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: ENST00000299155
MT speed 0 s - this script 2.73056 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AMN	disease_causing_automatic	0.108594184748572	simple_aae		affected	0	T41I	single base exchange	rs119478058		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.108594184748572 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM030407)
known disease mutation: rs4770 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:103390126C>TN/A show variant in all transcripts IGV

HGNC symbol

AMN

Ensembl transcript ID

ENST00000299155

Genbank transcript ID

NM_030943

UniProt peptide

Q9BXJ7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.122C>T
cDNA.155C>T
g.1134C>T

AA changes

T41I Score: 89 explain score(s)

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

frameshift

known variant

Reference ID: rs119478058

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

known disease mutation: rs4770 (pathogenic for Imerslund-Gräsbeck syndrome 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM030407)

known disease mutation at this position, please check HGMD for details (HGMD ID CM030407)
known disease mutation at this position, please check HGMD for details (HGMD ID CM030407)

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.69	1
	2.142	1
(flanking)	0.019	0.999

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	1141	wt: 0.23 / mu: 0.26	wt: AGCCAGAACCGGACCCCGTGCGCCGGCGGCGCCGTTGAGTT mu: AGCCAGAACCGGATCCCGTGCGCCGGCGGCGCCGTTGAGTT	gtgc\|GCCG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000006747

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000018741

Mmusculus

all identical

ENSMUSG00000021278

Ggallus

not conserved

ENSGALG00000011391

Trubripes

not conserved

ENSTRUG00000012116

Drerio

not conserved

ENSDARG00000062947

Dmelanogaster

not conserved

FBgn0025686

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000012751

protein features

start (aa)	end (aa)	feature	details
20	357	TOPO_DOM	Extracellular (Potential).	lost
202	254	DOMAIN	VWFC.	might get lost (downstream of altered splice site)
241	241	CONFLICT	S -> F (in Ref. 1; AAK28532).	might get lost (downstream of altered splice site)
358	378	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
379	453	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1362 / 1362

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

454 / 454

position of stopcodon in wt / mu cDNA

1395 / 1395

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

34 / 34

chromosome

strand

last intron/exon boundary

1291

theoretical NMD boundary in CDS

1207

length of CDS

1362

coding sequence (CDS) position

122

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

155

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

1134

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

103390126

original gDNA sequence snippet

CAACTGGAGCCAGAACCGGACCCCGTGCGCCGGCGGCGCCG

altered gDNA sequence snippet

CAACTGGAGCCAGAACCGGATCCCGTGCGCCGGCGGCGCCG

original cDNA sequence snippet

CAACTGGAGCCAGAACCGGACCCCGTGCGCCGGCGGCGCCG

altered cDNA sequence snippet

CAACTGGAGCCAGAACCGGATCCCGTGCGCCGGCGGCGCCG

wildtype AA sequence

MGVLGRVLLW LQLCALTQAV SKLWVPNTDF DVAANWSQNR TPCAGGAVEF PADKMVSVLV
QEGHAVSDML LPLDGELVLA SGAGFGVSDV GSHLDCGAGE PAVFRDSDRF SWHDPHLWRS
GDEAPGLFFV DAERVPCRHD DVFFPPSASF RVGLGPGASP VRVRSISALG RTFTRDEDLA
VFLASRAGRL RFHGPGALSV GPEDCADPSG CVCGNAEAQP WICAALLQPL GGRCPQAACH
SALRPQGQCC DLCGAVVLLT HGPAFDLERY RARILDTFLG LPQYHGLQVA VSKVPRSSRL
READTEIQVV LVENGPETGG AGRLARALLA DVAENGEALG VLEATMRESG AHVWGSSAAG
LAGGVAAAVL LALLVLLVAP PLLRRAGRLR WRRHEAAAPA GAPLGFRNPV FDVTASEELP
LPRRLSLVPK AAADSTSHSY FVNPLFAGAE AEA*

mutated AA sequence

MGVLGRVLLW LQLCALTQAV SKLWVPNTDF DVAANWSQNR IPCAGGAVEF PADKMVSVLV
QEGHAVSDML LPLDGELVLA SGAGFGVSDV GSHLDCGAGE PAVFRDSDRF SWHDPHLWRS
GDEAPGLFFV DAERVPCRHD DVFFPPSASF RVGLGPGASP VRVRSISALG RTFTRDEDLA
VFLASRAGRL RFHGPGALSV GPEDCADPSG CVCGNAEAQP WICAALLQPL GGRCPQAACH
SALRPQGQCC DLCGAVVLLT HGPAFDLERY RARILDTFLG LPQYHGLQVA VSKVPRSSRL
READTEIQVV LVENGPETGG AGRLARALLA DVAENGEALG VLEATMRESG AHVWGSSAAG
LAGGVAAAVL LALLVLLVAP PLLRRAGRLR WRRHEAAAPA GAPLGFRNPV FDVTASEELP
LPRRLSLVPK AAADSTSHSY FVNPLFAGAE AEA*

speed

0.71 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