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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: ENST00000329434
MT speed 0.76 s - this script 2.800804 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
OR5P2polymorphism_automatic0.000260534782917987simple_aaeaffectedC213Ssingle base exchangers76615008show file

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Prediction

polymorphism

 Model: simple_aae, prob: 0.999739465217082 (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) chr11:7817852C>GN/A show variant in all transcripts   IGV
HGNC symbol OR5P2
Ensembl transcript ID ENST00000329434
Genbank transcript ID NM_153444
UniProt peptide Q8WZ92
alteration type single base exchange
alteration region CDS
DNA changes c.638G>C
cDNA.669G>C
g.669G>C
AA changes C213S Score: 112 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 213
frameshift no
known variant Reference ID: rs76615008
databasehomozygous (G/G)heterozygousallele carriers
1000G253679932
ExAC51402039825538
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3680.997
2.8380.998
(flanking)1.690.931
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased675wt: 0.30 / mu: 0.57wt: TGTCATAGCCGTCTGCTACATCTATATCCTCATCACCATCC
mu: TGTCATAGCCGTCTCCTACATCTATATCCTCATCACCATCC		 acat|CTAT
Acc increased679wt: 0.33 / mu: 0.58wt: ATAGCCGTCTGCTACATCTATATCCTCATCACCATCCTGAA
mu: ATAGCCGTCTCCTACATCTATATCCTCATCACCATCCTGAA		 ctat|ATCC
Acc increased677wt: 0.32 / mu: 0.62wt: TCATAGCCGTCTGCTACATCTATATCCTCATCACCATCCTG
mu: TCATAGCCGTCTCCTACATCTATATCCTCATCACCATCCTG		 atct|ATAT
Acc gained6730.65mu: TGTGTCATAGCCGTCTCCTACATCTATATCCTCATCACCAT ctac|ATCT
distance from splice site 401
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      213IIVVTVCVIAVCYIYILITILKMR
mutated  not conserved    213IIVVTVCVIAVSYIYILITILKM
Ptroglodytes  not conserved  ENSPTRG00000003320  213IIVVTVCVVAVSYIYILITILKM
Mmulatta  not conserved  ENSMMUG00000011135  220IIVVTMCVIAISYIYILITIMKM
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000058014  220IIIVTIFVIAVSYIYILITILKM
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 
193213TRANSMEMHelical; Name=5; (Potential).lost
214233TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
234254TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
255267TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
259259CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
268288TRANSMEMHelical; Name=7; (Potential).might get lost (downstream of altered splice site)
289322TOPO_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 969 / 969
position (AA) of stopcodon in wt / mu AA sequence 323 / 323
position of stopcodon in wt / mu cDNA 1000 / 1000
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 32 / 32
chromosome 11
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 969
coding sequence (CDS) position 638
cDNA position
(for ins/del: last normal base / first normal base)		 669
gDNA position
(for ins/del: last normal base / first normal base)		 669
chromosomal position
(for ins/del: last normal base / first normal base)		 7817852
original gDNA sequence snippet TGTGTGTGTCATAGCCGTCTGCTACATCTATATCCTCATCA
altered gDNA sequence snippet TGTGTGTGTCATAGCCGTCTCCTACATCTATATCCTCATCA
original cDNA sequence snippet TGTGTGTGTCATAGCCGTCTGCTACATCTATATCCTCATCA
altered cDNA sequence snippet TGTGTGTGTCATAGCCGTCTCCTACATCTATATCCTCATCA
wildtype AA sequence MNSLKDGNHT ALTGFILLGL TDDPILRVIL FMIILSGNLS IIILIRISSQ LHHPMYFFLS
HLAFADMAYS SSVTPNMLVN FLVERNTVSY LGCAIQLGSA AFFATVECVL LAAMAYDRFV
AICSPLLYST KMSTQVSVQL LLVVYIAGFL IAVSYTTSFY FLLFCGPNQV NHFFCDFAPL
LELSCSDISV STVVLSFSSG SIIVVTVCVI AVCYIYILIT ILKMRSTEGH HKAFSTCTSH
LTVVTLFYGT ITFIYVMPNF SYSTDQNKVV SVLYTVVIPM LNPLIYSLRN KEIKGALKRE
LVRKILSHDA CYFSRTSNND IT*
mutated AA sequence MNSLKDGNHT ALTGFILLGL TDDPILRVIL FMIILSGNLS IIILIRISSQ LHHPMYFFLS
HLAFADMAYS SSVTPNMLVN FLVERNTVSY LGCAIQLGSA AFFATVECVL LAAMAYDRFV
AICSPLLYST KMSTQVSVQL LLVVYIAGFL IAVSYTTSFY FLLFCGPNQV NHFFCDFAPL
LELSCSDISV STVVLSFSSG SIIVVTVCVI AVSYIYILIT ILKMRSTEGH HKAFSTCTSH
LTVVTLFYGT ITFIYVMPNF SYSTDQNKVV SVLYTVVIPM LNPLIYSLRN KEIKGALKRE
LVRKILSHDA CYFSRTSNND IT*
speed 0.76 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