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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: ENST00000377981
MT speed 0 s - this script 2.444416 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
OR13J1polymorphism_automatic8.39356395498925e-09simple_aaeH133Rsingle base exchangers7044405show file

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Prediction

polymorphism

 Model: simple_aae, prob: 0.999999991606436 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:35870001T>CN/A show variant in all transcripts   IGV
HGNC symbol OR13J1
Ensembl transcript ID ENST00000377981
Genbank transcript ID NM_001004487
UniProt peptide Q8NGT2
alteration type single base exchange
alteration region CDS
DNA changes c.398A>G
cDNA.461A>G
g.461A>G
AA changes H133R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 133
frameshift no
known variant Reference ID: rs7044405
databasehomozygous (C/C)heterozygousallele carriers
1000G105011342184
ExAC23411-140559356
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.6660.001
0.2810.192
(flanking)2.7440.991
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 increased455wt: 0.6349 / mu: 0.6679 (marginal change - not scored)wt: GGCCATCTGCCAGCCACTCAGGTACCACGTGCTCATGAGCC
mu: GGCCATCTGCCAGCCACTCAGGTACCGCGTGCTCATGAGCC		 tcag|GTAC
distance from splice site 461
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      133RYLAICQPLRYHVLMSHRLCVLLM
mutated  not conserved    133RYLAICQPLRYRVLMSHRLCVLL
Ptroglodytes  not conserved  ENSPTRG00000020925  133RYLAICQPLRYRVLMSHRHCVLL
Mmulatta  not conserved  ENSMMUG00000016340  133RYLAICQPLRYRVLMNHRLCVLL
Fcatus  not conserved  ENSFCAG00000012759  133RYLAICRPLRYPVLMSHRLCFFL
Mmusculus  not conserved  ENSMUSG00000046450  133RYLAICQPLRYPVLMSHRLCLML
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000020546  130AICYPLYYGRLMSSKMCYLM
protein features
start (aa)end (aa)featuredetails 
121139TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 939 / 939
position (AA) of stopcodon in wt / mu AA sequence 313 / 313
position of stopcodon in wt / mu cDNA 1002 / 1002
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 64 / 64
chromosome 9
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 939
coding sequence (CDS) position 398
cDNA position
(for ins/del: last normal base / first normal base)		 461
gDNA position
(for ins/del: last normal base / first normal base)		 461
chromosomal position
(for ins/del: last normal base / first normal base)		 35870001
original gDNA sequence snippet CTGCCAGCCACTCAGGTACCACGTGCTCATGAGCCACCGGC
altered gDNA sequence snippet CTGCCAGCCACTCAGGTACCGCGTGCTCATGAGCCACCGGC
original cDNA sequence snippet CTGCCAGCCACTCAGGTACCACGTGCTCATGAGCCACCGGC
altered cDNA sequence snippet CTGCCAGCCACTCAGGTACCGCGTGCTCATGAGCCACCGGC
wildtype AA sequence MEPLNRTEVS EFFLKGFSGY PALEHLLFPL CSAMYLVTLL GNTAIMAVSV LDIHLHTPVY
FFLGNLSTLD ICYTPTFVPL MLVHLLSSRK TISFAVCAIQ MCLSLSTGST ECLLLAITAY
DRYLAICQPL RYHVLMSHRL CVLLMGAAWV LCLLKSVTEM VISMRLPFCG HHVVSHFTCK
ILAVLKLACG NTSVSEDFLL AGSILLLPVP LAFICLSYLL ILATILRVPS AARCCKAFST
CLAHLAVVLL FYGTIIFMYL KPKSKEAHIS DEVFTVLYAM VTTMLNPTIY SLRNKEVKEA
ARKVWGRSRA SR*
mutated AA sequence MEPLNRTEVS EFFLKGFSGY PALEHLLFPL CSAMYLVTLL GNTAIMAVSV LDIHLHTPVY
FFLGNLSTLD ICYTPTFVPL MLVHLLSSRK TISFAVCAIQ MCLSLSTGST ECLLLAITAY
DRYLAICQPL RYRVLMSHRL CVLLMGAAWV LCLLKSVTEM VISMRLPFCG HHVVSHFTCK
ILAVLKLACG NTSVSEDFLL AGSILLLPVP LAFICLSYLL ILATILRVPS AARCCKAFST
CLAHLAVVLL FYGTIIFMYL KPKSKEAHIS DEVFTVLYAM VTTMLNPTIY SLRNKEVKEA
ARKVWGRSRA SR*
speed 0.44 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