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 2.506364 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AGXT	disease_causing	0.969285724057093	simple_aae		affected		Q282R	single base exchange	rs180177280		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.969285724057093 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM093808)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:241815420A>GN/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.845A>G
cDNA.1232A>G
g.7525A>G

AA changes

Q282R Score: 43 explain score(s)

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

282

frameshift

known variant

Reference ID: rs180177280
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation at this position, please check HGMD for details (HGMD ID CM093808)

known disease mutation at this position, please check HGMD for details (HGMD ID CM093808)
known disease mutation at this position, please check HGMD for details (HGMD ID CM093808)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.261	0.744
	1.377	0.971
(flanking)	4.682	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	7525	sequence motif lost	-	wt: ACAG\|gtgc mu: ACGG.gtgc
Acc increased	7521	wt: 0.59 / mu: 0.73	wt: AGAGCCTGGCCCTCATTGCGGAACAGGTGCATGGGCTGCAC mu: AGAGCCTGGCCCTCATTGCGGAACGGGTGCATGGGCTGCAC	gcgg\|AACA
Acc marginally increased	7519	wt: 0.4298 / mu: 0.4600 (marginal change - not scored)	wt: AGAGAGCCTGGCCCTCATTGCGGAACAGGTGCATGGGCTGC mu: AGAGAGCCTGGCCCTCATTGCGGAACGGGTGCATGGGCTGC	ttgc\|GGAA
Donor lost	7525	0.58	wt: GGAACAGGTGCATGG	AACA\|ggtg
Donor increased	7519	wt: 0.26 / mu: 0.96	wt: CATTGCGGAACAGGT mu: CATTGCGGAACGGGT	TTGC\|ggaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

282

mutated

all conserved

282

Ptroglodytes

not conserved

ENSPTRG00000013113

244

Mmulatta

all identical

ENSMMUG00000023435

304

Fcatus

all identical

ENSFCAG00000010448

282

Mmusculus

all identical

ENSMUSG00000026272

304

Ggallus

not conserved

ENSGALG00000020943

305

Trubripes

all conserved

ENSTRUG00000007149

312

Drerio

not conserved

ENSDARG00000018478

312

Dmelanogaster

not conserved

FBgn0014031

278

Celegans

all conserved

T14D7.1

299

Xtropicalis

all identical

ENSXETG00000012149

305

protein features

start (aa)	end (aa)	feature	details
266	282	HELIX		lost
284	305	HELIX		might get lost (downstream of altered splice site)
309	311	STRAND		might get lost (downstream of altered splice site)
314	316	HELIX		might get lost (downstream of altered splice site)
321	325	STRAND		might get lost (downstream of altered splice site)
332	343	HELIX		might get lost (downstream of altered splice site)
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

845

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

1232

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

7525

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

241815420

original gDNA sequence snippet

CCTGGCCCTCATTGCGGAACAGGTGCATGGGCTGCACTCCA

altered gDNA sequence snippet

CCTGGCCCTCATTGCGGAACGGGTGCATGGGCTGCACTCCA

original cDNA sequence snippet

CCTGGCCCTCATTGCGGAACAGGGCCTGGAGAACAGCTGGC

altered cDNA sequence snippet

CCTGGCCCTCATTGCGGAACGGGGCCTGGAGAACAGCTGGC

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 ERGLENSWRQ HREAAAYLHG
RLQALGLQLF VKDPALRLPT VTTVAVPAGY DWRDIVSYVI DHFDIEIMGG LGPSTGKVLR
IGLLGCNATR ENVDRVTEAL RAALQHCPKK KL*

speed

0.49 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
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MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

Problems