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: ENST00000282561
MT speed 0 s - this script 2.732746 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GJA1	disease_causing_automatic	0.99999999201383	simple_aae			0	S18P	single base exchange	rs104893962		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999999201383 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM030452)
known disease mutation: rs16983 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:121768045T>CN/A show variant in all transcripts IGV

HGNC symbol

GJA1

Ensembl transcript ID

ENST00000282561

Genbank transcript ID

NM_000165

UniProt peptide

P17302

alteration type

single base exchange

alteration region

CDS

DNA changes

c.52T>C
cDNA.209T>C
g.11208T>C

AA changes

S18P Score: 74 explain score(s)

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

frameshift

known variant

Reference ID: rs104893962
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs16983 (pathogenic for Oculodentodigital dysplasia) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM030452)

known disease mutation at this position, please check HGMD for details (HGMD ID CM030452)
known disease mutation at this position, please check HGMD for details (HGMD ID CM030452)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.51	1
	5.302	1
(flanking)	6.42	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	11209	wt: 0.2988 / mu: 0.3184 (marginal change - not scored)	wt: TGACAAGGTTCAAGCCTACTCAACTGCTGGAGGGAAGGTGT mu: TGACAAGGTTCAAGCCTACCCAACTGCTGGAGGGAAGGTGT	actc\|AACT
Donor marginally increased	11206	wt: 0.8971 / mu: 0.8978 (marginal change - not scored)	wt: AGCCTACTCAACTGC mu: AGCCTACCCAACTGC	CCTA\|ctca

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

all identical

ENSPTRG00000018560

Mmulatta

all identical

ENSMMUG00000005225

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000050953

Ggallus

all identical

ENSGALG00000014873

Trubripes

no homologue

Drerio

all identical

ENSDARG00000041799

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000025411

protein features

start (aa)	end (aa)	feature	details
14	36	TRANSMEM	Helical; (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1149 / 1149

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

383 / 383

position of stopcodon in wt / mu cDNA

1306 / 1306

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

158 / 158

chromosome

strand

last intron/exon boundary

142

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

1149

coding sequence (CDS) position

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

209

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

11208

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

121768045

original gDNA sequence snippet

TTGACAAGGTTCAAGCCTACTCAACTGCTGGAGGGAAGGTG

altered gDNA sequence snippet

TTGACAAGGTTCAAGCCTACCCAACTGCTGGAGGGAAGGTG

original cDNA sequence snippet

TTGACAAGGTTCAAGCCTACTCAACTGCTGGAGGGAAGGTG

altered cDNA sequence snippet

TTGACAAGGTTCAAGCCTACCCAACTGCTGGAGGGAAGGTG

wildtype AA sequence

MGDWSALGKL LDKVQAYSTA GGKVWLSVLF IFRILLLGTA VESAWGDEQS AFRCNTQQPG
CENVCYDKSF PISHVRFWVL QIIFVSVPTL LYLAHVFYVM RKEEKLNKKE EELKVAQTDG
VNVDMHLKQI EIKKFKYGIE EHGKVKMRGG LLRTYIISIL FKSIFEVAFL LIQWYIYGFS
LSAVYTCKRD PCPHQVDCFL SRPTEKTIFI IFMLVVSLVS LALNIIELFY VFFKGVKDRV
KGKSDPYHAT SGALSPAKDC GSQKYAYFNG CSSPTAPLSP MSPPGYKLVT GDRNNSSCRN
YNKQASEQNW ANYSAEQNRM GQAGSTISNS HAQPFDFPDD NQNSKKLAAG HELQPLAIVD
QRPSSRASSR ASSRPRPDDL EI*

mutated AA sequence

MGDWSALGKL LDKVQAYPTA GGKVWLSVLF IFRILLLGTA VESAWGDEQS AFRCNTQQPG
CENVCYDKSF PISHVRFWVL QIIFVSVPTL LYLAHVFYVM RKEEKLNKKE EELKVAQTDG
VNVDMHLKQI EIKKFKYGIE EHGKVKMRGG LLRTYIISIL FKSIFEVAFL LIQWYIYGFS
LSAVYTCKRD PCPHQVDCFL SRPTEKTIFI IFMLVVSLVS LALNIIELFY VFFKGVKDRV
KGKSDPYHAT SGALSPAKDC GSQKYAYFNG CSSPTAPLSP MSPPGYKLVT GDRNNSSCRN
YNKQASEQNW ANYSAEQNRM GQAGSTISNS HAQPFDFPDD NQNSKKLAAG HELQPLAIVD
QRPSSRASSR ASSRPRPDDL EI*

speed

0.72 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

disease causing

Problems