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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: ENST00000343870
MT speed 0 s - this script 2.992571 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
OR6C74polymorphism_automatic6.26054763586126e-13simple_aaeaffectedY75Csingle base exchangers4388990show file

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Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999374 (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) chr12:55641295A>GN/A show variant in all transcripts   IGV
HGNC symbol OR6C74
Ensembl transcript ID ENST00000343870
Genbank transcript ID NM_001005490
UniProt peptide A6NCV1
alteration type single base exchange
alteration region CDS
DNA changes c.224A>G
cDNA.314A>G
g.314A>G
AA changes Y75C Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 75
frameshift no
known variant Reference ID: rs4388990
databasehomozygous (G/G)heterozygousallele carriers
1000G1528771029
ExAC50812260527686
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9640.005
0.3150.002
(flanking)-1.3140
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased322wt: 0.44 / mu: 0.54wt: TCACAACTGTCTACATTCCCAAATTTCTTGTTAGTATGGCA
mu: TCACAACTGTCTGCATTCCCAAATTTCTTGTTAGTATGGCA		 ccca|AATT
Acc marginally increased323wt: 0.7041 / mu: 0.7446 (marginal change - not scored)wt: CACAACTGTCTACATTCCCAAATTTCTTGTTAGTATGGCAA
mu: CACAACTGTCTGCATTCCCAAATTTCTTGTTAGTATGGCAA		 ccaa|ATTT
distance from splice site 314
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      75FSFLEVSFTTVYIPKFLVSMATGD
mutated  not conserved    75FSFLEVSFTTVCIPKFLVSMATG
Ptroglodytes  not conserved  ENSPTRG00000005050  75FSFLEVSFTTACIPKFLVSMATG
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000044897  75FSFLEISFTTVCIPKFLVSMATG
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 
6484TRANSMEMHelical; Name=2; (Potential).lost
8595TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
9595DISULFIDBy similarity.might get lost (downstream of altered splice site)
96116TRANSMEMHelical; Name=3; (Potential).might get lost (downstream of altered splice site)
117140TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
141161TRANSMEMHelical; Name=4; (Potential).might get lost (downstream of altered splice site)
162194TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
177177DISULFIDBy similarity.might get lost (downstream of altered splice site)
195215TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
216237TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
238258TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
259269TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
270290TRANSMEMHelical; Name=7; (Potential).might get lost (downstream of altered splice site)
291312TOPO_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 939 / 939
position (AA) of stopcodon in wt / mu AA sequence 313 / 313
position of stopcodon in wt / mu cDNA 1029 / 1029
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 91 / 91
chromosome 12
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 224
cDNA position
(for ins/del: last normal base / first normal base)		 314
gDNA position
(for ins/del: last normal base / first normal base)		 314
chromosomal position
(for ins/del: last normal base / first normal base)		 55641295
original gDNA sequence snippet AGTCTCATTCACAACTGTCTACATTCCCAAATTTCTTGTTA
altered gDNA sequence snippet AGTCTCATTCACAACTGTCTGCATTCCCAAATTTCTTGTTA
original cDNA sequence snippet AGTCTCATTCACAACTGTCTACATTCCCAAATTTCTTGTTA
altered cDNA sequence snippet AGTCTCATTCACAACTGTCTGCATTCCCAAATTTCTTGTTA
wildtype AA sequence MRNHTTVANF ILLGLTDDPQ LQVIIFLLLF FTYMLSITGN LTIITLTLLD LHLKTPMYFF
LRNFSFLEVS FTTVYIPKFL VSMATGDKTI SYNDCAAQLF FTILLGATEF FLLAAMSYER
YVAICKPLHY TTIMSSRVCS LLVFASWMAG FLIIFPPLLM GLQLDFCAAN TVDHFFCDVS
PILQLSCTDT DIIELMMLLS AILTLLVTLV LVILSYTNII RTILKIPSSQ QRKKAFSTCS
SHMVVVSISY GSCIFMYVKP SAKERVSLNK GIALLSTSVA PMLNPFIYTL RNKQVKDVFK
HTVKKIELFS MK*
mutated AA sequence MRNHTTVANF ILLGLTDDPQ LQVIIFLLLF FTYMLSITGN LTIITLTLLD LHLKTPMYFF
LRNFSFLEVS FTTVCIPKFL VSMATGDKTI SYNDCAAQLF FTILLGATEF FLLAAMSYER
YVAICKPLHY TTIMSSRVCS LLVFASWMAG FLIIFPPLLM GLQLDFCAAN TVDHFFCDVS
PILQLSCTDT DIIELMMLLS AILTLLVTLV LVILSYTNII RTILKIPSSQ QRKKAFSTCS
SHMVVVSISY GSCIFMYVKP SAKERVSLNK GIALLSTSVA PMLNPFIYTL RNKQVKDVFK
HTVKKIELFS MK*
speed 0.92 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