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 2.477814 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AGXT	disease_causing_automatic	0.99989353804393	simple_aae		affected	0	G41R	single base exchange	rs121908523		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99989353804393 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM1615662)
known disease mutation at this position (HGMD CM930013)
known disease mutation: rs5644 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:241808403G>AN/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.121G>A
cDNA.508G>A
g.508G>A

AA changes

G41R Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs121908523

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

known disease mutation: rs5644 (pathogenic for Nephrolithiasis|Nephrocalcinosis|Primary hyperoxaluria, type I|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM1615662)

known disease mutation at this position, please check HGMD for details (HGMD ID CM1615662)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930013)

known disease mutation at this position, please check HGMD for details (HGMD ID CM1615662)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930013)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930013)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
TAF1, Transcription Factor, TAF1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.552	0.048
	2.673	0.496
(flanking)	2.716	0.496

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	504	wt: 0.74 / mu: 0.94	wt: ATGGCAGCCGGGGGG mu: ATGGCAGCCAGGGGG	GGCA\|gccg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000013113

Mmulatta

all identical

ENSMMUG00000023435

Fcatus

all identical

ENSFCAG00000010448

Mmusculus

all identical

ENSMUSG00000026272

Ggallus

all identical

ENSGALG00000020943

Trubripes

all identical

ENSTRUG00000007149

Drerio

all identical

ENSDARG00000018478

Dmelanogaster

not conserved

FBgn0014031

Celegans

not conserved

T14D7.1

Xtropicalis

all identical

ENSXETG00000012149

protein features

start (aa)	end (aa)	feature	details
35	40	HELIX		might get lost (downstream of altered splice site)
51	68	HELIX		might get lost (downstream of altered splice site)
73	80	STRAND		might get lost (downstream of altered splice site)
82	93	HELIX		might get lost (downstream of altered splice site)
100	106	STRAND		might get lost (downstream of altered splice site)
107	118	HELIX		might get lost (downstream of altered splice site)
123	127	STRAND		might get lost (downstream of altered splice site)
136	146	HELIX		might get lost (downstream of altered splice site)
149	157	STRAND		might get lost (downstream of altered splice site)
158	161	TURN		might get lost (downstream of altered splice site)
169	175	HELIX		might get lost (downstream of altered splice site)
179	183	STRAND		might get lost (downstream of altered splice site)
185	190	TURN		might get lost (downstream of altered splice site)
195	199	TURN		might get lost (downstream of altered splice site)
201	209	STRAND		might get lost (downstream of altered splice site)
209	209	MUTAGEN	K->R: Affects pyridoxal phosphate binding.	might get lost (downstream of altered splice site)
209	209	MOD_RES	N6-(pyridoxal phosphate)lysine.	might get lost (downstream of altered splice site)
218	222	STRAND		might get lost (downstream of altered splice site)
224	232	HELIX		might get lost (downstream of altered splice site)
244	250	HELIX		might get lost (downstream of altered splice site)
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

121

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

508

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

508

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

241808403

original gDNA sequence snippet

CTCCTCGCATCATGGCAGCCGGGGGGCTGCAGATGATCGGG

altered gDNA sequence snippet

CTCCTCGCATCATGGCAGCCAGGGGGCTGCAGATGATCGGG

original cDNA sequence snippet

CTCCTCGCATCATGGCAGCCGGGGGGCTGCAGATGATCGGG

altered cDNA sequence snippet

CTCCTCGCATCATGGCAGCCAGGGGGCTGCAGATGATCGGG

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 RGLQMIGSMS 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*

speed

0.36 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