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: ENST00000412585
MT speed 0 s - this script 3.190419 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
HLA-B	polymorphism_automatic	7.69051489157846e-13	simple_aae				A95T	single base exchange	rs1131213		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999231 (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)

chr6:31324525C>TN/A show variant in all transcripts IGV

HGNC symbol

HLA-B

Ensembl transcript ID

ENST00000412585

Genbank transcript ID

NM_005514

UniProt peptide

P30481

alteration type

single base exchange

alteration region

CDS

DNA changes

c.283G>A
cDNA.312G>A
g.441G>A

AA changes

A95T Score: 58 explain score(s)

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

frameshift

known variant

Reference ID: rs1131213

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1404	790	2194
ExAC	2	3	5

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2AK9ac, Histone, Histone 2A Lysine 9 Acetylation
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 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
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.154	0
	-0.052	0
(flanking)	-1.153	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	439	wt: 0.9145 / mu: 0.9627 (marginal change - not scored)	wt: GGCCCAGGCACAGAC mu: GGCCCAGACACAGAC	CCCA\|ggca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000038986

Mmulatta

not conserved

ENSMMUG00000029841

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
25	114	REGION	Alpha-1.	lost
25	309	TOPO_DOM	Extracellular (Potential).	lost
81	108	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1089 / 1089

position (AA) of stopcodon in wt / mu AA sequence

363 / 363

position of stopcodon in wt / mu cDNA

1118 / 1118

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

30 / 30

chromosome

strand

-1

last intron/exon boundary

1123

theoretical NMD boundary in CDS

1043

length of CDS

1089

coding sequence (CDS) position

283

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

312

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

441

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

31324525

original gDNA sequence snippet

CACAGATCTACAAGGCCCAGGCACAGACTGACCGAGAGAGC

altered gDNA sequence snippet

CACAGATCTACAAGGCCCAGACACAGACTGACCGAGAGAGC

original cDNA sequence snippet

CACAGATCTACAAGGCCCAGGCACAGACTGACCGAGAGAGC

altered cDNA sequence snippet

CACAGATCTACAAGGCCCAGACACAGACTGACCGAGAGAGC

wildtype AA sequence

MLVMAPRTVL LLLSAALALT ETWAGSHSMR YFYTSVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPREE PRAPWIEQEG PEYWDRNTQI YKAQAQTDRE SLRNLRGYYN QSEAGSHTLQ
SMYGCDVGPD GRLLRGHDQY AYDGKDYIAL NEDLRSWTAA DTAAQITQRK WEAAREAEQR
RAYLEGECVE WLRRYLENGK DKLERADPPK THVTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDRTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEP
SSQSTVPIVG IVAGLAVLAV VVIGAVVAAV MCRRKSSGGK GGSYSQAACS DSAQGSDVSL
TA*

mutated AA sequence

MLVMAPRTVL LLLSAALALT ETWAGSHSMR YFYTSVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPREE PRAPWIEQEG PEYWDRNTQI YKAQTQTDRE SLRNLRGYYN QSEAGSHTLQ
SMYGCDVGPD GRLLRGHDQY AYDGKDYIAL NEDLRSWTAA DTAAQITQRK WEAAREAEQR
RAYLEGECVE WLRRYLENGK DKLERADPPK THVTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDRTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEP
SSQSTVPIVG IVAGLAVLAV VVIGAVVAAV MCRRKSSGGK GGSYSQAACS DSAQGSDVSL
TA*

speed

1.18 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