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: ENST00000366714
MT speed 0 s - this script 2.699845 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GJC2	disease_causing_automatic	0.999999813723797	simple_aae		affected	0	M286T	single base exchange	rs74315311		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999813723797 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM041779)
known disease mutation: rs2071 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:228346316T>CN/A show variant in all transcripts IGV

HGNC symbol

GJC2

Ensembl transcript ID

ENST00000366714

Genbank transcript ID

NM_020435

UniProt peptide

Q5T442

alteration type

single base exchange

alteration region

CDS

DNA changes

c.857T>C
cDNA.1032T>C
g.8764T>C

AA changes

M286T Score: 81 explain score(s)

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

286

frameshift

known variant

Reference ID: rs74315311
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs2071 (pathogenic for Leukodystrophy, hypomyelinating, 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM041779)

known disease mutation at this position, please check HGMD for details (HGMD ID CM041779)
known disease mutation at this position, please check HGMD for details (HGMD ID CM041779)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.433	1
	4.433	1
(flanking)	3.73	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 increased	8759	wt: 0.48 / mu: 0.57	wt: TGCCTGCTGCTCAACCTCTGTGAGATGGCCCACCTGGGCTT mu: TGCCTGCTGCTCAACCTCTGTGAGACGGCCCACCTGGGCTT	ctgt\|GAGA
Acc marginally increased	8761	wt: 0.9346 / mu: 0.9517 (marginal change - not scored)	wt: CCTGCTGCTCAACCTCTGTGAGATGGCCCACCTGGGCTTGG mu: CCTGCTGCTCAACCTCTGTGAGACGGCCCACCTGGGCTTGG	gtga\|GATG
Donor marginally increased	8759	wt: 0.9784 / mu: 0.9906 (marginal change - not scored)	wt: CTCTGTGAGATGGCC mu: CTCTGTGAGACGGCC	CTGT\|gaga

distance from splice site

876

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

286

mutated

not conserved

286

Ptroglodytes

all identical

ENSPTRG00000002070

286

Mmulatta

all identical

ENSMMUG00000023086

286

Fcatus

all identical

ENSFCAG00000007130

281

Mmusculus

all identical

ENSMUSG00000043448

285

Ggallus

all identical

ENSGALG00000005331

251

Trubripes

no homologue

Drerio

all identical

ENSDARG00000073896

250

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000006175

250

protein features

start (aa)	end (aa)	feature	details
266	286	TRANSMEM	Helical; (Potential).	lost
287	439	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
371	371	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1320 / 1320

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

440 / 440

position of stopcodon in wt / mu cDNA

1495 / 1495

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

176 / 176

chromosome

strand

last intron/exon boundary

157

theoretical NMD boundary in CDS

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

length of CDS

1320

coding sequence (CDS) position

857

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

1032

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

8764

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

228346316

original gDNA sequence snippet

GCTGCTCAACCTCTGTGAGATGGCCCACCTGGGCTTGGGCA

altered gDNA sequence snippet

GCTGCTCAACCTCTGTGAGACGGCCCACCTGGGCTTGGGCA

original cDNA sequence snippet

GCTGCTCAACCTCTGTGAGATGGCCCACCTGGGCTTGGGCA

altered cDNA sequence snippet

GCTGCTCAACCTCTGTGAGACGGCCCACCTGGGCTTGGGCA

wildtype AA sequence

MTNMSWSFLT RLLEEIHNHS TFVGKVWLTV LVVFRIVLTA VGGEAIYSDE QAKFTCNTRQ
PGCDNVCYDA FAPLSHVRFW VFQIVVISTP SVMYLGYAVH RLARASEQER RRALRRRPGP
RRAPRAHLPP PHAGWPEPAD LGEEEPMLGL GEEEEEEETG AAEGAGEEAE EAGAEEACTK
AVGADGKAAG TPGPTGQHDG RRRIQREGLM RVYVAQLVAR AAFEVAFLVG QYLLYGFEVR
PFFPCSRQPC PHVVDCFVSR PTEKTVFLLV MYVVSCLCLL LNLCEMAHLG LGSAQDAVRG
RRGPPASAPA PAPRPPPCAF PAAAAGLACP PDYSLVVRAA ERARAHDQNL ANLALQALRD
GAAAGDRDRD SSPCVGLPAA SRGPPRAGAP ASRTGSATSA GTVGEQGRPG THERPGAKPR
AGSEKGSASS RDGKTTVWI*

mutated AA sequence

MTNMSWSFLT RLLEEIHNHS TFVGKVWLTV LVVFRIVLTA VGGEAIYSDE QAKFTCNTRQ
PGCDNVCYDA FAPLSHVRFW VFQIVVISTP SVMYLGYAVH RLARASEQER RRALRRRPGP
RRAPRAHLPP PHAGWPEPAD LGEEEPMLGL GEEEEEEETG AAEGAGEEAE EAGAEEACTK
AVGADGKAAG TPGPTGQHDG RRRIQREGLM RVYVAQLVAR AAFEVAFLVG QYLLYGFEVR
PFFPCSRQPC PHVVDCFVSR PTEKTVFLLV MYVVSCLCLL LNLCETAHLG LGSAQDAVRG
RRGPPASAPA PAPRPPPCAF PAAAAGLACP PDYSLVVRAA ERARAHDQNL ANLALQALRD
GAAAGDRDRD SSPCVGLPAA SRGPPRAGAP ASRTGSATSA GTVGEQGRPG THERPGAKPR
AGSEKGSASS RDGKTTVWI*

speed

0.67 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