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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: ENST00000392899
MT speed 0 s - this script 2.677133 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
OR2F1polymorphism_automatic0.000930059826823038simple_aaeaffectedH137Rsingle base exchangers2072165show file

Taster files

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 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999069940173177 (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
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:143657473A>GN/A show variant in all transcripts   IGV
HGNC symbol OR2F1
Ensembl transcript ID ENST00000392899
Genbank transcript ID NM_012369
UniProt peptide Q13607
alteration type single base exchange
alteration region CDS
DNA changes c.410A>G
cDNA.447A>G
g.447A>G
AA changes H137R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 137
frameshift no
known variant Reference ID: rs2072165
databasehomozygous (G/G)heterozygousallele carriers
1000G172788960
ExAC20381430916347
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.0830.972
0.1690.149
(flanking)0.4230.043
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased446wt: 0.84 / mu: 0.93wt: TGCGATACTCGGCCATCATGCATGGAGGGCTGTGTGCTAGG
mu: TGCGATACTCGGCCATCATGCGTGGAGGGCTGTGTGCTAGG		 atgc|ATGG
Donor increased446wt: 0.54 / mu: 0.98wt: TCATGCATGGAGGGC
mu: TCATGCGTGGAGGGC		 ATGC|atgg
distance from splice site 447
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      137VCDALRYSAIMHGGLCARLAITSW
mutated  not conserved    137VCDALRYSAIMRGGLCARLAITS
Ptroglodytes  all identical  ENSPTRG00000019819  137VCDALRYSAIMHGGLCARLAITS
Mmulatta  all identical  ENSMMUG00000019855  137VCDPLRYSAIMHGALCARLAITS
Fcatus  all identical  ENSFCAG00000016323  137VCDPLRYSVIMHGGLCTRLAITS
Mmusculus  all identical  ENSMUSG00000095236  137VCDPLRYSVIMHAGLCTRLVITS
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 
121139TOPO_DOMCytoplasmic (Potential).lost
140160TRANSMEMHelical; Name=4; (Potential).might get lost (downstream of altered splice site)
161200TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
189189DISULFIDBy similarity.might get lost (downstream of altered splice site)
201222TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
211211CONFLICTF -> L (in Ref. 1; AAB01215).might get lost (downstream of altered splice site)
223236TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
237261TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
262272TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
273292TRANSMEMHelical; Name=7; (Potential).might get lost (downstream of altered splice site)
293317TOPO_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 954 / 954
position (AA) of stopcodon in wt / mu AA sequence 318 / 318
position of stopcodon in wt / mu cDNA 991 / 991
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 38 / 38
chromosome 7
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 954
coding sequence (CDS) position 410
cDNA position
(for ins/del: last normal base / first normal base)		 447
gDNA position
(for ins/del: last normal base / first normal base)		 447
chromosomal position
(for ins/del: last normal base / first normal base)		 143657473
original gDNA sequence snippet GCGATACTCGGCCATCATGCATGGAGGGCTGTGTGCTAGGT
altered gDNA sequence snippet GCGATACTCGGCCATCATGCGTGGAGGGCTGTGTGCTAGGT
original cDNA sequence snippet GCGATACTCGGCCATCATGCATGGAGGGCTGTGTGCTAGGT
altered cDNA sequence snippet GCGATACTCGGCCATCATGCGTGGAGGGCTGTGTGCTAGGT
wildtype AA sequence MGTDNQTWVS EFILLGLSSD WDTRVSLFVL FLVMYVVTVL GNCLIVLLIR LDSRLHTPMY
FFLTNLSLVD VSYATSVVPQ LLAHFLAEHK AIPFQSCAAQ LFFSLALGGI EFVLLAVMAY
DRYVAVCDAL RYSAIMHGGL CARLAITSWV SGFISSPVQT AITFQLPMCR NKFIDHISCE
LLAVVRLACV DTSSNEVTIM VSSIVLLMTP FCLVLLSYIQ IISTILKIQS REGRKKAFHT
CASHLTVVAL CYGVAIFTYI QPHSSPSVLQ EKLFSVFYAI LTPMLNPMIY SLRNKEVKGA
WQKLLWKFSG LTSKLAT*
mutated AA sequence MGTDNQTWVS EFILLGLSSD WDTRVSLFVL FLVMYVVTVL GNCLIVLLIR LDSRLHTPMY
FFLTNLSLVD VSYATSVVPQ LLAHFLAEHK AIPFQSCAAQ LFFSLALGGI EFVLLAVMAY
DRYVAVCDAL RYSAIMRGGL CARLAITSWV SGFISSPVQT AITFQLPMCR NKFIDHISCE
LLAVVRLACV DTSSNEVTIM VSSIVLLMTP FCLVLLSYIQ IISTILKIQS REGRKKAFHT
CASHLTVVAL CYGVAIFTYI QPHSSPSVLQ EKLFSVFYAI LTPMLNPMIY SLRNKEVKGA
WQKLLWKFSG LTSKLAT*
speed 0.61 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