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: ENST00000310160
MT speed 0 s - this script 2.354523 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FUT1	disease_causing_automatic	0.339384193751019	simple_aae		affected	0	L164H	single base exchange	rs104894687		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.339384193751019 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM940790)
known disease mutation: rs12140 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:49254048A>TN/A show variant in all transcripts IGV

HGNC symbol

FUT1

Ensembl transcript ID

ENST00000310160

Genbank transcript ID

NM_000148

UniProt peptide

P19526

alteration type

single base exchange

alteration region

CDS

DNA changes

c.491T>A
cDNA.1466T>A
g.4600T>A

AA changes

L164H Score: 99 explain score(s)

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

164

frameshift

known variant

Reference ID: rs104894687
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs12140 (pathogenic for Para-Bombay phenotype) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940790)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940790)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940790)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.106	0.001
	2.738	0.55
(flanking)	0.403	0.568

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 gained	4594	0.32	mu: GGACTTGAGAGATCCTTTCCTGAAGCACTCTGGCTTCCCCT	tcct\|GAAG

distance from splice site

493

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

164

mutated

not conserved

164

Ptroglodytes

all identical

ENSPTRG00000011256

165

Mmulatta

all identical

ENSMMUG00000004020

165

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000008461

166

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

all conserved

B0205.4

183

Xtropicalis

all identical

ENSXETG00000004564

161

protein features

start (aa)	end (aa)	feature	details
26	365	TOPO_DOM	Lumenal (Potential).	lost
327	327	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1098 / 1098

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

366 / 366

position of stopcodon in wt / mu cDNA

2073 / 2073

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

976 / 976

chromosome

strand

-1

last intron/exon boundary

974

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

1098

coding sequence (CDS) position

491

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

1466

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

4600

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

49254048

original gDNA sequence snippet

GAGAGATCCTTTCCTGAAGCTCTCTGGCTTCCCCTGCTCTT

altered gDNA sequence snippet

GAGAGATCCTTTCCTGAAGCACTCTGGCTTCCCCTGCTCTT

original cDNA sequence snippet

GAGAGATCCTTTCCTGAAGCTCTCTGGCTTCCCCTGCTCTT

altered cDNA sequence snippet

GAGAGATCCTTTCCTGAAGCACTCTGGCTTCCCCTGCTCTT

wildtype AA sequence

MWLRSHRQLC LAFLLVCVLS VIFFLHIHQD SFPHGLGLSI LCPDRRLVTP PVAIFCLPGT
AMGPNASSSC PQHPASLSGT WTVYPNGRFG NQMGQYATLL ALAQLNGRRA FILPAMHAAL
APVFRITLPV LAPEVDSRTP WRELQLHDWM SEEYADLRDP FLKLSGFPCS WTFFHHLREQ
IRREFTLHDH LREEAQSVLG QLRLGRTGDR PRTFVGVHVR RGDYLQVMPQ RWKGVVGDSA
YLRQAMDWFR ARHEAPVFVV TSNGMEWCKE NIDTSQGDVT FAGDGQEATP WKDFALLTQC
NHTIMTIGTF GFWAAYLAGG DTVYLANFTL PDSEFLKIFK PEAAFLPEWV GINADLSPLW
TLAKP*

mutated AA sequence

MWLRSHRQLC LAFLLVCVLS VIFFLHIHQD SFPHGLGLSI LCPDRRLVTP PVAIFCLPGT
AMGPNASSSC PQHPASLSGT WTVYPNGRFG NQMGQYATLL ALAQLNGRRA FILPAMHAAL
APVFRITLPV LAPEVDSRTP WRELQLHDWM SEEYADLRDP FLKHSGFPCS WTFFHHLREQ
IRREFTLHDH LREEAQSVLG QLRLGRTGDR PRTFVGVHVR RGDYLQVMPQ RWKGVVGDSA
YLRQAMDWFR ARHEAPVFVV TSNGMEWCKE NIDTSQGDVT FAGDGQEATP WKDFALLTQC
NHTIMTIGTF GFWAAYLAGG DTVYLANFTL PDSEFLKIFK PEAAFLPEWV GINADLSPLW
TLAKP*

speed

0.29 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