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 3.232985 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AGXT	disease_causing_automatic	0.00773852397071229	simple_aae		affected	0	V336D	single base exchange	rs180177155		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.00773852397071229 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM042937)
known disease mutation: rs204143 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:241817503T>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.1007T>A
cDNA.1394T>A
g.9608T>A

AA changes

V336D Score: 152 explain score(s)

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

336

frameshift

known variant

Reference ID: rs180177155
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs204143 (pathogenic for Primary hyperoxaluria, type I) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM042937)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042937)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042937)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.458	0.145
	0.736	0.096
(flanking)	0.042	0.019

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
Donor marginally increased	9610	wt: 0.9984 / mu: 0.9986 (marginal change - not scored)	wt: TCGTCAGCTACGTCA mu: TCGACAGCTACGTCA	GTCA\|gcta
Donor increased	9600	wt: 0.39 / mu: 0.57	wt: TGGAGAGACATCGTC mu: TGGAGAGACATCGAC	GAGA\|gaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

336

mutated

not conserved

336

Ptroglodytes

all identical

ENSPTRG00000013113

256

Mmulatta

all identical

ENSMMUG00000023435

358

Fcatus

all identical

ENSFCAG00000010448

336

Mmusculus

all identical

ENSMUSG00000026272

358

Ggallus

not conserved

ENSGALG00000020943

359

Trubripes

all conserved

ENSTRUG00000007149

367

Drerio

all conserved

ENSDARG00000018478

367

Dmelanogaster

not conserved

FBgn0014031

332

Celegans

not conserved

T14D7.1

353

Xtropicalis

not conserved

ENSXETG00000012149

359

protein features

start (aa)	end (aa)	feature	details
332	343	HELIX		lost
352	354	HELIX		might get lost (downstream of altered splice site)
355	357	TURN		might get lost (downstream of altered splice site)
358	362	STRAND		might get lost (downstream of altered splice site)
360	360	BINDING	Substrate.	might get lost (downstream of altered splice site)
365	367	HELIX		might get lost (downstream of altered splice site)
370	386	HELIX		might get lost (downstream of altered splice site)

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

1007

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

1394

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

9608

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

241817503

original gDNA sequence snippet

CTATGACTGGAGAGACATCGTCAGCTACGTCATAGACCACT

altered gDNA sequence snippet

CTATGACTGGAGAGACATCGACAGCTACGTCATAGACCACT

original cDNA sequence snippet

CTATGACTGGAGAGACATCGTCAGCTACGTCATAGACCACT

altered cDNA sequence snippet

CTATGACTGGAGAGACATCGACAGCTACGTCATAGACCACT

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

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 DWRDIDSYVI DHFDIEIMGG LGPSTGKVLR
IGLLGCNATR ENVDRVTEAL RAALQHCPKK KL*

speed

1.21 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