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 2.485979 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AGXT	disease_causing_automatic	0.999510901883266	simple_aae			0	S205P	single base exchange	rs121908520		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999510901883266 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM910017)
known disease mutation: rs5640 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:241813412T>CN/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.613T>C
cDNA.1000T>C
g.5517T>C

AA changes

S205P Score: 74 explain score(s)

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

205

frameshift

known variant

Reference ID: rs121908520
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs5640 (pathogenic for Primary hyperoxaluria, type I|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910017)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910017)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910017)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
HNF4A, Transcription Factor, HNF4A Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.305	1
	0.243	0.998
(flanking)	3.415	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 marginally increased	5518	wt: 0.3744 / mu: 0.3865 (marginal change - not scored)	wt: AGGCATCGACATCCTGTACTCGGGCTCCCAGAAGGCCCTGA mu: AGGCATCGACATCCTGTACCCGGGCTCCCAGAAGGCCCTGA	actc\|GGGC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

205

mutated

not conserved

205

Ptroglodytes

all identical

ENSPTRG00000013113

181

Mmulatta

all identical

ENSMMUG00000023435

227

Fcatus

all identical

ENSFCAG00000010448

205

Mmusculus

all identical

ENSMUSG00000026272

227

Ggallus

all conserved

ENSGALG00000020943

228

Trubripes

all conserved

ENSTRUG00000007149

235

Drerio

all conserved

ENSDARG00000018478

235

Dmelanogaster

all conserved

FBgn0014031

201

Celegans

all identical

T14D7.1

222

Xtropicalis

all identical

ENSXETG00000012149

228

protein features

start (aa)	end (aa)	feature	details
201	209	STRAND		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

613

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

1000

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

5517

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

241813412

original gDNA sequence snippet

CAGGCATCGACATCCTGTACTCGGGCTCCCAGAAGGCCCTG

altered gDNA sequence snippet

CAGGCATCGACATCCTGTACCCGGGCTCCCAGAAGGCCCTG

original cDNA sequence snippet

AAGGCATCGACATCCTGTACTCGGGCTCCCAGAAGGCCCTG

altered cDNA sequence snippet

AAGGCATCGACATCCTGTACCCGGGCTCCCAGAAGGCCCTG

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 DILYPGSQKA LNAPPGTSLI SFSDKAKKKM YSRKTKPFSF
YLDIKWLANF WGCDDQPRMY HHTIPVISLY SLRESLALIA EQGLENSWRQ HREAAAYLHG
RLQALGLQLF VKDPALRLPT VTTVAVPAGY DWRDIVSYVI DHFDIEIMGG LGPSTGKVLR
IGLLGCNATR ENVDRVTEAL RAALQHCPKK KL*

speed

0.47 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