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: ENST00000307503
MT speed 0 s - this script 3.086421 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AGXT	disease_causing	0.999999999833813	simple_aae				R360Q	single base exchange	rs180177161		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999833813 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs204147 (probable pathogenic)
known disease mutation at this position (HGMD CM093814)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:241818138G>AN/A show variant in all transcripts IGV

HGNC symbol

AGXT

Ensembl transcript ID

ENST00000307503

Genbank transcript ID

NM_000030

UniProt peptide

P21549

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1079G>A
cDNA.1466G>A
g.10243G>A

AA changes

R360Q Score: 43 explain score(s)

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

360

frameshift

known variant

Reference ID: rs180177161
Allele 'A' was neither found in ExAC nor 1000G.
known as potential disease variant: rs204147 (probable pathogenic for Primary hyperoxaluria, type I) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM093814)

known disease mutation at this position, please check HGMD for details (HGMD ID CM093814)
known disease mutation at this position, please check HGMD for details (HGMD ID CM093814)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.507	0.998
	3.747	1
(flanking)	0.279	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 marginally decreased	10235	wt: 0.9049 / mu: 0.8255 (marginal change - not scored)	wt: AGCCCGCCCTGTGCCCCCCAGGTGCTGCGGATCGGCCTGCT mu: AGCCCGCCCTGTGCCCCCCAGGTGCTGCAGATCGGCCTGCT	ccag\|GTGC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

360

mutated

all conserved

360

Ptroglodytes

all identical

ENSPTRG00000013113

280

Mmulatta

all identical

ENSMMUG00000023435

382

Fcatus

all identical

ENSFCAG00000010448

360

Mmusculus

all identical

ENSMUSG00000026272

382

Ggallus

all identical

ENSGALG00000020943

383

Trubripes

all identical

ENSTRUG00000007149

391

Drerio

all identical

ENSDARG00000018478

391

Dmelanogaster

all identical

FBgn0014031

356

Celegans

all identical

T14D7.1

377

Xtropicalis

all identical

ENSXETG00000012149

383

protein features

start (aa)	end (aa)	feature	details
358	362	STRAND		lost
360	360	BINDING	Substrate.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1179 / 1179

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

393 / 393

position of stopcodon in wt / mu cDNA

1566 / 1566

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

388 / 388

chromosome

strand

last intron/exon boundary

1459

theoretical NMD boundary in CDS

1021

length of CDS

1179

coding sequence (CDS) position

1079

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

1466

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

10243

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

241818138

original gDNA sequence snippet

CTGTGCCCCCCAGGTGCTGCGGATCGGCCTGCTGGGCTGCA

altered gDNA sequence snippet

CTGTGCCCCCCAGGTGCTGCAGATCGGCCTGCTGGGCTGCA

original cDNA sequence snippet

CTCCACGGGGAAGGTGCTGCGGATCGGCCTGCTGGGCTGCA

altered cDNA sequence snippet

CTCCACGGGGAAGGTGCTGCAGATCGGCCTGCTGGGCTGCA

wildtype AA sequence

MASHKLLVTP PKALLKPLSI PNQLLLGPGP SNLPPRIMAA GGLQMIGSMS KDMYQIMDEI
KEGIQYVFQT RNPLTLVISG SGHCALEAAL VNVLEPGDSF LVGANGIWGQ RAVDIGERIG
ARVHPMTKDP GGHYTLQEVE EGLAQHKPVL LFLTHGESST GVLQPLDGFG ELCHRYKCLL
LVDSVASLGG TPLYMDRQGI DILYSGSQKA LNAPPGTSLI SFSDKAKKKM YSRKTKPFSF
YLDIKWLANF WGCDDQPRMY HHTIPVISLY SLRESLALIA EQGLENSWRQ HREAAAYLHG
RLQALGLQLF VKDPALRLPT VTTVAVPAGY DWRDIVSYVI DHFDIEIMGG LGPSTGKVLR
IGLLGCNATR ENVDRVTEAL RAALQHCPKK KL*

mutated AA sequence

speed

0.89 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