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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: ENST00000538986
MT speed 1.33 s - this script 4.498902 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
TAS2R20polymorphism_automatic5.79536418854332e-14simple_aaeaffectedF252Ssingle base exchangers10845280show file

Taster files

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Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999942 (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) chr12:11149720A>GN/A show variant in all transcripts   IGV
HGNC symbol TAS2R20
Ensembl transcript ID ENST00000538986
Genbank transcript ID NM_176889
UniProt peptide P59543
alteration type single base exchange
alteration region CDS
DNA changes c.755T>C
cDNA.755T>C
g.755T>C
AA changes F252S Score: 155 explain score(s)
position(s) of altered AA
if AA alteration in CDS
252
frameshift no
known variant Reference ID: rs10845280
databasehomozygous (G/G)heterozygousallele carriers
1000G6248701494
ExAC11833910120934
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.8530.002
-1.5640
(flanking)0.4250.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased750wt: 0.33 / mu: 0.39wt: TGTCTAATCATATCGTTTTGGAATTTTAAGATGCGACCAAA
mu: TGTCTAATCATATCGTTTTGGAATTCTAAGATGCGACCAAA
 ttgg|AATT
distance from splice site 627
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      252YFLCLIISFWNFKMRPKEIVLMLC
mutated  not conserved    252YFLCLIISFWNSKMRPKEIVLML
Ptroglodytes  not conserved  ENSPTRG00000032536  252YFLCLITSFWNSKMRPKEIVLML
Mmulatta  all conserved  ENSMMUG00000021004  252YFLCLIVSFWNYKKQQKELVLIL
Fcatus  no alignment  ENSFCAG00000018426  n/a
Mmusculus  not conserved  ENSMUSG00000059382  251SSCVIISGWSLQNAP---VFLF
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 
251259TOPO_DOMExtracellular (Potential).lost
260280TRANSMEMHelical; Name=7; (Potential).might get lost (downstream of altered splice site)
281309TOPO_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 930 / 930
position (AA) of stopcodon in wt / mu AA sequence 310 / 310
position of stopcodon in wt / mu cDNA 930 / 930
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 1 / 1
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 930
coding sequence (CDS) position 755
cDNA position
(for ins/del: last normal base / first normal base)
755
gDNA position
(for ins/del: last normal base / first normal base)
755
chromosomal position
(for ins/del: last normal base / first normal base)
11149720
original gDNA sequence snippet AATCATATCGTTTTGGAATTTTAAGATGCGACCAAAAGAAA
altered gDNA sequence snippet AATCATATCGTTTTGGAATTCTAAGATGCGACCAAAAGAAA
original cDNA sequence snippet AATCATATCGTTTTGGAATTTTAAGATGCGACCAAAAGAAA
altered cDNA sequence snippet AATCATATCGTTTTGGAATTCTAAGATGCGACCAAAAGAAA
wildtype AA sequence MMSFLHIVFS ILVVVAFILG NFANGFIALI NFIAWVKRQK ISSADQIIAA LAVSRVGLLW
VILLHWYSTV LNPTSSNLKV IIFISNAWAV TNHFSIWLAT SLSIFYLLKI VNFSRLIFHH
LKRKAKSVVL VIVLGSLFFL VCHLVMKHTY INVWTEECEG NVTWKIKLRN AMHLSNLTVA
MLANLIPFTL TLISFLLLIY SLCKHLKKMQ LHGKGSQDPS TKIHIKALQT VTSFLILLAI
YFLCLIISFW NFKMRPKEIV LMLCQAFGII YPSFHSFILI WGNKTLKQTF LSVLWQVTCW
AKGQNQSTP*
mutated AA sequence MMSFLHIVFS ILVVVAFILG NFANGFIALI NFIAWVKRQK ISSADQIIAA LAVSRVGLLW
VILLHWYSTV LNPTSSNLKV IIFISNAWAV TNHFSIWLAT SLSIFYLLKI VNFSRLIFHH
LKRKAKSVVL VIVLGSLFFL VCHLVMKHTY INVWTEECEG NVTWKIKLRN AMHLSNLTVA
MLANLIPFTL TLISFLLLIY SLCKHLKKMQ LHGKGSQDPS TKIHIKALQT VTSFLILLAI
YFLCLIISFW NSKMRPKEIV LMLCQAFGII YPSFHSFILI WGNKTLKQTF LSVLWQVTCW
AKGQNQSTP*
speed 1.33 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