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 2.681905 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AGXT	disease_causing_automatic	0.0581556465579034	simple_aae		affected	0	I244T	single base exchange	rs121908525		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.0581556465579034 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM970066)
known disease mutation: rs5646 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:241814576T>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.731T>C
cDNA.1118T>C
g.6681T>C

AA changes

I244T Score: 89 explain score(s)

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

244

frameshift

known variant

Reference ID: rs121908525

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	4	4

known disease mutation: rs5646 (pathogenic for Nephrolithiasis|Nephrocalcinosis|Primary hyperoxaluria|Primary hyperoxaluria, type I|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970066)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970066)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970066)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.158	0.554
	3.763	0.571
(flanking)	-0.067	0.268

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	6676	wt: 0.8245 / mu: 0.8981 (marginal change - not scored)	wt: AAGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCAA mu: AAGCCCTTCTCCTTCTACCTGGACACCAAGTGGCTGGCCAA	cctg\|GACA
Acc marginally increased	6672	wt: 0.5402 / mu: 0.5899 (marginal change - not scored)	wt: GACGAAGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGG mu: GACGAAGCCCTTCTCCTTCTACCTGGACACCAAGTGGCTGG	tcta\|CCTG
Acc marginally increased	6675	wt: 0.9694 / mu: 0.9754 (marginal change - not scored)	wt: GAAGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCA mu: GAAGCCCTTCTCCTTCTACCTGGACACCAAGTGGCTGGCCA	acct\|GGAC
Acc marginally increased	6673	wt: 0.9557 / mu: 0.9695 (marginal change - not scored)	wt: ACGAAGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGC mu: ACGAAGCCCTTCTCCTTCTACCTGGACACCAAGTGGCTGGC	ctac\|CTGG
Donor marginally increased	6684	wt: 0.6476 / mu: 0.6869 (marginal change - not scored)	wt: CATCAAGTGGCTGGC mu: CACCAAGTGGCTGGC	TCAA\|gtgg
Donor gained	6676	0.38	mu: TACCTGGACACCAAG	CCTG\|gaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

244

mutated

not conserved

244

Ptroglodytes

not conserved

ENSPTRG00000013113

206

Mmulatta

all identical

ENSMMUG00000023435

266

Fcatus

not conserved

ENSFCAG00000010448

244

Mmusculus

all identical

ENSMUSG00000026272

266

Ggallus

all conserved

ENSGALG00000020943

267

Trubripes

all conserved

ENSTRUG00000007149

274

Drerio

all conserved

ENSDARG00000018478

274

Dmelanogaster

all identical

FBgn0014031

240

Celegans

not conserved

T14D7.1

261

Xtropicalis

all conserved

ENSXETG00000012149

267

protein features

start (aa)	end (aa)	feature	details
244	250	HELIX		lost
254	256	STRAND		might get lost (downstream of altered splice site)
266	282	HELIX		might get lost (downstream of altered splice site)
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

731

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

1118

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

6681

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

241814576

original gDNA sequence snippet

CTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCAACTTCT

altered gDNA sequence snippet

CTTCTCCTTCTACCTGGACACCAAGTGGCTGGCCAACTTCT

original cDNA sequence snippet

CTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCAACTTCT

altered cDNA sequence snippet

CTTCTCCTTCTACCTGGACACCAAGTGGCTGGCCAACTTCT

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
YLDTKWLANF WGCDDQPRMY HHTIPVISLY SLRESLALIA EQGLENSWRQ HREAAAYLHG
RLQALGLQLF VKDPALRLPT VTTVAVPAGY DWRDIVSYVI DHFDIEIMGG LGPSTGKVLR
IGLLGCNATR ENVDRVTEAL RAALQHCPKK KL*

speed

0.62 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