MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000376630
MT speed 0 s - this script 2.900275 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
HLA-E	polymorphism_automatic	0.011349315326213	simple_aae		affected		G128R	single base exchange	rs1264457		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.988650684673787 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM076230)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:30458064G>AN/A show variant in all transcripts IGV

HGNC symbol

HLA-E

Ensembl transcript ID

ENST00000376630

Genbank transcript ID

NM_005516

UniProt peptide

P13747

alteration type

single base exchange

alteration region

CDS

DNA changes

c.382G>A
cDNA.447G>A
g.821G>A

AA changes

G128R Score: 125 explain score(s)

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

128

frameshift

known variant

Reference ID: rs1264457

database	homozygous (A/A)	heterozygous	allele carriers
1000G	674	1228	1902
ExAC	17148	-1529	15619

known disease mutation at this position, please check HGMD for details (HGMD ID CM076230)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-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
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.239	0.848
	0.269	0.883
(flanking)	1.239	0.918

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 increased	817	wt: 0.20 / mu: 0.97	wt: GGGCCCGACGGGCGC mu: GGGCCCGACAGGCGC	GCCC\|gacg
Donor gained	821	0.75	mu: CCGACAGGCGCTTCC	GACA\|ggcg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

128

mutated

not conserved

128

Ptroglodytes

all identical

ENSPTRG00000017912

128

Mmulatta

no homologue

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
22	305	TOPO_DOM	Extracellular (Potential).	lost
112	203	REGION	Alpha-2.	lost
128	139	STRAND		lost
142	147	STRAND		might get lost (downstream of altered splice site)
151	158	STRAND		might get lost (downstream of altered splice site)
159	161	HELIX		might get lost (downstream of altered splice site)
162	170	HELIX		might get lost (downstream of altered splice site)
171	173	TURN		might get lost (downstream of altered splice site)
174	182	HELIX		might get lost (downstream of altered splice site)
184	195	HELIX		might get lost (downstream of altered splice site)
185	185	DISULFID		might get lost (downstream of altered splice site)
197	200	HELIX		might get lost (downstream of altered splice site)
204	295	REGION	Alpha-3.	might get lost (downstream of altered splice site)
206	294	DOMAIN	Ig-like C1-type.	might get lost (downstream of altered splice site)
207	214	STRAND		might get lost (downstream of altered splice site)
216	232	STRAND		might get lost (downstream of altered splice site)
224	224	DISULFID		might get lost (downstream of altered splice site)
235	239	STRAND		might get lost (downstream of altered splice site)
241	243	TURN		might get lost (downstream of altered splice site)
249	251	STRAND		might get lost (downstream of altered splice site)
258	260	STRAND		might get lost (downstream of altered splice site)
262	271	STRAND		might get lost (downstream of altered splice site)
275	277	HELIX		might get lost (downstream of altered splice site)
279	283	STRAND		might get lost (downstream of altered splice site)
280	280	DISULFID		might get lost (downstream of altered splice site)
287	289	STRAND		might get lost (downstream of altered splice site)
291	293	STRAND		might get lost (downstream of altered splice site)
296	305	REGION	Connecting peptide.	might get lost (downstream of altered splice site)
306	329	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
330	358	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1077 / 1077

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

359 / 359

position of stopcodon in wt / mu cDNA

1142 / 1142

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

66 / 66

chromosome

strand

last intron/exon boundary

1145

theoretical NMD boundary in CDS

1029

length of CDS

1077

coding sequence (CDS) position

382

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

447

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

821

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

30458064

original gDNA sequence snippet

GCTGCGAGCTGGGGCCCGACGGGCGCTTCCTCCGCGGGTAT

altered gDNA sequence snippet

GCTGCGAGCTGGGGCCCGACAGGCGCTTCCTCCGCGGGTAT

original cDNA sequence snippet

GCTGCGAGCTGGGGCCCGACGGGCGCTTCCTCCGCGGGTAT

altered cDNA sequence snippet

GCTGCGAGCTGGGGCCCGACAGGCGCTTCCTCCGCGGGTAT

wildtype AA sequence

MVDGTLLLLL SEALALTQTW AGSHSLKYFH TSVSRPGRGE PRFISVGYVD DTQFVRFDND
AASPRMVPRA PWMEQEGSEY WDRETRSARD TAQIFRVNLR TLRGYYNQSE AGSHTLQWMH
GCELGPDGRF LRGYEQFAYD GKDYLTLNED LRSWTAVDTA AQISEQKSND ASEAEHQRAY
LEDTCVEWLH KYLEKGKETL LHLEPPKTHV THHPISDHEA TLRCWALGFY PAEITLTWQQ
DGEGHTQDTE LVETRPAGDG TFQKWAAVVV PSGEEQRYTC HVQHEGLPEP VTLRWKPASQ
PTIPIVGIIA GLVLLGSVVS GAVVAAVIWR KKSSGGKGGS YSKAEWSDSA QGSESHSL*

mutated AA sequence

MVDGTLLLLL SEALALTQTW AGSHSLKYFH TSVSRPGRGE PRFISVGYVD DTQFVRFDND
AASPRMVPRA PWMEQEGSEY WDRETRSARD TAQIFRVNLR TLRGYYNQSE AGSHTLQWMH
GCELGPDRRF LRGYEQFAYD GKDYLTLNED LRSWTAVDTA AQISEQKSND ASEAEHQRAY
LEDTCVEWLH KYLEKGKETL LHLEPPKTHV THHPISDHEA TLRCWALGFY PAEITLTWQQ
DGEGHTQDTE LVETRPAGDG TFQKWAAVVV PSGEEQRYTC HVQHEGLPEP VTLRWKPASQ
PTIPIVGIIA GLVLLGSVVS GAVVAAVIWR KKSSGGKGGS YSKAEWSDSA QGSESHSL*

speed

0.84 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