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: ENST00000252809
MT speed 0 s - this script 2.653735 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GDF15	polymorphism_automatic	2.19454998617863e-09	simple_aae		affected		H202D	single base exchange	rs1058587		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999780545 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM046071)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:18499422C>GN/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.604C>G
cDNA.636C>G
g.2455C>G

AA changes

H202D Score: 81 explain score(s)

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

202

frameshift

known variant

Reference ID: rs1058587

database	homozygous (G/G)	heterozygous	allele carriers
1000G	161	834	995
ExAC	3173	19602	22775

known disease mutation at this position, please check HGMD for details (HGMD ID CM046071)

regulatory features

ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Max, Transcription Factor, Max TF binding
Gabp, Transcription Factor, Gabp TF binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Srf, Transcription Factor, Srf TF binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
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
Cjun, Transcription Factor, Cjun TF 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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.024	0.552
	0.06	0.009
(flanking)	-2.9	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 gained	2449	0.90	mu: GCAACGGGGACGACT	AACG\|ggga

distance from splice site

327

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

202

mutated

not conserved

202

Ptroglodytes

all identical

ENSPTRG00000010707

202

Mmulatta

not conserved

ENSMMUG00000021180

202

Fcatus

not conserved

ENSFCAG00000009733

201

Mmusculus

not conserved

ENSMUSG00000038508

197

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000010311

258

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

all conserved

B0412.2

243

Xtropicalis

not conserved

ENSXETG00000034009

239

protein features

start (aa)	end (aa)	feature	details
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

604

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

636

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

2455

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

18499422

original gDNA sequence snippet

CGCGTGCGCGCAACGGGGACCACTGTCCGCTCGGGCCCGGG

altered gDNA sequence snippet

CGCGTGCGCGCAACGGGGACGACTGTCCGCTCGGGCCCGGG

original cDNA sequence snippet

CGCGTGCGCGCAACGGGGACCACTGTCCGCTCGGGCCCGGG

altered cDNA sequence snippet

CGCGTGCGCGCAACGGGGACGACTGTCCGCTCGGGCCCGGG

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

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

speed

0.60 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