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: ENST00000075503
MT speed 0 s - this script 2.881817 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
STYK1	polymorphism_automatic	0.00103780005751497	simple_aae				S204G	single base exchange	rs3759259		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.998962199942485 (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)

chr12:10782115T>CN/A show variant in all transcripts IGV

HGNC symbol

STYK1

Ensembl transcript ID

ENST00000075503

Genbank transcript ID

NM_018423

UniProt peptide

Q6J9G0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.610A>G
cDNA.1131A>G
g.44803A>G

AA changes

S204G Score: 56 explain score(s)

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

204

frameshift

known variant

Reference ID: rs3759259

database	homozygous (C/C)	heterozygous	allele carriers
1000G	982	1034	2016
ExAC	24145	-15523	8622

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.094	0.994
	1.686	1
(flanking)	1.185	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	44813	wt: 0.8645 / mu: 0.8831 (marginal change - not scored)	wt: GGACCTGCTCAGCTTTCTCTGGACCTGTCGGCGGGTGAGCA mu: GGACCTGCTCGGCTTTCTCTGGACCTGTCGGCGGGTGAGCA	tctg\|GACC
Acc marginally increased	44814	wt: 0.8603 / mu: 0.8908 (marginal change - not scored)	wt: GACCTGCTCAGCTTTCTCTGGACCTGTCGGCGGGTGAGCAG mu: GACCTGCTCGGCTTTCTCTGGACCTGTCGGCGGGTGAGCAG	ctgg\|ACCT
Acc marginally increased	44812	wt: 0.8451 / mu: 0.9025 (marginal change - not scored)	wt: GGGACCTGCTCAGCTTTCTCTGGACCTGTCGGCGGGTGAGC mu: GGGACCTGCTCGGCTTTCTCTGGACCTGTCGGCGGGTGAGC	ctct\|GGAC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

204

mutated

not conserved

204

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000015484

204

Fcatus

all identical

ENSFCAG00000008388

205

Mmusculus

all identical

ENSMUSG00000032899

209

Ggallus

not conserved

ENSGALG00000014759

212

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000070950

219

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000016240

214

protein features

start (aa)	end (aa)	feature	details
114	384	DOMAIN	Protein kinase.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1269 / 1269

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

423 / 423

position of stopcodon in wt / mu cDNA

1790 / 1790

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

522 / 522

chromosome

strand

-1

last intron/exon boundary

1586

theoretical NMD boundary in CDS

1014

length of CDS

1269

coding sequence (CDS) position

610

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

1131

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

44803

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

10782115

original gDNA sequence snippet

TGGCCCAGGGGGACCTGCTCAGCTTTCTCTGGACCTGTCGG

altered gDNA sequence snippet

TGGCCCAGGGGGACCTGCTCGGCTTTCTCTGGACCTGTCGG

original cDNA sequence snippet

TGGCCCAGGGGGACCTGCTCAGCTTTCTCTGGACCTGTCGG

altered cDNA sequence snippet

TGGCCCAGGGGGACCTGCTCGGCTTTCTCTGGACCTGTCGG

wildtype AA sequence

MGMTRMLLEC SLSDKLCVIQ EKQYEVIIVP TLLVTIFLIL LGVILWLFIR EQRTQQQRSG
PQGIAPVPPP RDLSWEAGHG GNVALPLKET SVENFLGATT PALAKLQVPR EQLSEVLEQI
CSGSCGPIFR ANMNTGDPSK PKSVILKALK EPAGLHEVQD FLGRIQFHQY LGKHKNLVQL
EGCCTEKLPL YMVLEDVAQG DLLSFLWTCR RDVMTMDGLL YDLTEKQVYH IGKQVLLALE
FLQEKHLFHG DVAARNILMQ SDLTAKLCGL GLAYEVYTRG AISSTQTIPL KWLAPERLLL
RPASIRADVW SFGILLYEMV TLGAPPYPEV PPTSILEHLQ RRKIMKRPSS CTHTMYSIMK
SCWRWREADR PSPRELRLRL EAAIKTADDE AVLQVPELVV PELYAAVAGI RVESLFYNYS
ML*

mutated AA sequence

MGMTRMLLEC SLSDKLCVIQ EKQYEVIIVP TLLVTIFLIL LGVILWLFIR EQRTQQQRSG
PQGIAPVPPP RDLSWEAGHG GNVALPLKET SVENFLGATT PALAKLQVPR EQLSEVLEQI
CSGSCGPIFR ANMNTGDPSK PKSVILKALK EPAGLHEVQD FLGRIQFHQY LGKHKNLVQL
EGCCTEKLPL YMVLEDVAQG DLLGFLWTCR RDVMTMDGLL YDLTEKQVYH IGKQVLLALE
FLQEKHLFHG DVAARNILMQ SDLTAKLCGL GLAYEVYTRG AISSTQTIPL KWLAPERLLL
RPASIRADVW SFGILLYEMV TLGAPPYPEV PPTSILEHLQ RRKIMKRPSS CTHTMYSIMK
SCWRWREADR PSPRELRLRL EAAIKTADDE AVLQVPELVV PELYAAVAGI RVESLFYNYS
ML*

speed

0.87 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