Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 5.96986418915874e-05 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:32632820C>GN/A show variant in all transcripts   IGV
HGNC symbol HLA-DQB1
Ensembl transcript ID ENST00000399082
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.3341G>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs1130375
databasehomozygous (G/G)heterozygousallele carriers
1000G2597821041
ExAC42801624220522
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)0.1340.125
0.8430.614
(flanking)1.5990.793
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased3338wt: 0.7836 / mu: 0.8457 (marginal change - not scored)wt: GGATTTCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCA
mu: GGATTTCGTGTTCCAGTTTAAGGCCATGTGCTACTTCACCA		 ttaa|GGGC
Acc marginally increased3332wt: 0.6695 / mu: 0.6722 (marginal change - not scored)wt: CGCAGAGGATTTCGTGTTCCAGTTTAAGGGCATGTGCTACT
mu: CGCAGAGGATTTCGTGTTCCAGTTTAAGGCCATGTGCTACT		 tcca|GTTT
Donor marginally increased3339wt: 0.9965 / mu: 0.9973 (marginal change - not scored)wt: TTTAAGGGCATGTGC
mu: TTTAAGGCCATGTGC		 TAAG|ggca
Donor marginally increased3333wt: 0.9605 / mu: 0.9611 (marginal change - not scored)wt: TTCCAGTTTAAGGGC
mu: TTCCAGTTTAAGGCC		 CCAG|ttta
distance from splice site 1456
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features N/A
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 46 / 46
chromosome 6
strand -1
last intron/exon boundary 437
theoretical NMD boundary in CDS 341
length of CDS 405
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 3341
chromosomal position
(for ins/del: last normal base / first normal base)		 32632820
original gDNA sequence snippet TTTCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCAACG
altered gDNA sequence snippet TTTCGTGTTCCAGTTTAAGGCCATGTGCTACTTCACCAACG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MSWKKALRIP GDLRVATVTL MLAMLSSLLA EGRDSPVEPT VTISPSRTEA LNHHNLLVCS
VTDFYPGQIK VRWFRNDQEE TAGVVSTPLI RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP
SLQSPITVEW RLLH*
mutated AA sequence N/A
speed 0.44 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