mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.999997887009913 (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)

chr6:32632647T>CN/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.3514A>G

AA changes

N/A

position(s) of altered AA
if AA alteration in CDS

N/A

frameshift

N/A

known variant

Reference ID: rs1130390

database	homozygous (C/C)	heterozygous	allele carriers
1000G	254	623	877
ExAC	2346	8958	11304

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

	PhyloP	PhastCons
(flanking)	-0.519	0
	-1.182	0
(flanking)	0.095	0

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor marginally increased	3519	wt: 0.9111 / mu: 0.9201 (marginal change - not scored)	wt: ACCCGGGCGGAGTTG mu: GCCCGGGCGGAGTTG	CCGG\|gcgg

distance from splice site

1629

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

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)

3514

chromosomal position
(for ins/del: last normal base / first normal base)

32632647

original gDNA sequence snippet

AGAAGGAAGTCCTGGAGGGGACCCGGGCGGAGTTGGACACG

altered gDNA sequence snippet

AGAAGGAAGTCCTGGAGGGGGCCCGGGCGGAGTTGGACACG

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

0.98 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