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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: ENST00000377175
MT speed 2.19 s - this script 6.136836 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
OR2W1polymorphism_automatic0.996687639783558simple_aaeaffectedD296Nsingle base exchangers35771565show file

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Prediction

polymorphism

Model: simple_aae, prob: 0.00331236021644215 (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 CM141898)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:29012067C>TN/A show variant in all transcripts   IGV
HGNC symbol OR2W1
Ensembl transcript ID ENST00000377175
Genbank transcript ID NM_030903
UniProt peptide Q9Y3N9
alteration type single base exchange
alteration region CDS
DNA changes c.886G>A
cDNA.951G>A
g.951G>A
AA changes D296N Score: 23 explain score(s)
position(s) of altered AA
if AA alteration in CDS
296
frameshift no
known variant Reference ID: rs35771565
databasehomozygous (T/T)heterozygousallele carriers
1000G1749011075
ExAC22521592318175

known disease mutation at this position, please check HGMD for details (HGMD ID CM141898)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.2131
3.5321
(flanking)0.5770.947
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 increased942wt: 0.8550 / mu: 0.8764 (marginal change - not scored)wt: ACCCGCTCATTTACACCTTAAGAAATAAGGACATGAAGGAT
mu: ACCCGCTCATTTACACCTTAAGAAATAAGAACATGAAGGAT
 ttaa|GAAA
Donor marginally increased942wt: 0.8354 / mu: 0.8884 (marginal change - not scored)wt: CCTTAAGAAATAAGG
mu: CCTTAAGAAATAAGA
 TTAA|gaaa
Donor marginally increased953wt: 0.8562 / mu: 0.9486 (marginal change - not scored)wt: AAGGACATGAAGGAT
mu: AAGAACATGAAGGAT
 GGAC|atga
Donor increased954wt: 0.51 / mu: 0.59wt: AGGACATGAAGGATG
mu: AGAACATGAAGGATG
 GACA|tgaa
distance from splice site 78
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      296LNPLIYTLRNKDMKDALKKLMRFH
mutated  all conserved    296LNPLIYTLRNKNMKDA
Ptroglodytes  all identical  ENSPTRG00000017886  296LNPLIYTLRNKDMKDA
Mmulatta  all identical  ENSMMUG00000004377  296LNPLIYTLRNKDMKDA
Fcatus  all identical  ENSFCAG00000010634  296LNPLVYTLRNKDMKNA
Mmusculus  all identical  ENSMUSG00000071522  296LNPLIYTLRNRDMKDA
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 
293320TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 963 / 963
position (AA) of stopcodon in wt / mu AA sequence 321 / 321
position of stopcodon in wt / mu cDNA 1028 / 1028
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 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 963
coding sequence (CDS) position 886
cDNA position
(for ins/del: last normal base / first normal base)
951
gDNA position
(for ins/del: last normal base / first normal base)
951
chromosomal position
(for ins/del: last normal base / first normal base)
29012067
original gDNA sequence snippet TTTACACCTTAAGAAATAAGGACATGAAGGATGCCCTGAAG
altered gDNA sequence snippet TTTACACCTTAAGAAATAAGAACATGAAGGATGCCCTGAAG
original cDNA sequence snippet TTTACACCTTAAGAAATAAGGACATGAAGGATGCCCTGAAG
altered cDNA sequence snippet TTTACACCTTAAGAAATAAGAACATGAAGGATGCCCTGAAG
wildtype AA sequence MDQSNYSSLH GFILLGFSNH PKMEMILSGV VAIFYLITLV GNTAIILASL LDSQLHTPMY
FFLRNLSFLD LCFTTSIIPQ MLVNLWGPDK TISYVGCIIQ LYVYMWLGSV ECLLLAVMSY
DRFTAICKPL HYFVVMNPHL CLKMIIMIWS ISLANSVVLC TLTLNLPTCG NNILDHFLCE
LPALVKIACV DTTTVEMSVF ALGIIIVLTP LILILISYGY IAKAVLRTKS KASQRKAMNT
CGSHLTVVSM FYGTIIYMYL QPGNRASKDQ GKFLTLFYTV ITPSLNPLIY TLRNKDMKDA
LKKLMRFHHK STKIKRNCKS *
mutated AA sequence MDQSNYSSLH GFILLGFSNH PKMEMILSGV VAIFYLITLV GNTAIILASL LDSQLHTPMY
FFLRNLSFLD LCFTTSIIPQ MLVNLWGPDK TISYVGCIIQ LYVYMWLGSV ECLLLAVMSY
DRFTAICKPL HYFVVMNPHL CLKMIIMIWS ISLANSVVLC TLTLNLPTCG NNILDHFLCE
LPALVKIACV DTTTVEMSVF ALGIIIVLTP LILILISYGY IAKAVLRTKS KASQRKAMNT
CGSHLTVVSM FYGTIIYMYL QPGNRASKDQ GKFLTLFYTV ITPSLNPLIY TLRNKNMKDA
LKKLMRFHHK STKIKRNCKS *
speed 2.19 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