76001
alteration type single base exchange
alteration region CDS
DNA changes c.677G>A
cDNA.677G>A
g.677G>A
AA changes R226Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 226
frameshift no
known variant Reference ID: rs3749977
databasehomozygous (A/A)heterozygousallele carriers
1000G40610491455
ExAC58792100926888

known disease mutation at this position, please check HGMD for details (HGMD ID CM1212921)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0990
-1.0070
(flanking)-0.1580
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased678wt: 0.5138 / mu: 0.5370 (marginal change - not scored)wt: TCTTATGGTGCCATCGTCCGAGCTATACTGAGGATGCAGTC
mu: TCTTATGGTGCCATCGTCCAAGCTATACTGAGGATGCAGTC		 ccga|GCTA
Donor increased678wt: 0.52 / mu: 0.60wt: GTCCGAGCTATACTG
mu: GTCCAAGCTATACTG		 CCGA|gcta
Donor increased673wt: 0.50 / mu: 0.94wt: CCATCGTCCGAGCTA
mu: CCATCGTCCAAGCTA		 ATCG|tccg
distance from splice site 260
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      226ILILTSYGAIVRAILRMQSTTGLQ
mutated  all conserved    226ILILTSYGAIVQAILRMQSTTGL
Ptroglodytes  all identical  ENSPTRG00000024029  226ILILTSYGAIVRAVLRMQSTTGL
Mmulatta  all conserved  ENSMMUG00000029883  224ILILTSYGAIVQAVLRMQSTTGL
Fcatus  not conserved  ENSFCAG00000005124  224ILILSSYGAIAWAVLRMQSSAGL
Mmusculus  not conserved  ENSMUSG00000054940  224ILILSSYAAIAWTVLEMQSTTRL
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
223239TOPO_DOMCytoplasmic (Potential).lost
240262TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
263275TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
276295TRANSMEMHelical; Name=7; (Potential).might get lost (downstream of altered splice site)
296311TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 936 / 936
position (AA) of stopcodon in wt / mu AA sequence 312 / 312
position of stopcodon in wt / mu cDNA 936 / 936
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 1 / 1
chromosome 6
strand 1
last intron/exon boundary 1
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 936
coding sequence (CDS) position 677
cDNA position
(for ins/del: last normal base / first normal base)		 677
gDNA position
(for ins/del: last normal base / first normal base)		 677
chromosomal position
(for ins/del: last normal base / first normal base)		 29080344
original gDNA sequence snippet TTCTTATGGTGCCATCGTCCGAGCTATACTGAGGATGCAGT
altered gDNA sequence snippet TTCTTATGGTGCCATCGTCCAAGCTATACTGAGGATGCAGT
original cDNA sequence snippet TTCTTATGGTGCCATCGTCCGAGCTATACTGAGGATGCAGT
altered cDNA sequence snippet TTCTTATGGTGCCATCGTCCAAGCTATACTGAGGATGCAGT
wildtype AA sequence MNDDGKVNAS SEGYFILVGF SNWPHLEVVI FVVVLIFYLM TLIGNLFIII LSYLDSHLHT
PMYFFLSNLS FLDLCYTTSS IPQLLVNLWG PEKTISYAGC MIQLYFVLAL GTTECVLLVV
MSYDRYAAVC RPLHYTVLMH PRFCHLLAVA SWVSGFTNSA LHSSFTFWVP LCGHRQVDHF
FCEVPALLRL SCVDTHVNEL TLMITSSIFV LIPLILILTS YGAIVRAILR MQSTTGLQKV
FGTCGAHLMA VSLFFIPAMC MYLQPPSGNS QDQGKFIALF YTVVTPSLNP LIYTLRNKVV
RGAVKRLMGW E*
mutated AA sequence MNDDGKVNAS SEGYFILVGF SNWPHLEVVI FVVVLIFYLM TLIGNLFIII LSYLDSHLHT
PMYFFLSNLS FLDLCYTTSS IPQLLVNLWG PEKTISYAGC MIQLYFVLAL GTTECVLLVV
MSYDRYAAVC RPLHYTVLMH PRFCHLLAVA SWVSGFTNSA LHSSFTFWVP LCGHRQVDHF
FCEVPALLRL SCVDTHVNEL TLMITSSIFV LIPLILILTS YGAIVQAILR MQSTTGLQKV
FGTCGAHLMA VSLFFIPAMC MYLQPPSGNS QDQGKFIALF YTVVTPSLNP LIYTLRNKVV
RGAVKRLMGW E*
speed 0.74 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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