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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: ENST00000304865
MT speed 0.8 s - this script 2.852647 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
OR1L8polymorphism_automatic2.06919987799647e-06simple_aaeT27Psingle base exchangers10985704show file

Taster files

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Prediction

polymorphism

Model: simple_aae, prob: 0.999997930800122 (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) chr9:125330678T>GN/A show variant in all transcripts   IGV
HGNC symbol OR1L8
Ensembl transcript ID ENST00000304865
Genbank transcript ID NM_001004454
UniProt peptide Q8NGR8
alteration type single base exchange
alteration region CDS
DNA changes c.79A>C
cDNA.161A>C
g.161A>C
AA changes T27P Score: 38 explain score(s)
position(s) of altered AA
if AA alteration in CDS
27
frameshift no
known variant Reference ID: rs10985704
databasehomozygous (G/G)heterozygousallele carriers
1000G11739852158
ExAC22428-1208910339
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.6590.61
1.6240.566
(flanking)-0.9910.003
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased154wt: 0.8510 / mu: 0.8890 (marginal change - not scored)wt: GAGGACCAAAAGACA
mu: GAGGACCAAAAGCCA
 GGAC|caaa
distance from splice site 161
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      27LGLSSRPEDQKTLFVLFLIVYLVT
mutated  not conserved    27LGLSSRPEDQKPLFVLFLIVYLV
Ptroglodytes  not conserved  ENSPTRG00000021330  27LGLSSRPEDQKPFFVLFLIVYLV
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000075380  27LGLSPRPEDQKPLFILFLTIYLV
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 
2750TRANSMEMHelical; Name=1; (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 930 / 930
position (AA) of stopcodon in wt / mu AA sequence 310 / 310
position of stopcodon in wt / mu cDNA 1012 / 1012
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 83 / 83
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 930
coding sequence (CDS) position 79
cDNA position
(for ins/del: last normal base / first normal base)
161
gDNA position
(for ins/del: last normal base / first normal base)
161
chromosomal position
(for ins/del: last normal base / first normal base)
125330678
original gDNA sequence snippet CCCGGCCTGAGGACCAAAAGACACTCTTTGTTCTCTTCCTC
altered gDNA sequence snippet CCCGGCCTGAGGACCAAAAGCCACTCTTTGTTCTCTTCCTC
original cDNA sequence snippet CCCGGCCTGAGGACCAAAAGACACTCTTTGTTCTCTTCCTC
altered cDNA sequence snippet CCCGGCCTGAGGACCAAAAGCCACTCTTTGTTCTCTTCCTC
wildtype AA sequence MERINHTSSV SEFILLGLSS RPEDQKTLFV LFLIVYLVTI TGNLLIILAI RFNPHLQTPM
YFFLSFLSLT DICFTTSVVP KMLMNFLSEK KTISYAGCLT QMYFLYALGN SDSCLLAVMA
FDRYVAVCDP FHYVTTMSHH HCVLLVAFSC SFPHLHSLLH TLLLNRLTFC DSNVIHHFLC
DLSPVLKLSC SSIFVNEIVQ MTEAPIVLVT RFLCIAFSYI RILTTVLKIP STSGKRKAFS
TCGFYLTVVT LFYGSIFCVY LQPPSTYAVK DHVATIVYTV LSSMLNPFIY SLRNKDLKQG
LRKLMSKRS*
mutated AA sequence MERINHTSSV SEFILLGLSS RPEDQKPLFV LFLIVYLVTI TGNLLIILAI RFNPHLQTPM
YFFLSFLSLT DICFTTSVVP KMLMNFLSEK KTISYAGCLT QMYFLYALGN SDSCLLAVMA
FDRYVAVCDP FHYVTTMSHH HCVLLVAFSC SFPHLHSLLH TLLLNRLTFC DSNVIHHFLC
DLSPVLKLSC SSIFVNEIVQ MTEAPIVLVT RFLCIAFSYI RILTTVLKIP STSGKRKAFS
TCGFYLTVVT LFYGSIFCVY LQPPSTYAVK DHVATIVYTV LSSMLNPFIY SLRNKDLKQG
LRKLMSKRS*
speed 0.80 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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