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: ENST00000252809
MT speed 0 s - this script 2.813239 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GDF15	polymorphism_automatic	0	simple_aae		affected		V9L	single base exchange	rs1059519		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1 (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)

chr19:18497024G>CN/A show variant in all transcripts IGV

HGNC symbol

GDF15

Ensembl transcript ID

ENST00000252809

Genbank transcript ID

NM_004864

UniProt peptide

Q99988

alteration type

single base exchange

alteration region

CDS

DNA changes

c.25G>C
cDNA.57G>C
g.57G>C

AA changes

V9L Score: 32 explain score(s)

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

frameshift

known variant

Reference ID: rs1059519

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1293	980	2273
ExAC	28749	-24731	4018

regulatory features

p300, Transcription Factor, p300 Transcription Factor Binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Max, Transcription Factor, Max TF binding
GTF2B, Transcription Factor, GTF2B Transcription Factor Binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
NELFe, Transcription Factor, NELFe Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
HNF4G, Transcription Factor, HNF4G Transcription Factor Binding
SP1, Transcription Factor, SP1 Transcription Factor Binding
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
Tcf12, Transcription Factor, Tcf12 Transcription Factor Binding
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Cmyc, Transcription Factor, Cmyc TF binding
Jund, Transcription Factor, Jund TF binding
FOXA1, Transcription Factor, FOXA1 Transcription Factor Binding
Cjun, Transcription Factor, Cjun TF binding
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
FOXA2, Transcription Factor, FOXA2 Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
CTCFL, Transcription Factor, CTCFL Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
TFIIIC-110, Transcription Factor, TFIIIC-110 Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Rad21, Transcription Factor, Rad21 Transcription Factor Binding
ZBTB7A, Transcription Factor, ZBTB7A Transcription Factor Binding
HNF4A, Transcription Factor, HNF4A Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.83	0
	-0.43	0
(flanking)	-0.196	0

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 increased	55	wt: 0.35 / mu: 0.60	wt: CAGGACGGTGAATGG mu: CAGGACGCTGAATGG	GGAC\|ggtg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000010707

Mmulatta

all conserved

ENSMMUG00000021180

Fcatus

not conserved

ENSFCAG00000009733

Mmusculus

not conserved

ENSMUSG00000038508

LRFLLFL

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000010311

n/a

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no alignment

B0412.2

n/a

Xtropicalis

no alignment

ENSXETG00000034009

n/a

protein features

start (aa)	end (aa)	feature	details
1	29	SIGNAL	Potential.	lost
30	194	PROPEP	Potential. /FTId=PRO_0000033992.	might get lost (downstream of altered splice site)
70	70	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
211	211	DISULFID	By similarity.	might get lost (downstream of altered splice site)
240	240	DISULFID	By similarity.	might get lost (downstream of altered splice site)
244	244	DISULFID	By similarity.	might get lost (downstream of altered splice site)
269	269	CONFLICT	V -> E (in Ref. 1; AAB88913).	might get lost (downstream of altered splice site)
273	273	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
273	273	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
274	274	DISULFID	By similarity.	might get lost (downstream of altered splice site)
288	288	CONFLICT	T -> A (in Ref. 10; AAF89834).	might get lost (downstream of altered splice site)
305	305	DISULFID	By similarity.	might get lost (downstream of altered splice site)
307	307	DISULFID	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

927 / 927

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

309 / 309

position of stopcodon in wt / mu cDNA

959 / 959

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

33 / 33

chromosome

strand

last intron/exon boundary

310

theoretical NMD boundary in CDS

227

length of CDS

927

coding sequence (CDS) position

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

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

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

18497024

original gDNA sequence snippet

CCGGGCAAGAACTCAGGACGGTGAATGGCTCTCAGATGCTC

altered gDNA sequence snippet

CCGGGCAAGAACTCAGGACGCTGAATGGCTCTCAGATGCTC

original cDNA sequence snippet

CCGGGCAAGAACTCAGGACGGTGAATGGCTCTCAGATGCTC

altered cDNA sequence snippet

CCGGGCAAGAACTCAGGACGCTGAATGGCTCTCAGATGCTC

wildtype AA sequence

MPGQELRTVN GSQMLLVLLV LSWLPHGGAL SLAEASRASF PGPSELHSED SRFRELRKRY
EDLLTRLRAN QSWEDSNTDL VPAPAVRILT PEVRLGSGGH LHLRISRAAL PEGLPEASRL
HRALFRLSPT ASRSWDVTRP LRRQLSLARP QAPALHLRLS PPPSQSDQLL AESSSARPQL
ELHLRPQAAR GRRRARARNG DHCPLGPGRC CRLHTVRASL EDLGWADWVL SPREVQVTMC
IGACPSQFRA ANMHAQIKTS LHRLKPDTVP APCCVPASYN PMVLIQKTDT GVSLQTYDDL
LAKDCHCI*

mutated AA sequence

MPGQELRTLN GSQMLLVLLV LSWLPHGGAL SLAEASRASF PGPSELHSED SRFRELRKRY
EDLLTRLRAN QSWEDSNTDL VPAPAVRILT PEVRLGSGGH LHLRISRAAL PEGLPEASRL
HRALFRLSPT ASRSWDVTRP LRRQLSLARP QAPALHLRLS PPPSQSDQLL AESSSARPQL
ELHLRPQAAR GRRRARARNG DHCPLGPGRC CRLHTVRASL EDLGWADWVL SPREVQVTMC
IGACPSQFRA ANMHAQIKTS LHRLKPDTVP APCCVPASYN PMVLIQKTDT GVSLQTYDDL
LAKDCHCI*

speed

0.75 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