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 2.477346 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AGXT	disease_causing	0.9999770209694	simple_aae		affected		R289C	single base exchange	rs180177290		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.9999770209694 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM993608)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:241816972C>TN/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.865C>T
cDNA.1252C>T
g.9077C>T

AA changes

R289C Score: 180 explain score(s)

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

289

frameshift

known variant

Reference ID: rs180177290

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	12	12

known disease mutation at this position, please check HGMD for details (HGMD ID CM993608)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993608)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993608)

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)	3.783	0.998
	0.645	0.743
(flanking)	-0.023	0.362

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 increased	9081	wt: 0.31 / mu: 0.52	wt: GCGCCAGCACCGCGA mu: GTGCCAGCACCGCGA	GCCA\|gcac

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

289

mutated

not conserved

289

Ptroglodytes

not conserved

ENSPTRG00000013113

251

Mmulatta

all identical

ENSMMUG00000023435

311

Fcatus

not conserved

ENSFCAG00000010448

289

Mmusculus

all identical

ENSMUSG00000026272

311

Ggallus

all conserved

ENSGALG00000020943

312

Trubripes

all identical

ENSTRUG00000007149

319

Drerio

all identical

ENSDARG00000018478

319

Dmelanogaster

all identical

FBgn0014031

285

Celegans

all conserved

T14D7.1

306

Xtropicalis

not conserved

ENSXETG00000012149

312

protein features

start (aa)	end (aa)	feature	details
284	305	HELIX		lost
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

865

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

1252

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

9077

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

241816972

original gDNA sequence snippet

AGGGCCTGGAGAACAGCTGGCGCCAGCACCGCGAGGCCGCG

altered gDNA sequence snippet

AGGGCCTGGAGAACAGCTGGTGCCAGCACCGCGAGGCCGCG

original cDNA sequence snippet

AGGGCCTGGAGAACAGCTGGCGCCAGCACCGCGAGGCCGCG

altered cDNA sequence snippet

AGGGCCTGGAGAACAGCTGGTGCCAGCACCGCGAGGCCGCG

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

speed

0.46 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