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: ENST00000408903
MT speed 0 s - this script 2.844289 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MCC	polymorphism_automatic	1.11211759801222e-08	simple_aae		affected		S25G	single base exchange	rs348942		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999988878824 (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)

chr5:112824039T>CN/A show variant in all transcripts IGV

HGNC symbol

MCC

Ensembl transcript ID

ENST00000408903

Genbank transcript ID

NM_001085377

UniProt peptide

P23508

alteration type

single base exchange

alteration region

CDS

DNA changes

c.73A>G
cDNA.489A>G
g.489A>G

AA changes

S25G Score: 56 explain score(s)

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

frameshift

known variant

Reference ID: rs348942

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1437	912	2349
ExAC	15112	2543	17655

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2AZ, Histone, Histone 2A variant Z
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 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
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.444	0.679
	-0.15	0.679
(flanking)	0.188	0.695

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	483	0.41	mu: GCAGCGGCAGCGGCA	AGCG\|gcag

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

not conserved

ENSPTRG00000017140

Mmulatta

not conserved

ENSMMUG00000013557

Fcatus

not conserved

ENSFCAG00000001896

Mmusculus

not conserved

ENSMUSG00000071856

Ggallus

no alignment

ENSGALG00000000208

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000087450

n/a

Dmelanogaster

no alignment

FBgn0085433

n/a

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000021515

n/a

protein features

start (aa)	end (aa)	feature	details
294	294	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
353	353	CONFLICT	S -> G (in Ref. 5; BAC87521).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3060 / 3060

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

1020 / 1020

position of stopcodon in wt / mu cDNA

3476 / 3476

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

417 / 417

chromosome

strand

-1

last intron/exon boundary

3296

theoretical NMD boundary in CDS

2829

length of CDS

3060

coding sequence (CDS) position

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

489

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

489

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

112824039

original gDNA sequence snippet

GCGGCGGCGGCAGCGGCAGCAGCAGCAGCAGCAGCGACACG

altered gDNA sequence snippet

GCGGCGGCGGCAGCGGCAGCGGCAGCAGCAGCAGCGACACG

original cDNA sequence snippet

GCGGCGGCGGCAGCGGCAGCAGCAGCAGCAGCAGCGACACG

altered cDNA sequence snippet

GCGGCGGCGGCAGCGGCAGCGGCAGCAGCAGCAGCGACACG

wildtype AA sequence

MMAAAAAAAA GSSSSGGGGG GSGSSSSSSD TSSTGEEERM RRLFQTCDGD GDGYISRNDL
LMVCRQLNME ESVAEIMNQL GADENGKISF QDFTRCRMQL VREIRKEEVD LSAKSDNSCT
KKLRDRIASW PTSSDNSLGA LSAARESWEY DSGARDLQSP DVQSQSALQK LLEYGGSSLH
QQAALHKLLT QSPHIGNSVG GSYLELANTL HSAALASLKG DIVELNKRLQ QTERERDLLE
KKLAKAQCEQ SHLMREHEDV QERTTLRYEE RITELHSVIA ELNKKIDRLQ GTTIREEDEY
SELRSELSQS QHEVNEDSRS MDQDQTSVSI PENQSTMVTA DMDNCSDLNS ELQRVLTGLE
NVVCGRKKSS CSLSVAEVDK HIEQLTTASE HCDLAIKTVE EIEGVLGRDL YPNLAEERSR
WEKELAGLRE ENESLTAMLC SKEEELNRTK ATMNAIREER DRLRRRVREL QTRLQSVQAT
GPSSPGRLTS TNRPINPSTG ELSTSSSSND IPIAKIAERV KLSKTRSESS SSDRPVLGSE
ISSIGVSSSV AEHLAHSLQD CSNIQEIFQT LYSHGSAISE SKIREFEVET ERLNSRIEHL
KSQNDLLTIT LEECKSNAER MSMLVGKYES NATALRLALQ YSEQCIEAYE LLLALAESEQ
SLILGQFRAA GVGSSPGDQS GDENITQMLK RAHDCRKTAE NAAKALLMKL DGSCGGAFAV
AGCSVQPWES LSSNSHTSTT SSTASSCDTE FTKEDEQRLK DYIQQLKNDR AAVKLTMLEL
ESIHIDPLSY DVKPRGDSQR LDLENAVLMQ ELMAMKEEMA ELKAQLYLLE KEKKALELKL
STREAQEQAY LVHIEHLKSE VEEQKEQRMR SLSSTSSGSK DKPGKECADA ASPALSLAEL
RTTCSENELA AEFTNAIRRE KKLKARVQEL VSALERLTKS SEIRHQQSAE FVNDLKRANS
NLVAAYEKAK KKHQNKLKKL ESQMMAMVER HETQVRMLKQ RIALLEEENS RPHTNETSL*

mutated AA sequence

MMAAAAAAAA GSSSSGGGGG GSGSGSSSSD TSSTGEEERM RRLFQTCDGD GDGYISRNDL
LMVCRQLNME ESVAEIMNQL GADENGKISF QDFTRCRMQL VREIRKEEVD LSAKSDNSCT
KKLRDRIASW PTSSDNSLGA LSAARESWEY DSGARDLQSP DVQSQSALQK LLEYGGSSLH
QQAALHKLLT QSPHIGNSVG GSYLELANTL HSAALASLKG DIVELNKRLQ QTERERDLLE
KKLAKAQCEQ SHLMREHEDV QERTTLRYEE RITELHSVIA ELNKKIDRLQ GTTIREEDEY
SELRSELSQS QHEVNEDSRS MDQDQTSVSI PENQSTMVTA DMDNCSDLNS ELQRVLTGLE
NVVCGRKKSS CSLSVAEVDK HIEQLTTASE HCDLAIKTVE EIEGVLGRDL YPNLAEERSR
WEKELAGLRE ENESLTAMLC SKEEELNRTK ATMNAIREER DRLRRRVREL QTRLQSVQAT
GPSSPGRLTS TNRPINPSTG ELSTSSSSND IPIAKIAERV KLSKTRSESS SSDRPVLGSE
ISSIGVSSSV AEHLAHSLQD CSNIQEIFQT LYSHGSAISE SKIREFEVET ERLNSRIEHL
KSQNDLLTIT LEECKSNAER MSMLVGKYES NATALRLALQ YSEQCIEAYE LLLALAESEQ
SLILGQFRAA GVGSSPGDQS GDENITQMLK RAHDCRKTAE NAAKALLMKL DGSCGGAFAV
AGCSVQPWES LSSNSHTSTT SSTASSCDTE FTKEDEQRLK DYIQQLKNDR AAVKLTMLEL
ESIHIDPLSY DVKPRGDSQR LDLENAVLMQ ELMAMKEEMA ELKAQLYLLE KEKKALELKL
STREAQEQAY LVHIEHLKSE VEEQKEQRMR SLSSTSSGSK DKPGKECADA ASPALSLAEL
RTTCSENELA AEFTNAIRRE KKLKARVQEL VSALERLTKS SEIRHQQSAE FVNDLKRANS
NLVAAYEKAK KKHQNKLKKL ESQMMAMVER HETQVRMLKQ RIALLEEENS RPHTNETSL*

speed

0.78 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