Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999873 (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) chr6:32634306A>TN/A show variant in all transcripts   IGV
HGNC symbol HLA-DQB1
Ensembl transcript ID ENST00000374943
Genbank transcript ID NM_001243961
UniProt peptide P01920
alteration type single base exchange
alteration region CDS
DNA changes c.79T>A
cDNA.156T>A
g.1855T>A
AA changes S27T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 27
frameshift no
known variant Reference ID: rs1049060
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC14753326118014
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2AZ, Histone, Histone 2A variant Z
H2BK20ac, Histone, Histone 2B Lysine 20 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
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
POU2F2, Transcription Factor, POU2F2 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2240
-2.3230
(flanking)0.2570.087
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 increased1847wt: 0.8957 / mu: 0.9543 (marginal change - not scored)wt: GGCGATGCTGAGCTC
mu: GGCGATGCTGAGCAC		 CGAT|gctg
distance from splice site 31
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      27ATVTLMLAMLSSLLAEGRDSPEDF
mutated  all conserved    27ATVTLMLAMLSTLLAEGRDSPED
Ptroglodytes  all conserved  ENSPTRG00000018018  27ATVTLVLAMLSTPVAEGRDSPED
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000073421  23AAVVVLM-VLSSPGTEGGDSERH
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000079105  15LVILMLSTFTGTA-DGYYD
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
132SIGNALlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 810 / 810
position (AA) of stopcodon in wt / mu AA sequence 270 / 270
position of stopcodon in wt / mu cDNA 887 / 887
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 78 / 78
chromosome 6
strand -1
last intron/exon boundary 874
theoretical NMD boundary in CDS 746
length of CDS 810
coding sequence (CDS) position 79
cDNA position
(for ins/del: last normal base / first normal base)		 156
gDNA position
(for ins/del: last normal base / first normal base)		 1855
chromosomal position
(for ins/del: last normal base / first normal base)		 32634306
original gDNA sequence snippet TGATGCTGGCGATGCTGAGCTCCCTACTGGCTGAGGGCAGA
altered gDNA sequence snippet TGATGCTGGCGATGCTGAGCACCCTACTGGCTGAGGGCAGA
original cDNA sequence snippet TGATGCTGGCGATGCTGAGCTCCCTACTGGCTGAGGGCAGA
altered cDNA sequence snippet TGATGCTGGCGATGCTGAGCACCCTACTGGCTGAGGGCAGA
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 IRQRSQKGPQ GPPPAGLLH*
mutated AA sequence MSWKKALRIP GDLRVATVTL MLAMLSTLLA EGRDSPEDFV FQFKGMCYFT NGTERVRLVT
RYIYNREEYA RFDSDVGVYR AVTPQGRPDA EYWNSQKEVL EGTRAELDTV CRHNYEVAFR
GILQRRVEPT VTISPSRTEA LNHHNLLVCS VTDFYPGQIK VRWFRNDQEE TAGVVSTPLI
RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RAQSESAQSK MLSGVGGFVL
GLIFLGLGLI IRQRSQKGPQ GPPPAGLLH*
speed 1.02 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