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: ENST00000264914
MT speed 0 s - this script 2.402378 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ARSB	disease_causing_automatic	0.99999782851616	simple_aae		affected	0	C405Y	single base exchange	rs118203941		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999782851616 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM920109)
known disease mutation: rs880 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:78077797C>TN/A show variant in all transcripts IGV

HGNC symbol

ARSB

Ensembl transcript ID

ENST00000264914

Genbank transcript ID

NM_000046

UniProt peptide

P15848

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1214G>A
cDNA.1751G>A
g.204114G>A

AA changes

C405Y Score: 194 explain score(s)

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

405

frameshift

known variant

Reference ID: rs118203941

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

known disease mutation: rs880 (pathogenic for Mucopolysaccharidosis type 6|Metachromatic leukodystrophy|Mucopolysaccharidosis, type vi, severe|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920109)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920109)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920109)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.301	0.998
	2.967	1
(flanking)	2.069	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
Acceptor lost	204113.5	sequence motif lost	-	wt: ccca\|GGTC mu: ccca.GATC
Acc marginally increased	204119	wt: 0.7026 / mu: 0.7278 (marginal change - not scored)	wt: ACTATTTCTTCCCAGGTCCCAGGAACAGCATGGCTCCAGCA mu: ACTATTTCTTCCCAGATCCCAGGAACAGCATGGCTCCAGCA	ccca\|GGAA
Acc marginally increased	204111	wt: 0.7959 / mu: 0.8366 (marginal change - not scored)	wt: TCTTTCAAACTATTTCTTCCCAGGTCCCAGGAACAGCATGG mu: TCTTTCAAACTATTTCTTCCCAGATCCCAGGAACAGCATGG	tccc\|AGGT
Donor marginally increased	204119	wt: 0.9100 / mu: 0.9332 (marginal change - not scored)	wt: GTCCCAGGAACAGCA mu: ATCCCAGGAACAGCA	CCCA\|ggaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

405

mutated

not conserved

405

Ptroglodytes

all identical

ENSPTRG00000017019

407

Mmulatta

all identical

ENSMMUG00000006792

406

Fcatus

not conserved

ENSFCAG00000011879

407

Mmusculus

all identical

ENSMUSG00000042082

406

Ggallus

all identical

ENSGALG00000004438

398

Trubripes

all identical

ENSTRUG00000003412

385

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000000542

399

protein features

start (aa)	end (aa)	feature	details
405	405	DISULFID		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1602 / 1602

position (AA) of stopcodon in wt / mu AA sequence

534 / 534

position of stopcodon in wt / mu cDNA

2139 / 2139

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

538 / 538

chromosome

strand

-1

last intron/exon boundary

1874

theoretical NMD boundary in CDS

1286

length of CDS

1602

coding sequence (CDS) position

1214

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

1751

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

204114

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

78077797

original gDNA sequence snippet

TTCAAACTATTTCTTCCCAGGTCCCAGGAACAGCATGGCTC

altered gDNA sequence snippet

TTCAAACTATTTCTTCCCAGATCCCAGGAACAGCATGGCTC

original cDNA sequence snippet

CTTCGTGGACTCTTCACCGTGTCCCAGGAACAGCATGGCTC

altered cDNA sequence snippet

CTTCGTGGACTCTTCACCGTATCCCAGGAACAGCATGGCTC

wildtype AA sequence

MGPRGAASLP RGPGPRRLLL PVVLPLLLLL LLAPPGSGAG ASRPPHLVFL LADDLGWNDV
GFHGSRIRTP HLDALAAGGV LLDNYYTQPL CTPSRSQLLT GRYQIRTGLQ HQIIWPCQPS
CVPLDEKLLP QLLKEAGYTT HMVGKWHLGM YRKECLPTRR GFDTYFGYLL GSEDYYSHER
CTLIDALNVT RCALDFRDGE EVATGYKNMY STNIFTKRAI ALITNHPPEK PLFLYLALQS
VHEPLQVPEE YLKPYDFIQD KNRHHYAGMV SLMDEAVGNV TAALKSSGLW NNTVFIFSTD
NGGQTLAGGN NWPLRGRKWS LWEGGVRGVG FVASPLLKQK GVKNRELIHI SDWLPTLVKL
ARGHTNGTKP LDGFDVWKTI SEGSPSPRIE LLHNIDPNFV DSSPCPRNSM APAKDDSSLP
EYSAFNTSVH AAIRHGNWKL LTGYPGCGYW FPPPSQYNVS EIPSSDPPTK TLWLFDIDRD
PEERHDLSRE YPHIVTKLLS RLQFYHKHSV PVYFPAQDPR CDPKATGVWG PWM*

mutated AA sequence

MGPRGAASLP RGPGPRRLLL PVVLPLLLLL LLAPPGSGAG ASRPPHLVFL LADDLGWNDV
GFHGSRIRTP HLDALAAGGV LLDNYYTQPL CTPSRSQLLT GRYQIRTGLQ HQIIWPCQPS
CVPLDEKLLP QLLKEAGYTT HMVGKWHLGM YRKECLPTRR GFDTYFGYLL GSEDYYSHER
CTLIDALNVT RCALDFRDGE EVATGYKNMY STNIFTKRAI ALITNHPPEK PLFLYLALQS
VHEPLQVPEE YLKPYDFIQD KNRHHYAGMV SLMDEAVGNV TAALKSSGLW NNTVFIFSTD
NGGQTLAGGN NWPLRGRKWS LWEGGVRGVG FVASPLLKQK GVKNRELIHI SDWLPTLVKL
ARGHTNGTKP LDGFDVWKTI SEGSPSPRIE LLHNIDPNFV DSSPYPRNSM APAKDDSSLP
EYSAFNTSVH AAIRHGNWKL LTGYPGCGYW FPPPSQYNVS EIPSSDPPTK TLWLFDIDRD
PEERHDLSRE YPHIVTKLLS RLQFYHKHSV PVYFPAQDPR CDPKATGVWG PWM*

speed

0.34 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