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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: ENST00000360004
MT speed 1.16 s - this script 4.403883 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
HLA-DRB1polymorphism_automatic9.66580149253105e-11simple_aaeY61Hsingle base exchangers1064664show file

Taster files

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documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999903342 (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) chr6:32552075A>GN/A show variant in all transcripts   IGV
HGNC symbol HLA-DRB1
Ensembl transcript ID ENST00000360004
Genbank transcript ID NM_002124
UniProt peptide P13761
alteration type single base exchange
alteration region CDS
DNA changes c.181T>C
cDNA.287T>C
g.5551T>C
AA changes Y61H Score: 83 explain score(s)
position(s) of altered AA
if AA alteration in CDS
61
frameshift no
known variant Reference ID: rs1064664
databasehomozygous (G/G)heterozygousallele carriers
1000G2999521251
ExAC57621953525297
regulatory features H2AZ, Histone, Histone 2A variant Z
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)2.2960.032
-0.1710.009
(flanking)0.2190.007
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 increased5542wt: 0.9450 / mu: 0.9548 (marginal change - not scored)wt: TGGACAGATACTTCT
mu: TGGACAGATACTTCC
 GACA|gata
Donor marginally increased5554wt: 0.2963 / mu: 0.3036 (marginal change - not scored)wt: TCTATAACCAGGAGG
mu: TCCATAACCAGGAGG
 TATA|acca
Donor marginally increased5556wt: 0.8736 / mu: 0.9071 (marginal change - not scored)wt: TATAACCAGGAGGAG
mu: CATAACCAGGAGGAG
 TAAC|cagg
distance from splice site 81
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      61TERVRFLDRYFYNQEESVRFDSDV
mutated  all conserved    61HNQEESVRFDSD
Ptroglodytes  all identical  ENSPTRG00000018001  61YNQEEFMRFDSD
Mmulatta  all conserved  ENSMMUG00000029799  61HNQEEYARFDSD
Fcatus  no alignment  ENSFCAG00000001348  n/a
Mmusculus  all identical  ENSMUSG00000060586  59TQRVRLLERYFYNLEE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000079105  49YLASYSFNKVVDTQFNSS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
30124REGIONBeta-1.lost
30227TOPO_DOMExtracellular (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 801 / 801
position (AA) of stopcodon in wt / mu AA sequence 267 / 267
position of stopcodon in wt / mu cDNA 907 / 907
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 107 / 107
chromosome 6
strand -1
last intron/exon boundary 894
theoretical NMD boundary in CDS 737
length of CDS 801
coding sequence (CDS) position 181
cDNA position
(for ins/del: last normal base / first normal base)
287
gDNA position
(for ins/del: last normal base / first normal base)
5551
chromosomal position
(for ins/del: last normal base / first normal base)
32552075
original gDNA sequence snippet GGTTCCTGGACAGATACTTCTATAACCAGGAGGAGTCCGTG
altered gDNA sequence snippet GGTTCCTGGACAGATACTTCCATAACCAGGAGGAGTCCGTG
original cDNA sequence snippet GGTTCCTGGACAGATACTTCTATAACCAGGAGGAGTCCGTG
altered cDNA sequence snippet GGTTCCTGGACAGATACTTCCATAACCAGGAGGAGTCCGTG
wildtype AA sequence MVCLKLPGGS CMTALTVTLM VLSSPLALSG DTRPRFLWQP KRECHFFNGT ERVRFLDRYF
YNQEESVRFD SDVGEFRAVT ELGRPDAEYW NSQKDILEQA RAAVDTYCRH NYGVVESFTV
QRRVQPKVTV YPSKTQPLQH HNLLVCSVSG FYPGSIEVRW FLNGQEEKAG MVSTGLIQNG
DWTFQTLVML ETVPRSGEVY TCQVEHPSVT SPLTVEWRAR SESAQSKMLS GVGGFVLGLL
FLGAGLFIYF RNQKGHSGLQ PTGFLS*
mutated AA sequence MVCLKLPGGS CMTALTVTLM VLSSPLALSG DTRPRFLWQP KRECHFFNGT ERVRFLDRYF
HNQEESVRFD SDVGEFRAVT ELGRPDAEYW NSQKDILEQA RAAVDTYCRH NYGVVESFTV
QRRVQPKVTV YPSKTQPLQH HNLLVCSVSG FYPGSIEVRW FLNGQEEKAG MVSTGLIQNG
DWTFQTLVML ETVPRSGEVY TCQVEHPSVT SPLTVEWRAR SESAQSKMLS GVGGFVLGLL
FLGAGLFIYF RNQKGHSGLQ PTGFLS*
speed 1.16 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