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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: ENST00000319340
MT speed 1.51 s - this script 6.653579 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CHST13polymorphism_automatic0.991366273168593simple_aaeA271Vsingle base exchangers1056523show file

Taster files

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documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.00863372683140704 (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) chr3:126261207C>TN/A show variant in all transcripts   IGV
HGNC symbol CHST13
Ensembl transcript ID ENST00000319340
Genbank transcript ID NM_152889
UniProt peptide Q8NET6
alteration type single base exchange
alteration region CDS
DNA changes c.812C>T
cDNA.862C>T
g.18082C>T
AA changes A271V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS
271
frameshift no
known variant Reference ID: rs1056523
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC18881222514113
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)4.91
1.7820.985
(flanking)-0.9670.734
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 632
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      271RYDVVGKFETLAEDAAFVLGLAGA
mutated  not conserved    271RYDVVGKFETLVEDAAFVLGLAG
Ptroglodytes  all identical  ENSPTRG00000015335  270RYDVVGKFETLAEDAAFVLGLAG
Mmulatta  all identical  ENSMMUG00000004201  271RYDIVGKFETLAEDAAFVLGLAG
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000056643  266RYDVVGKFETIADDAAFVLDLVG
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000000576  281HYDVVGKYETLEQDSRYVLQLAG
Drerio  all identical  ENSDARG00000004018  271HYDVVGKYETLAQDSRYILKLAG
Dmelanogaster  not conserved  FBgn0032618  259KYNVVGKYDTLLDDSALALYLAG
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000004792  268HYDVVGKYETLEEDAEYLLQLIG
protein features
start (aa)end (aa)featuredetails 
31341TOPO_DOMLumenal (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1026 / 1026
position (AA) of stopcodon in wt / mu AA sequence 342 / 342
position of stopcodon in wt / mu cDNA 1076 / 1076
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 51 / 51
chromosome 3
strand 1
last intron/exon boundary 231
theoretical NMD boundary in CDS 130
length of CDS 1026
coding sequence (CDS) position 812
cDNA position
(for ins/del: last normal base / first normal base)
862
gDNA position
(for ins/del: last normal base / first normal base)
18082
chromosomal position
(for ins/del: last normal base / first normal base)
126261207
original gDNA sequence snippet GGGCAAGTTCGAGACGCTGGCGGAGGACGCGGCCTTCGTGC
altered gDNA sequence snippet GGGCAAGTTCGAGACGCTGGTGGAGGACGCGGCCTTCGTGC
original cDNA sequence snippet GGGCAAGTTCGAGACGCTGGCGGAGGACGCGGCCTTCGTGC
altered cDNA sequence snippet GGGCAAGTTCGAGACGCTGGTGGAGGACGCGGCCTTCGTGC
wildtype AA sequence MGRRCCRRRV LAAACLGAAL LLLCAAPRSL RPAFGNRALG SSWLGGEKRS PLQKLYDLDQ
DPRSTLAKVH RQRRDLLNSA CSRHSRRQRL LQPEDLRHVL VDDAHGLLYC YVPKVACTNW
KRVLLALSGQ ARGDPRAISA QEAHAPGRLP SLADFSPAEI NRRLRAYLAF LFVREPFERL
ASAYRNKLAR PYSAAFQRRY GARIVQRLRP RALPDARARG HDVRFAEFLA YLLDPRTRRE
EPFNEHWERA HALCHPCRLR YDVVGKFETL AEDAAFVLGL AGASDLSFPG PPRPRGAAAS
RDLAARLFRD ISPFYQRRLF DLYKMDFLLF NYSAPSYLRL L*
mutated AA sequence MGRRCCRRRV LAAACLGAAL LLLCAAPRSL RPAFGNRALG SSWLGGEKRS PLQKLYDLDQ
DPRSTLAKVH RQRRDLLNSA CSRHSRRQRL LQPEDLRHVL VDDAHGLLYC YVPKVACTNW
KRVLLALSGQ ARGDPRAISA QEAHAPGRLP SLADFSPAEI NRRLRAYLAF LFVREPFERL
ASAYRNKLAR PYSAAFQRRY GARIVQRLRP RALPDARARG HDVRFAEFLA YLLDPRTRRE
EPFNEHWERA HALCHPCRLR YDVVGKFETL VEDAAFVLGL AGASDLSFPG PPRPRGAAAS
RDLAARLFRD ISPFYQRRLF DLYKMDFLLF NYSAPSYLRL L*
speed 1.51 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