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: ENST00000339480
MT speed 1.1 s - this script 3.153393 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GJB4	disease_causing_automatic	0.998052093122719	simple_aae			0	F189Y	single base exchange	rs80358213		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.998052093122719 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM035050)
known disease mutation: rs5009 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:35227421T>AN/A show variant in all transcripts IGV

HGNC symbol

GJB4

Ensembl transcript ID

ENST00000339480

Genbank transcript ID

NM_153212

UniProt peptide

Q9NTQ9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.566T>A
cDNA.936T>A
g.2080T>A

AA changes

F189Y Score: 22 explain score(s)

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

189

frameshift

known variant

Reference ID: rs80358213
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs5009 (pathogenic for Erythrokeratodermia variabilis et progressiva 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM035050)

known disease mutation at this position, please check HGMD for details (HGMD ID CM035050)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035050)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.504	1
	5.088	1
(flanking)	3.412	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	2083	wt: 0.8598 / mu: 0.8911 (marginal change - not scored)	wt: GAAGGTCTTCACCTACTTCATGGTGACCACAGCTGCCATCT mu: GAAGGTCTTCACCTACTACATGGTGACCACAGCTGCCATCT	tcat\|GGTG
Donor marginally increased	2084	wt: 0.3561 / mu: 0.4419 (marginal change - not scored)	wt: TTCATGGTGACCACA mu: TACATGGTGACCACA	CATG\|gtga

distance from splice site

888

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

189

mutated

all conserved

189

Ptroglodytes

all identical

ENSPTRG00000022950

189

Mmulatta

all identical

ENSMMUG00000001860

189

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000046623

189

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
188	210	TRANSMEM	Helical; (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

801 / 801

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

267 / 267

position of stopcodon in wt / mu cDNA

1171 / 1171

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

371 / 371

chromosome

strand

last intron/exon boundary

theoretical NMD boundary in CDS

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

length of CDS

801

coding sequence (CDS) position

566

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

936

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

2080

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

35227421

original gDNA sequence snippet

GAAGAAGGTCTTCACCTACTTCATGGTGACCACAGCTGCCA

altered gDNA sequence snippet

GAAGAAGGTCTTCACCTACTACATGGTGACCACAGCTGCCA

original cDNA sequence snippet

GAAGAAGGTCTTCACCTACTTCATGGTGACCACAGCTGCCA

altered cDNA sequence snippet

GAAGAAGGTCTTCACCTACTACATGGTGACCACAGCTGCCA

wildtype AA sequence

MNWAFLQGLL SGVNKYSTVL SRIWLSVVFI FRVLVYVVAA EEVWDDEQKD FVCNTKQPGC
PNVCYDEFFP VSHVRLWALQ LILVTCPSLL VVMHVAYREE RERKHHLKHG PNAPSLYDNL
SKKRGGLWWT YLLSLIFKAA VDAGFLYIFH RLYKDYDMPR VVACSVEPCP HTVDCYISRP
TEKKVFTYFM VTTAAICILL NLSEVFYLVG KRCMEIFGPR HRRPRCRECL PDTCPPYVLS
QGGHPEDGNS VLMKAGSAPV DAGGYP*

mutated AA sequence

MNWAFLQGLL SGVNKYSTVL SRIWLSVVFI FRVLVYVVAA EEVWDDEQKD FVCNTKQPGC
PNVCYDEFFP VSHVRLWALQ LILVTCPSLL VVMHVAYREE RERKHHLKHG PNAPSLYDNL
SKKRGGLWWT YLLSLIFKAA VDAGFLYIFH RLYKDYDMPR VVACSVEPCP HTVDCYISRP
TEKKVFTYYM VTTAAICILL NLSEVFYLVG KRCMEIFGPR HRRPRCRECL PDTCPPYVLS
QGGHPEDGNS VLMKAGSAPV DAGGYP*

speed

1.10 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