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: ENST00000330794
MT speed 0 s - this script 2.815235 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
STING1	polymorphism_automatic	0.999995470217916	simple_aae		affected		R293Q	single base exchange	rs7380824		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 4.52978208419833e-06 (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 CM114287)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:138856982C>TN/A show variant in all transcripts IGV

HGNC symbol

STING1

Ensembl transcript ID

ENST00000330794

Genbank transcript ID

NM_198282

UniProt peptide

Q86WV6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.878G>A
cDNA.1212G>A
g.5539G>A

AA changes

R293Q Score: 43 explain score(s)

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

293

frameshift

known variant

Reference ID: rs7380824

database	homozygous (T/T)	heterozygous	allele carriers
1000G	210	957	1167
ExAC	3140	18541	21681

known disease mutation at this position, please check HGMD for details (HGMD ID CM114287)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.73	1
	4.171	1
(flanking)	2.266	1

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
Acc marginally increased	5540	wt: 0.2248 / mu: 0.2402 (marginal change - not scored)	wt: CAGGCCAAACTCTTCTGCCGGACACTTGAGGACATCCTGGC mu: CAGGCCAAACTCTTCTGCCAGACACTTGAGGACATCCTGGC	ccgg\|ACAC
Acc increased	5539	wt: 0.59 / mu: 0.66	wt: GCAGGCCAAACTCTTCTGCCGGACACTTGAGGACATCCTGG mu: GCAGGCCAAACTCTTCTGCCAGACACTTGAGGACATCCTGG	gccg\|GACA
Donor increased	5539	wt: 0.33 / mu: 0.86	wt: CTGCCGGACACTTGA mu: CTGCCAGACACTTGA	GCCG\|gaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

293

mutated

all conserved

293

Ptroglodytes

all identical

ENSPTRG00000017301

293

Mmulatta

all identical

ENSMMUG00000012048

293

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000024349

292

Ggallus

all identical

ENSGALG00000000852

298

Trubripes

no homologue

Drerio

all identical

ENSDARG00000091058

284

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000016088

275

protein features

start (aa)	end (aa)	feature	details
174	379	TOPO_DOM	Cytoplasmic (Potential).	lost
281	301	HELIX		lost
303	306	HELIX		might get lost (downstream of altered splice site)
309	314	STRAND		might get lost (downstream of altered splice site)
318	320	STRAND		might get lost (downstream of altered splice site)
324	326	MUTAGEN	SLS->ALA: Induces a decrease in phosphorylation by TBK1.	might get lost (downstream of altered splice site)
325	333	HELIX		might get lost (downstream of altered splice site)
334	336	TURN		might get lost (downstream of altered splice site)
358	358	MOD_RES	Phosphoserine; by TBK1.	might get lost (downstream of altered splice site)
358	358	MUTAGEN	S->A: Induces a decrease in phosphorylation by TBK1 and ability to activate IRF-E.	might get lost (downstream of altered splice site)
363	363	CONFLICT	L -> F (in Ref. 2; BAF83350).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1140 / 1140

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

380 / 380

position of stopcodon in wt / mu cDNA

1474 / 1474

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

335 / 335

chromosome

strand

-1

last intron/exon boundary

1281

theoretical NMD boundary in CDS

896

length of CDS

1140

coding sequence (CDS) position

878

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

1212

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

5539

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

138856982

original gDNA sequence snippet

GCAGGCCAAACTCTTCTGCCGGACACTTGAGGACATCCTGG

altered gDNA sequence snippet

GCAGGCCAAACTCTTCTGCCAGACACTTGAGGACATCCTGG

original cDNA sequence snippet

GCAGGCCAAACTCTTCTGCCGGACACTTGAGGACATCCTGG

altered cDNA sequence snippet

GCAGGCCAAACTCTTCTGCCAGACACTTGAGGACATCCTGG

wildtype AA sequence

MPHSSLHPSI PCPRGHGAQK AALVLLSACL VTLWGLGEPP EHTLRYLVLH LASLQLGLLL
NGVCSLAEEL RHIHSRYRGS YWRTVRACLG CPLRRGALLL LSIYFYYSLP NAVGPPFTWM
LALLGLSQAL NILLGLKGLA PAEISAVCEK GNFNVAHGLA WSYYIGYLRL ILPELQARIR
TYNQHYNNLL RGAVSQRLYI LLPLDCGVPD NLSMADPNIR FLDKLPQQTG DHAGIKDRVY
SNSIYELLEN GQRAGTCVLE YATPLQTLFA MSQYSQAGFS REDRLEQAKL FCRTLEDILA
DAPESQNNCR LIAYQEPADD SSFSLSQEVL RHLRQEEKEE VTVGSLKTSA VPSTSTMSQE
PELLISGMEK PLPLRTDFS*

mutated AA sequence

MPHSSLHPSI PCPRGHGAQK AALVLLSACL VTLWGLGEPP EHTLRYLVLH LASLQLGLLL
NGVCSLAEEL RHIHSRYRGS YWRTVRACLG CPLRRGALLL LSIYFYYSLP NAVGPPFTWM
LALLGLSQAL NILLGLKGLA PAEISAVCEK GNFNVAHGLA WSYYIGYLRL ILPELQARIR
TYNQHYNNLL RGAVSQRLYI LLPLDCGVPD NLSMADPNIR FLDKLPQQTG DHAGIKDRVY
SNSIYELLEN GQRAGTCVLE YATPLQTLFA MSQYSQAGFS REDRLEQAKL FCQTLEDILA
DAPESQNNCR LIAYQEPADD SSFSLSQEVL RHLRQEEKEE VTVGSLKTSA VPSTSTMSQE
PELLISGMEK PLPLRTDFS*

speed

0.75 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