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: ENST00000287020
MT speed 0 s - this script 2.137868 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GDF6	disease_causing_automatic	4.22869001904859e-07	simple_aae			0	Q253L	single base exchange	rs121909355		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 4.22869001904859e-07 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM0910798)
known disease mutation: rs8375 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr8:97157401T>AN/A show variant in all transcripts IGV

HGNC symbol

GDF6

Ensembl transcript ID

ENST00000287020

Genbank transcript ID

NM_001001557

UniProt peptide

Q6KF10

alteration type

single base exchange

alteration region

CDS

DNA changes

c.758A>T
cDNA.858A>T
g.15620A>T

AA changes

Q253L Score: 113 explain score(s)

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

253

frameshift

known variant

Reference ID: rs121909355

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

known disease mutation: rs8375 (pathogenic for Microphthalmia, isolated 4) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM0910798)

known disease mutation at this position, please check HGMD for details (HGMD ID CM0910798)
known disease mutation at this position, please check HGMD for details (HGMD ID CM0910798)

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
Max, Transcription Factor, Max TF binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Rad21, Transcription Factor, Rad21 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.308	0.564
	-0.064	0.206
(flanking)	0.513	0.177

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

352

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

253

mutated

not conserved

253

Ptroglodytes

not conserved

ENSPTRG00000020439

253

Mmulatta

all identical

ENSMMUG00000011267

253

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000051279

256

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000004399

249

Drerio

not conserved

ENSDARG00000053479

222

Dmelanogaster

not conserved

FBgn0000490

428

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
23	330	PROPEP	Potential. /FTId=PRO_0000342206.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1368 / 1368

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

456 / 456

position of stopcodon in wt / mu cDNA

1468 / 1468

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

101 / 101

chromosome

strand

-1

last intron/exon boundary

507

theoretical NMD boundary in CDS

356

length of CDS

1368

coding sequence (CDS) position

758

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

858

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

15620

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

97157401

original gDNA sequence snippet

GGCGCGCGCGCGGGGACCCCAGCAACCGCCGCCCCCGGACC

altered gDNA sequence snippet

GGCGCGCGCGCGGGGACCCCTGCAACCGCCGCCCCCGGACC

original cDNA sequence snippet

GGCGCGCGCGCGGGGACCCCAGCAACCGCCGCCCCCGGACC

altered cDNA sequence snippet

GGCGCGCGCGCGGGGACCCCTGCAACCGCCGCCCCCGGACC

wildtype AA sequence

MDTPRVLLSA VFLISFLWDL PGFQQASISS SSSSAELGST KGMRSRKEGK MQRAPRDSDA
GREGQEPQPR PQDEPRAQQP RAQEPPGRGP RVVPHEYMLS IYRTYSIAEK LGINASFFQS
SKSANTITSF VDRGLDDLSH TPLRRQKYLF DVSMLSDKEE LVGAELRLFR QAPSAPWGPP
AGPLHVQLFP CLSPLLLDAR TLDPQGAPPA GWEVFDVWQG LRHQPWKQLC LELRAAWGEL
DAGEAEARAR GPQQPPPPDL RSLGFGRRVR PPQERALLVV FTRSQRKNLF AEMREQLGSA
EAAGPGAGAE GSWPPPSGAP DARPWLPSPG RRRRRTAFAS RHGKRHGKKS RLRCSKKPLH
VNFKELGWDD WIIAPLEYEA YHCEGVCDFP LRSHLEPTNH AIIQTLMNSM DPGSTPPSCC
VPTKLTPISI LYIDAGNNVV YKQYEDMVVE SCGCR*

mutated AA sequence

MDTPRVLLSA VFLISFLWDL PGFQQASISS SSSSAELGST KGMRSRKEGK MQRAPRDSDA
GREGQEPQPR PQDEPRAQQP RAQEPPGRGP RVVPHEYMLS IYRTYSIAEK LGINASFFQS
SKSANTITSF VDRGLDDLSH TPLRRQKYLF DVSMLSDKEE LVGAELRLFR QAPSAPWGPP
AGPLHVQLFP CLSPLLLDAR TLDPQGAPPA GWEVFDVWQG LRHQPWKQLC LELRAAWGEL
DAGEAEARAR GPLQPPPPDL RSLGFGRRVR PPQERALLVV FTRSQRKNLF AEMREQLGSA
EAAGPGAGAE GSWPPPSGAP DARPWLPSPG RRRRRTAFAS RHGKRHGKKS RLRCSKKPLH
VNFKELGWDD WIIAPLEYEA YHCEGVCDFP LRSHLEPTNH AIIQTLMNSM DPGSTPPSCC
VPTKLTPISI LYIDAGNNVV YKQYEDMVVE SCGCR*

speed

0.12 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