MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000264914
Querying Taster for transcript #2: ENST00000396151
Querying Taster for transcript #3: ENST00000565165
MT speed 0 s - this script 3.078993 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ARSB	disease_causing_automatic	0.999999969553137	simple_aae			0	R95Q	single base exchange	rs118203942		show file
ARSB	disease_causing_automatic	0.999999969553137	simple_aae			0	R95Q	single base exchange	rs118203942		show file
ARSB	disease_causing_automatic	0.999999969553137	simple_aae			0	R95Q	single base exchange	rs118203942		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999969553137 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960080)
known disease mutation: rs884 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:78280788C>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.284G>A
cDNA.821G>A
g.1123G>A

AA changes

R95Q Score: 43 explain score(s)

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

frameshift

known variant

Reference ID: rs118203942
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs884 (pathogenic for Mucopolysaccharidosis type 6|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960080)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960080)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960080)

regulatory features

Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
Egr1, Transcription Factor, Egr1 Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Znf263, Transcription Factor, Znf263 TF binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.021	0.994
	5.685	1
(flanking)	1.865	1

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 marginally increased	1125	wt: 0.8697 / mu: 0.8933 (marginal change - not scored)	wt: CGCGGAGCCAGCTGC mu: CGCAGAGCCAGCTGC	CGGA\|gcca
Donor marginally increased	1120	wt: 0.8569 / mu: 0.8685 (marginal change - not scored)	wt: GCCGTCGCGGAGCCA mu: GCCGTCGCAGAGCCA	CGTC\|gcgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000017019

Mmulatta

all identical

ENSMMUG00000006792

Fcatus

all identical

ENSFCAG00000011879

Mmusculus

all identical

ENSMUSG00000042082

Ggallus

all identical

ENSGALG00000004438

Trubripes

all identical

ENSTRUG00000003412

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000000542

protein features

start (aa)	end (aa)	feature	details
93	100	HELIX		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

284

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

821

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

1123

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

78280788

original gDNA sequence snippet

GCCGCTGTGCACGCCGTCGCGGAGCCAGCTGCTCACTGGCC

altered gDNA sequence snippet

GCCGCTGTGCACGCCGTCGCAGAGCCAGCTGCTCACTGGCC

original cDNA sequence snippet

GCCGCTGTGCACGCCGTCGCGGAGCCAGCTGCTCACTGGCC

altered cDNA sequence snippet

GCCGCTGTGCACGCCGTCGCAGAGCCAGCTGCTCACTGGCC

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 CTPSQSQLLT 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*

speed

0.33 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

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999969553137 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960080)
known disease mutation: rs884 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:78280788C>TN/A show variant in all transcripts IGV

HGNC symbol

ARSB

Ensembl transcript ID

ENST00000396151

Genbank transcript ID

NM_198709

UniProt peptide

P15848

alteration type

single base exchange

alteration region

CDS

DNA changes

c.284G>A
cDNA.783G>A
g.1123G>A

AA changes

R95Q Score: 43 explain score(s)

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

frameshift

known variant

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.021	0.994
	5.685	1
(flanking)	1.865	1

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 marginally increased	1125	wt: 0.8697 / mu: 0.8933 (marginal change - not scored)	wt: CGCGGAGCCAGCTGC mu: CGCAGAGCCAGCTGC	CGGA\|gcca
Donor marginally increased	1120	wt: 0.8569 / mu: 0.8685 (marginal change - not scored)	wt: GCCGTCGCGGAGCCA mu: GCCGTCGCAGAGCCA	CGTC\|gcgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000017019

Mmulatta

all identical

ENSMMUG00000006792

Fcatus

all identical

ENSFCAG00000011879

Mmusculus

all identical

ENSMUSG00000042082

Ggallus

all identical

ENSGALG00000004438

Trubripes

all identical

ENSTRUG00000003412

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000000542

protein features

start (aa)	end (aa)	feature	details
93	100	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1242 / 1242

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

414 / 414

position of stopcodon in wt / mu cDNA

1741 / 1741

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

500 / 500

chromosome

strand

-1

last intron/exon boundary

1713

theoretical NMD boundary in CDS

1163

length of CDS

1242

coding sequence (CDS) position

284

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

783

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

1123

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

78280788

original gDNA sequence snippet

GCCGCTGTGCACGCCGTCGCGGAGCCAGCTGCTCACTGGCC

altered gDNA sequence snippet

GCCGCTGTGCACGCCGTCGCAGAGCCAGCTGCTCACTGGCC

original cDNA sequence snippet

GCCGCTGTGCACGCCGTCGCGGAGCCAGCTGCTCACTGGCC

altered cDNA sequence snippet

GCCGCTGTGCACGCCGTCGCAGAGCCAGCTGCTCACTGGCC

wildtype AA sequence

mutated AA sequence

speed

0.78 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999969553137 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960080)
known disease mutation: rs884 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:78280788C>TN/A show variant in all transcripts IGV

HGNC symbol

ARSB

Ensembl transcript ID

ENST00000565165

Genbank transcript ID

N/A

UniProt peptide

P15848

alteration type

single base exchange

alteration region

CDS

DNA changes

c.284G>A
cDNA.783G>A
g.1123G>A

AA changes

R95Q Score: 43 explain score(s)

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

frameshift

known variant

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.021	0.994
	5.685	1
(flanking)	1.865	1

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 marginally increased	1125	wt: 0.8697 / mu: 0.8933 (marginal change - not scored)	wt: CGCGGAGCCAGCTGC mu: CGCAGAGCCAGCTGC	CGGA\|gcca
Donor marginally increased	1120	wt: 0.8569 / mu: 0.8685 (marginal change - not scored)	wt: GCCGTCGCGGAGCCA mu: GCCGTCGCAGAGCCA	CGTC\|gcgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000017019

Mmulatta

all identical

ENSMMUG00000006792

Fcatus

all identical

ENSFCAG00000011879

Mmusculus

all identical

ENSMUSG00000042082

Ggallus

all identical

ENSGALG00000004438

Trubripes

all identical

ENSTRUG00000003412

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000000542

protein features

start (aa)	end (aa)	feature	details
93	100	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1242 / 1242

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

414 / 414

position of stopcodon in wt / mu cDNA

1741 / 1741

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

500 / 500

chromosome

strand

-1

last intron/exon boundary

1713

theoretical NMD boundary in CDS

1163

length of CDS

1242

coding sequence (CDS) position

284

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

783

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

1123

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

78280788

original gDNA sequence snippet

GCCGCTGTGCACGCCGTCGCGGAGCCAGCTGCTCACTGGCC

altered gDNA sequence snippet

GCCGCTGTGCACGCCGTCGCAGAGCCAGCTGCTCACTGGCC

original cDNA sequence snippet

GCCGCTGTGCACGCCGTCGCGGAGCCAGCTGCTCACTGGCC

altered cDNA sequence snippet

GCCGCTGTGCACGCCGTCGCAGAGCCAGCTGCTCACTGGCC

wildtype AA sequence

mutated AA sequence

speed

0.22 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems