Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999997916935 (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
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analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:32632608C>GN/A show variant in all transcripts   IGV
HGNC symbol HLA-DQB1
Ensembl transcript ID ENST00000434651
Genbank transcript ID NM_002123
UniProt peptide P01920
alteration type single base exchange
alteration region CDS
DNA changes c.346G>C
cDNA.433G>C
g.3553G>C
AA changes E116Q Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 116
frameshift no
known variant Reference ID: rs1140316
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC304629295975
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0980.001
-2.0540.001
(flanking)0.4140.43
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 increased3555wt: 0.9778 / mu: 0.9779 (marginal change - not scored)wt: TACGAGGTGGCGTTC
mu: TACCAGGTGGCGTTC		 CGAG|gtgg
distance from splice site 34
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      116AELDTVCRHNYEVAFRGILQRRVE
mutated  all conserved    116AELDTVCRHNYQVAFR
Ptroglodytes  all conserved  ENSPTRG00000018018  116AELDTVCRHNYQLELR
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000073421  111AELDTVCRHNYEGPETHTSLR
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000079105  101AQVDTFCRHNAQIWDSAVRDKAV
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
33126REGIONBeta-1.lost
33230TOPO_DOMExtracellular (Potential).lost
111119HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 786 / 786
position (AA) of stopcodon in wt / mu AA sequence 262 / 262
position of stopcodon in wt / mu cDNA 873 / 873
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 88 / 88
chromosome 6
strand -1
last intron/exon boundary 860
theoretical NMD boundary in CDS 722
length of CDS 786
coding sequence (CDS) position 346
cDNA position
(for ins/del: last normal base / first normal base)		 433
gDNA position
(for ins/del: last normal base / first normal base)		 3553
chromosomal position
(for ins/del: last normal base / first normal base)		 32632608
original gDNA sequence snippet CGGTGTGCAGACACAACTACGAGGTGGCGTTCCGCGGGATC
altered gDNA sequence snippet CGGTGTGCAGACACAACTACCAGGTGGCGTTCCGCGGGATC
original cDNA sequence snippet CGGTGTGCAGACACAACTACGAGGTGGCGTTCCGCGGGATC
altered cDNA sequence snippet CGGTGTGCAGACACAACTACCAGGTGGCGTTCCGCGGGATC
wildtype AA sequence MSWKKALRIP GDLRVATVTL MLAMLSSLLA EGRDSPEDFV FQFKGMCYFT NGTERVRLVT
RYIYNREEYA RFDSDVGVYR AVTPQGRPDA EYWNSQKEVL EGTRAELDTV CRHNYEVAFR
GILQRRVEPT VTISPSRTEA LNHHNLLVCS VTDFYPGQIK VRWFRNDQEE TAGVVSTPLI
RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RAQSESAQSK MLSGVGGFVL
GLIFLGLGLI IRQRSQKGLL H*
mutated AA sequence MSWKKALRIP GDLRVATVTL MLAMLSSLLA EGRDSPEDFV FQFKGMCYFT NGTERVRLVT
RYIYNREEYA RFDSDVGVYR AVTPQGRPDA EYWNSQKEVL EGTRAELDTV CRHNYQVAFR
GILQRRVEPT VTISPSRTEA LNHHNLLVCS VTDFYPGQIK VRWFRNDQEE TAGVVSTPLI
RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RAQSESAQSK MLSGVGGFVL
GLIFLGLGLI IRQRSQKGLL H*
speed 1.11 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