mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999432 (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)

chr6:31324100G>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.463C>A
cDNA.492C>A
g.866C>A

AA changes

R155S Score: 110 explain score(s)

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

155

frameshift

known variant

Reference ID: rs1050654

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	1033	30701	31734

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
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
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)	-0.531	0
	-0.762	0
(flanking)	0.061	0.003

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 gained	861	0.31	mu: CGAGGACCTGAGCTC	AGGA\|cctg

distance from splice site

120

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

155

mutated

not conserved

155

Ptroglodytes

not conserved

ENSPTRG00000038986

155

Mmulatta

all identical

ENSMMUG00000029841

150

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	309	TOPO_DOM	Extracellular (Potential).	lost
115	206	REGION	Alpha-2.	lost
157	161	STRAND		might get lost (downstream of altered splice site)
162	173	HELIX		might get lost (downstream of altered splice site)
176	185	HELIX		might get lost (downstream of altered splice site)
187	198	HELIX		might get lost (downstream of altered splice site)
188	188	DISULFID		might get lost (downstream of altered splice site)
200	203	HELIX		might get lost (downstream of altered splice site)
207	298	REGION	Alpha-3.	might get lost (downstream of altered splice site)
209	295	DOMAIN	Ig-like C1-type.	might get lost (downstream of altered splice site)
210	219	STRAND		might get lost (downstream of altered splice site)
222	235	STRAND		might get lost (downstream of altered splice site)
223	223	CONFLICT	V -> A (in Ref. 12; AAA59619).	might get lost (downstream of altered splice site)
227	227	DISULFID		might get lost (downstream of altered splice site)
229	229	CONFLICT	A -> S (in Ref. 12; AAA59619).	might get lost (downstream of altered splice site)
238	243	STRAND		might get lost (downstream of altered splice site)
249	251	HELIX		might get lost (downstream of altered splice site)
252	254	STRAND		might get lost (downstream of altered splice site)
261	263	STRAND		might get lost (downstream of altered splice site)
265	274	STRAND		might get lost (downstream of altered splice site)
278	280	HELIX		might get lost (downstream of altered splice site)
281	286	STRAND		might get lost (downstream of altered splice site)
283	283	DISULFID		might get lost (downstream of altered splice site)
290	292	STRAND		might get lost (downstream of altered splice site)
294	296	STRAND		might get lost (downstream of altered splice site)
299	309	REGION	Connecting peptide.	might get lost (downstream of altered splice site)
310	333	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
334	362	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

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

463

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

492

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

866

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

31324100

original gDNA sequence snippet

TCGCCCTGAACGAGGACCTGCGCTCCTGGACCGCCGCGGAC

altered gDNA sequence snippet

TCGCCCTGAACGAGGACCTGAGCTCCTGGACCGCCGCGGAC

original cDNA sequence snippet

TCGCCCTGAACGAGGACCTGCGCTCCTGGACCGCCGCGGAC

altered cDNA sequence snippet

TCGCCCTGAACGAGGACCTGAGCTCCTGGACCGCCGCGGAC

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 YKAQAQTDRE SLRNLRGYYN QSEAGSHTLQ
SMYGCDVGPD GRLLRGHDQY AYDGKDYIAL NEDLSSWTAA DTAAQITQRK WEAAREAEQR
RAYLEGECVE WLRRYLENGK DKLERADPPK THVTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDRTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEP
SSQSTVPIVG IVAGLAVLAV VVIGAVVAAV MCRRKSSGGK GGSYSQAACS DSAQGSDVSL
TA*

speed

1.02 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