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 4.555409 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ARSB	disease_causing_automatic	0.99999980434763	simple_aae			0	Y210C	single base exchange	rs118203943		show file
ARSB	disease_causing_automatic	0.99999980434763	simple_aae			0	Y210C	single base exchange	rs118203943		show file
ARSB	disease_causing_automatic	0.99999980434763	simple_aae			0	Y210C	single base exchange	rs118203943		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999980434763 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
heterozygous in TGP or ExAC
known disease mutation at this position (HGMD CM960081)
known disease mutation: rs885 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:78260300T>CN/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.629A>G
cDNA.1166A>G
g.21611A>G

AA changes

Y210C Score: 194 explain score(s)

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

210

frameshift

known variant

Reference ID: rs118203943

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	48	48

known disease mutation: rs885 (pathogenic for Mucopolysaccharidosis type 6|Metachromatic leukodystrophy|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960081)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960081)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960081)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.183	0.998
	4.417	1
(flanking)	4.417	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	21616	wt: 0.8597 / mu: 0.8619 (marginal change - not scored)	wt: ATTCAACAAACATAT mu: GTTCAACAAACATAT	TCAA\|caaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

210

mutated

not conserved

210

Ptroglodytes

all identical

ENSPTRG00000017019

212

Mmulatta

all identical

ENSMMUG00000006792

211

Fcatus

no alignment

ENSFCAG00000011879

n/a

Mmusculus

all identical

ENSMUSG00000042082

211

Ggallus

all identical

ENSGALG00000004438

203

Trubripes

all identical

ENSTRUG00000003412

190

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000000542

204

protein features

no protein features affected

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

629

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

1166

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

21611

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

78260300

original gDNA sequence snippet

AACAGGATATAAAAATATGTATTCAACAAACATATTCACCA

altered gDNA sequence snippet

AACAGGATATAAAAATATGTGTTCAACAAACATATTCACCA

original cDNA sequence snippet

AACAGGATATAAAAATATGTATTCAACAAACATATTCACCA

altered cDNA sequence snippet

AACAGGATATAAAAATATGTGTTCAACAAACATATTCACCA

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 EVATGYKNMC 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

1.20 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: 0.99999980434763 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
heterozygous in TGP or ExAC
known disease mutation at this position (HGMD CM960081)
known disease mutation: rs885 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:78260300T>CN/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.629A>G
cDNA.1128A>G
g.21611A>G

AA changes

Y210C Score: 194 explain score(s)

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

210

frameshift

known variant

Reference ID: rs118203943

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	48	48

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.183	0.998
	4.417	1
(flanking)	4.417	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	21616	wt: 0.8597 / mu: 0.8619 (marginal change - not scored)	wt: ATTCAACAAACATAT mu: GTTCAACAAACATAT	TCAA\|caaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

210

mutated

not conserved

210

Ptroglodytes

all identical

ENSPTRG00000017019

212

Mmulatta

all identical

ENSMMUG00000006792

211

Fcatus

no alignment

ENSFCAG00000011879

n/a

Mmusculus

all identical

ENSMUSG00000042082

211

Ggallus

all identical

ENSGALG00000004438

203

Trubripes

all identical

ENSTRUG00000003412

190

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000000542

204

protein features

no protein features affected

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

629

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

1128

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

21611

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

78260300

original gDNA sequence snippet

AACAGGATATAAAAATATGTATTCAACAAACATATTCACCA

altered gDNA sequence snippet

AACAGGATATAAAAATATGTGTTCAACAAACATATTCACCA

original cDNA sequence snippet

AACAGGATATAAAAATATGTATTCAACAAACATATTCACCA

altered cDNA sequence snippet

AACAGGATATAAAAATATGTGTTCAACAAACATATTCACCA

wildtype AA sequence

mutated AA sequence

MGPRGAASLP RGPGPRRLLL PVVLPLLLLL LLAPPGSGAG ASRPPHLVFL LADDLGWNDV
GFHGSRIRTP HLDALAAGGV LLDNYYTQPL CTPSRSQLLT GRYQIRTGLQ HQIIWPCQPS
CVPLDEKLLP QLLKEAGYTT HMVGKWHLGM YRKECLPTRR GFDTYFGYLL GSEDYYSHER
CTLIDALNVT RCALDFRDGE EVATGYKNMC STNIFTKRAI ALITNHPPEK PLFLYLALQS
VHEPLQVPEE YLKPYDFIQD KNRHHYAGMV SLMDEAVGNV TAALKSSGLW NNTVFIFSTD
NGGQTLAGGN NWPLRGRKWS LWEGGVRGVG FVASPLLKQK GVKNRELIHI SDWLPTLVKL
ARGHTNGTKP LDGFDVWKTI SEGSPSPRIE LLHNIDPNFV DSSPYWPECS LLL*

speed

1.32 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999980434763 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
heterozygous in TGP or ExAC
known disease mutation at this position (HGMD CM960081)
known disease mutation: rs885 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:78260300T>CN/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.629A>G
cDNA.1128A>G
g.21611A>G

AA changes

Y210C Score: 194 explain score(s)

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

210

frameshift

known variant

Reference ID: rs118203943

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	48	48

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.183	0.998
	4.417	1
(flanking)	4.417	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	21616	wt: 0.8597 / mu: 0.8619 (marginal change - not scored)	wt: ATTCAACAAACATAT mu: GTTCAACAAACATAT	TCAA\|caaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

210

mutated

not conserved

210

Ptroglodytes

all identical

ENSPTRG00000017019

212

Mmulatta

all identical

ENSMMUG00000006792

211

Fcatus

no alignment

ENSFCAG00000011879

n/a

Mmusculus

all identical

ENSMUSG00000042082

211

Ggallus

all identical

ENSGALG00000004438

203

Trubripes

all identical

ENSTRUG00000003412

190

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000000542

204

protein features

no protein features affected

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

629

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

1128

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

21611

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

78260300

original gDNA sequence snippet

AACAGGATATAAAAATATGTATTCAACAAACATATTCACCA

altered gDNA sequence snippet

AACAGGATATAAAAATATGTGTTCAACAAACATATTCACCA

original cDNA sequence snippet

AACAGGATATAAAAATATGTATTCAACAAACATATTCACCA

altered cDNA sequence snippet

AACAGGATATAAAAATATGTGTTCAACAAACATATTCACCA

wildtype AA sequence

mutated AA sequence

MGPRGAASLP RGPGPRRLLL PVVLPLLLLL LLAPPGSGAG ASRPPHLVFL LADDLGWNDV
GFHGSRIRTP HLDALAAGGV LLDNYYTQPL CTPSRSQLLT GRYQIRTGLQ HQIIWPCQPS
CVPLDEKLLP QLLKEAGYTT HMVGKWHLGM YRKECLPTRR GFDTYFGYLL GSEDYYSHER
CTLIDALNVT RCALDFRDGE EVATGYKNMC STNIFTKRAI ALITNHPPEK PLFLYLALQS
VHEPLQVPEE YLKPYDFIQD KNRHHYAGMV SLMDEAVGNV TAALKSSGLW NNTVFIFSTD
NGGQTLAGGN NWPLRGRKWS LWEGGVRGVG FVASPLLKQK GVKNRELIHI SDWLPTLVKL
ARGHTNGTKP LDGFDVWKTI SEGSPSPRIE LLHNIDPNFV DSSPYWPECS LLL*

speed

1.27 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