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: ENST00000029410
MT speed 0 s - this script 2.402605 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
B4GALT7	disease_causing_automatic	0.999999999997525	simple_aae		affected	0	L206P	single base exchange	rs121917818		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999997525 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM993493)
known disease mutation: rs5612 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:177034506T>CN/A show variant in all transcripts IGV

HGNC symbol

B4GALT7

Ensembl transcript ID

ENST00000029410

Genbank transcript ID

NM_007255

UniProt peptide

Q9UBV7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.617T>C
cDNA.728T>C
g.7406T>C

AA changes

L206P Score: 98 explain score(s)

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

206

frameshift

known variant

Reference ID: rs121917818
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs5612 (pathogenic for Ehlers-Danlos syndrome, spondylodysplastic type, 1) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993493)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993493)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993493)

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
CTCF, Transcription Factor, CCCTC-binding factor
CTCFL, Transcription Factor, CTCFL Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Rad21, Transcription Factor, Rad21 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.035	1
	4.173	1
(flanking)	0.451	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
Acc increased	7407	wt: 0.23 / mu: 0.25	wt: GTCGGCGGCATCCTGCTGCTCTCCAAGCAGCACTACCGGCT mu: GTCGGCGGCATCCTGCTGCCCTCCAAGCAGCACTACCGGCT	gctc\|TCCA
Donor increased	7407	wt: 0.78 / mu: 0.91	wt: CTGCTCTCCAAGCAG mu: CTGCCCTCCAAGCAG	GCTC\|tcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

206

mutated

not conserved

206

Ptroglodytes

all conserved

ENSPTRG00000017592

190

Mmulatta

all identical

ENSMMUG00000029662

206

Fcatus

not conserved

ENSFCAG00000007890

Mmusculus

all identical

ENSMUSG00000021504

206

Ggallus

all identical

ENSGALG00000024259

Trubripes

all identical

ENSTRUG00000008706

206

Drerio

all identical

ENSDARG00000021899

196

Dmelanogaster

all conserved

FBgn0039258

189

Celegans

all identical

R10E11.4

164

Xtropicalis

all identical

ENSXETG00000006736

201

protein features

start (aa)	end (aa)	feature	details
52	327	TOPO_DOM	Lumenal (Potential).	lost
257	257	METAL	Manganese (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

984 / 984

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

328 / 328

position of stopcodon in wt / mu cDNA

1095 / 1095

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

112 / 112

chromosome

strand

last intron/exon boundary

940

theoretical NMD boundary in CDS

778

length of CDS

984

coding sequence (CDS) position

617

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

728

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

7406

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

177034506

original gDNA sequence snippet

TGTCGGCGGCATCCTGCTGCTCTCCAAGCAGCACTACCGGC

altered gDNA sequence snippet

TGTCGGCGGCATCCTGCTGCCCTCCAAGCAGCACTACCGGC

original cDNA sequence snippet

TGTCGGCGGCATCCTGCTGCTCTCCAAGCAGCACTACCGGC

altered cDNA sequence snippet

TGTCGGCGGCATCCTGCTGCCCTCCAAGCAGCACTACCGGC

wildtype AA sequence

MFPSRRKAAQ LPWEDGRSGL LSGGLPRKCS VFHLFVACLS LGFFSLLWLQ LSCSGDVARA
VRGQGQETSG PPRACPPEPP PEHWEEDASW GPHRLAVLVP FRERFEELLV FVPHMRRFLS
RKKIRHHIYV LNQVDHFRFN RAALINVGFL ESSNSTDYIA MHDVDLLPLN EELDYGFPEA
GPFHVASPEL HPLYHYKTYV GGILLLSKQH YRLCNGMSNR FWGWGREDDE FYRRIKGAGL
QLFRPSGITT GYKTFRHLHD PAWRKRDQKR IAAQKQEQFK VDREGGLNTV KYHVASRTAL
SVGGAPCTVL NIMLDCDKTA TPWCTFS*

mutated AA sequence

MFPSRRKAAQ LPWEDGRSGL LSGGLPRKCS VFHLFVACLS LGFFSLLWLQ LSCSGDVARA
VRGQGQETSG PPRACPPEPP PEHWEEDASW GPHRLAVLVP FRERFEELLV FVPHMRRFLS
RKKIRHHIYV LNQVDHFRFN RAALINVGFL ESSNSTDYIA MHDVDLLPLN EELDYGFPEA
GPFHVASPEL HPLYHYKTYV GGILLPSKQH YRLCNGMSNR FWGWGREDDE FYRRIKGAGL
QLFRPSGITT GYKTFRHLHD PAWRKRDQKR IAAQKQEQFK VDREGGLNTV KYHVASRTAL
SVGGAPCTVL NIMLDCDKTA TPWCTFS*

speed

0.34 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