MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000334134
MT speed 0 s - this script 3.298622 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FGF3	disease_causing_automatic	0.999996299615377	simple_aae		affected	0	S156P	single base exchange	rs121917703		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999996299615377 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM070118)
known disease mutation: rs13837 (pathogenic)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:69625327A>GN/A show variant in all transcripts IGV

HGNC symbol

FGF3

Ensembl transcript ID

ENST00000334134

Genbank transcript ID

NM_005247

UniProt peptide

P11487

alteration type

single base exchange

alteration region

CDS

DNA changes

c.466T>C
cDNA.557T>C
g.8466T>C

AA changes

S156P Score: 74 explain score(s)

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

156

frameshift

known variant

Reference ID: rs121917703

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs13837 (pathogenic for Deafness with labyrinthine aplasia microtia and microdontia (LAMM)) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070118)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070118)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070118)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.307	1
	1.887	1
(flanking)	0.246	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
Donor marginally increased	8457	wt: 0.9683 / mu: 0.9844 (marginal change - not scored)	wt: GACTGTGGTACGTGT mu: GACTGTGGTACGTGC	CTGT\|ggta
Donor increased	8468	wt: 0.78 / mu: 0.86	wt: GTGTCTGTGAACGGC mu: GTGCCTGTGAACGGC	GTCT\|gtga

distance from splice site

142

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

156

mutated

not conserved

156

Ptroglodytes

all identical

ENSPTRG00000004001

156

Mmulatta

all identical

ENSMMUG00000002969

156

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000031074

156

Ggallus

all identical

ENSGALG00000007563

180

Trubripes

all identical

ENSTRUG00000015735

164

Drerio

all identical

ENSDARG00000068094

175

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000002761

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

720 / 720

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

240 / 240

position of stopcodon in wt / mu cDNA

811 / 811

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

92 / 92

chromosome

strand

-1

last intron/exon boundary

416

theoretical NMD boundary in CDS

274

length of CDS

720

coding sequence (CDS) position

466

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

557

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

8466

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

69625327

original gDNA sequence snippet

CCGAGAGACTGTGGTACGTGTCTGTGAACGGCAAGGGCCGG

altered gDNA sequence snippet

CCGAGAGACTGTGGTACGTGCCTGTGAACGGCAAGGGCCGG

original cDNA sequence snippet

CCGAGAGACTGTGGTACGTGTCTGTGAACGGCAAGGGCCGG

altered cDNA sequence snippet

CCGAGAGACTGTGGTACGTGCCTGTGAACGGCAAGGGCCGG

wildtype AA sequence

MGLIWLLLLS LLEPGWPAAG PGARLRRDAG GRGGVYEHLG GAPRRRKLYC ATKYHLQLHP
SGRVNGSLEN SAYSILEITA VEVGIVAIRG LFSGRYLAMN KRGRLYASEH YSAECEFVER
IHELGYNTYA SRLYRTVSST PGARRQPSAE RLWYVSVNGK GRPRRGFKTR RTQKSSLFLP
RVLDHRDHEM VRQLQSGLPR PPGKGVQPRR RRQKQSPDNL EPSHVQASRL GSQLEASAH*

mutated AA sequence

MGLIWLLLLS LLEPGWPAAG PGARLRRDAG GRGGVYEHLG GAPRRRKLYC ATKYHLQLHP
SGRVNGSLEN SAYSILEITA VEVGIVAIRG LFSGRYLAMN KRGRLYASEH YSAECEFVER
IHELGYNTYA SRLYRTVSST PGARRQPSAE RLWYVPVNGK GRPRRGFKTR RTQKSSLFLP
RVLDHRDHEM VRQLQSGLPR PPGKGVQPRR RRQKQSPDNL EPSHVQASRL GSQLEASAH*

speed

1.29 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