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: ENST00000382500
MT speed 0.9 s - this script 2.938348 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FOXD4	polymorphism_automatic	6.68418164195828e-06	simple_aae		affected		P231R	single base exchange	rs4742643		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999993315818358 (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)

chr9:117428G>CN/A show variant in all transcripts IGV

HGNC symbol

FOXD4

Ensembl transcript ID

ENST00000382500

Genbank transcript ID

NM_207305

UniProt peptide

Q12950

alteration type

single base exchange

alteration region

CDS

DNA changes

c.692C>G
cDNA.990C>G
g.990C>G

AA changes

P231R Score: 103 explain score(s)

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

231

frameshift

known variant

Reference ID: rs4742643

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	2515	17330	19845

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.071	0.264
	-0.042	0.308
(flanking)	1.163	0.649

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	993	wt: 0.2162 / mu: 0.2352 (marginal change - not scored)	wt: CAACCCCCGCCCAGGCCCTCTGCTTGGGGCCCCTGCCCCGC mu: CAACCCCCGCCCAGGCCGTCTGCTTGGGGCCCCTGCCCCGC	ctct\|GCTT
Acc increased	986	wt: 0.43 / mu: 0.49	wt: CCCTGCACAACCCCCGCCCAGGCCCTCTGCTTGGGGCCCCT mu: CCCTGCACAACCCCCGCCCAGGCCGTCTGCTTGGGGCCCCT	ccag\|GCCC

distance from splice site

990

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

231

mutated

not conserved

231

Ptroglodytes

all identical

ENSPTRG00000030377

231

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000051490

230

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000058133

n/a

Dmelanogaster

all identical

FBgn0004896

212

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000016337

n/a

protein features

start (aa)	end (aa)	feature	details
205	297	COMPBIAS	Pro-rich.	lost

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

1618 / 1618

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

299 / 299

chromosome

strand

-1

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

1320

coding sequence (CDS) position

692

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

990

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

990

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

117428

original gDNA sequence snippet

GCACAACCCCCGCCCAGGCCCTCTGCTTGGGGCCCCTGCCC

altered gDNA sequence snippet

GCACAACCCCCGCCCAGGCCGTCTGCTTGGGGCCCCTGCCC

original cDNA sequence snippet

GCACAACCCCCGCCCAGGCCCTCTGCTTGGGGCCCCTGCCC

altered cDNA sequence snippet

GCACAACCCCCGCCCAGGCCGTCTGCTTGGGGCCCCTGCCC

wildtype AA sequence

MNLPRAERLR STPQRSLRDS DGEDGKIDVL GEEEDEDEEE AASQQFLEQS LQPGLQVARW
GGVALPREHI EGGGGPSDPS EFGTEFRAPP RSAAASEDAR QPAKPPSSYI ALITMAILQS
PHKRLTLSGI CAFISDRFPY YRRKFPAWQN SIRHNLSLND CFVKIPREPG RPGKGNYWSL
DPASQDMFDN GSFLRRRKRF QRHQPTPGAH LPHPFPLPAA HAALHNPRPG PLLGAPAPPQ
PVPGAYPNTG PGRRPYALLH PHPPRYLLLS APAYAGAPKK AEGADLATPA PFPCCSPHLV
LSLGRRARVW RRHREADASL SALRVSCKGS GERVQGLRRV CPRPRGATAP CSSDRQACRT
ILQQQQRHQE EDCANGCAPT KGAVLGGHLS AASALLRYQA VAEGSGLTSL AAPLGGEGTS
PVFLVSPTPS SLAESAGPS*

mutated AA sequence

MNLPRAERLR STPQRSLRDS DGEDGKIDVL GEEEDEDEEE AASQQFLEQS LQPGLQVARW
GGVALPREHI EGGGGPSDPS EFGTEFRAPP RSAAASEDAR QPAKPPSSYI ALITMAILQS
PHKRLTLSGI CAFISDRFPY YRRKFPAWQN SIRHNLSLND CFVKIPREPG RPGKGNYWSL
DPASQDMFDN GSFLRRRKRF QRHQPTPGAH LPHPFPLPAA HAALHNPRPG RLLGAPAPPQ
PVPGAYPNTG PGRRPYALLH PHPPRYLLLS APAYAGAPKK AEGADLATPA PFPCCSPHLV
LSLGRRARVW RRHREADASL SALRVSCKGS GERVQGLRRV CPRPRGATAP CSSDRQACRT
ILQQQQRHQE EDCANGCAPT KGAVLGGHLS AASALLRYQA VAEGSGLTSL AAPLGGEGTS
PVFLVSPTPS SLAESAGPS*

speed

0.90 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