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 2.422225 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AGXT	disease_causing_automatic	0.99999999998691	simple_aae			0	W108R	single base exchange	rs180177197		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999999998691 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM983924)
known disease mutation: rs188891 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:241808743T>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.322T>C
cDNA.709T>C
g.848T>C

AA changes

W108R Score: 101 explain score(s)

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

108

frameshift

known variant

Reference ID: rs180177197

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs188891 (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 CM983924)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983924)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983924)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.479	1
	4.194	1
(flanking)	5.063	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

108

mutated

not conserved

108

Ptroglodytes

all identical

ENSPTRG00000013113

108

Mmulatta

all identical

ENSMMUG00000023435

130

Fcatus

all identical

ENSFCAG00000010448

108

Mmusculus

all identical

ENSMUSG00000026272

130

Ggallus

all identical

ENSGALG00000020943

132

Trubripes

all identical

ENSTRUG00000007149

138

Drerio

all identical

ENSDARG00000018478

138

Dmelanogaster

all identical

FBgn0014031

103

Celegans

all identical

T14D7.1

125

Xtropicalis

all identical

ENSXETG00000012149

131

protein features

start (aa)	end (aa)	feature	details
107	118	HELIX		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

322

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

709

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

848

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

241808743

original gDNA sequence snippet

TGGTTGGGGCCAATGGCATTTGGGGGCAGCGAGCCGTGGAC

altered gDNA sequence snippet

TGGTTGGGGCCAATGGCATTCGGGGGCAGCGAGCCGTGGAC

original cDNA sequence snippet

TGGTTGGGGCCAATGGCATTTGGGGGCAGCGAGCCGTGGAC

altered cDNA sequence snippet

TGGTTGGGGCCAATGGCATTCGGGGGCAGCGAGCCGTGGAC

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 LVGANGIRGQ 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*

speed

0.45 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