MutationTaster - study a chromosomal position

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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 0 s - this script 3.198232 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
HLA-DRB1	polymorphism_automatic	8.61977156318972e-13	simple_aae		affected		A100E	single base exchange	rs9269942		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999138 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:32551957G>TN/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.299C>A
cDNA.405C>A
g.5669C>A

AA changes

A100E Score: 107 explain score(s)

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

100

frameshift

known variant

Reference ID: rs9269942

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	1514	10895	12409

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

	PhyloP	PhastCons
(flanking)	0.304	0.049
	-2.842	0
(flanking)	-0.784	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	5666	wt: 0.6475 / mu: 0.6858 (marginal change - not scored)	wt: GGAGCAGGCGCGGGC mu: GGAGCAGGAGCGGGC	AGCA\|ggcg
Donor increased	5661	wt: 0.53 / mu: 0.66	wt: ATCCTGGAGCAGGCG mu: ATCCTGGAGCAGGAG	CCTG\|gagc
Donor gained	5664	0.69	mu: CTGGAGCAGGAGCGG	GGAG\|cagg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

100

mutated

not conserved

100

Ptroglodytes

all identical

ENSPTRG00000018001

100

Mmulatta

not conserved

ENSMMUG00000029799

100

Fcatus

not conserved

ENSFCAG00000001348

Mmusculus

not conserved

ENSMUSG00000060586

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000079105

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
30	124	REGION	Beta-1.	lost
30	227	TOPO_DOM	Extracellular (Potential).	lost
108	108	DISULFID	By similarity.	might get lost (downstream of altered splice site)
125	227	REGION	Beta-2.	might get lost (downstream of altered splice site)
126	216	DOMAIN	Ig-like C1-type.	might get lost (downstream of altered splice site)
146	146	DISULFID	By similarity.	might get lost (downstream of altered splice site)
202	202	DISULFID	By similarity.	might get lost (downstream of altered splice site)
228	250	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
251	266	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
254	254	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) (By similarity).	might get lost (downstream of altered splice site)

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

strand

-1

last intron/exon boundary

894

theoretical NMD boundary in CDS

737

length of CDS

801

coding sequence (CDS) position

299

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

405

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

5669

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

32551957

original gDNA sequence snippet

GAAGGACATCCTGGAGCAGGCGCGGGCCGCGGTGGACACCT

altered gDNA sequence snippet

GAAGGACATCCTGGAGCAGGAGCGGGCCGCGGTGGACACCT

original cDNA sequence snippet

GAAGGACATCCTGGAGCAGGCGCGGGCCGCGGTGGACACCT

altered cDNA sequence snippet

GAAGGACATCCTGGAGCAGGAGCGGGCCGCGGTGGACACCT

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
YNQEESVRFD SDVGEFRAVT ELGRPDAEYW NSQKDILEQE RAAVDTYCRH NYGVVESFTV
QRRVQPKVTV YPSKTQPLQH HNLLVCSVSG FYPGSIEVRW FLNGQEEKAG MVSTGLIQNG
DWTFQTLVML ETVPRSGEVY TCQVEHPSVT SPLTVEWRAR SESAQSKMLS GVGGFVLGLL
FLGAGLFIYF RNQKGHSGLQ PTGFLS*

speed

1.14 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
back to results table

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems