Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
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 3.723492 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ARSBdisease_causing_automatic0.999989210611541simple_aae0H393Psingle base exchangers118203944show file
ARSBdisease_causing_automatic0.999989210611541simple_aae0H393Psingle base exchangers118203944show file
ARSBdisease_causing_automatic0.999996545142112simple_aae0H393Psingle base exchangers118203944show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999989210611541 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM1513714)
  • known disease mutation at this position (HGMD CM960082)
  • known disease mutation: rs886 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:78135214T>GN/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.1178A>C
cDNA.1677A>C
g.146697A>C
AA changes H393P Score: 77 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 393
frameshift no
known variant Reference ID: rs118203944
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC033

known disease mutation: rs886 (pathogenic for Mucopolysaccharidosis type 6|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960082)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960082)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1513714)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960082)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1513714)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960082)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2280.991
1.7881
(flanking)3.8121
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 36
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      393EGSPSPRIELLHNIDPNFVDSSPY
mutated  not conserved    393EGSPSPRIELLPNIDPNFVDSSP
Ptroglodytes  all identical  ENSPTRG00000017019  395EGSPSPRIELLHNIDPNFVDSSP
Mmulatta  all identical  ENSMMUG00000006792  394EGSPSPRVELLHNIDPNFVDSSP
Fcatus  no alignment  ENSFCAG00000011879  n/a
Mmusculus  all identical  ENSMUSG00000042082  394EGHPSPRVELLHNIDQDFFDGLP
Ggallus  all identical  ENSGALG00000004438  386EGRPSPRVELLHNIDPMFVDDYP
Trubripes  all identical  ENSTRUG00000003412  373KGFASPRLELLHNIDPLYN
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000000542  387EGSPSPRVELLHNIDPLFEDSFP
protein features
start (aa)end (aa)featuredetails 
390396STRANDlost
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 5
strand -1
last intron/exon boundary 1713
theoretical NMD boundary in CDS 1163
length of CDS 1242
coding sequence (CDS) position 1178
cDNA position
(for ins/del: last normal base / first normal base)		 1677
gDNA position
(for ins/del: last normal base / first normal base)		 146697
chromosomal position
(for ins/del: last normal base / first normal base)		 78135214
original gDNA sequence snippet CCCCAGAATTGAGCTGCTGCATAATATTGACCCGAACTTCG
altered gDNA sequence snippet CCCCAGAATTGAGCTGCTGCCTAATATTGACCCGAACTTCG
original cDNA sequence snippet CCCCAGAATTGAGCTGCTGCATAATATTGACCCGAACTTCG
altered cDNA sequence snippet CCCCAGAATTGAGCTGCTGCCTAATATTGACCCGAACTTCG
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 DSSPYWPECS LLL*
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 LLPNIDPNFV DSSPYWPECS LLL*
speed 0.71 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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999989210611541 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM1513714)
  • known disease mutation at this position (HGMD CM960082)
  • known disease mutation: rs886 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:78135214T>GN/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.1178A>C
cDNA.1677A>C
g.146697A>C
AA changes H393P Score: 77 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 393
frameshift no
known variant Reference ID: rs118203944
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC033

known disease mutation: rs886 (pathogenic for Mucopolysaccharidosis type 6|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960082)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960082)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1513714)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960082)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1513714)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960082)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2280.991
1.7881
(flanking)3.8121
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 36
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      393EGSPSPRIELLHNIDPNFVDSSPY
mutated  not conserved    393EGSPSPRIELLPNIDPNFVDSSP
Ptroglodytes  all identical  ENSPTRG00000017019  395EGSPSPRIELLHNIDPNFVDSSP
Mmulatta  all identical  ENSMMUG00000006792  394EGSPSPRVELLHNIDPNFVDSSP
Fcatus  no alignment  ENSFCAG00000011879  n/a
Mmusculus  all identical  ENSMUSG00000042082  394EGHPSPRVELLHNIDQDFFDGLP
Ggallus  all identical  ENSGALG00000004438  386EGRPSPRVELLHNIDPMFVDDYP
Trubripes  all identical  ENSTRUG00000003412  373KGFASPRLELLHNIDPLYN
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000000542  387EGSPSPRVELLHNIDPLFEDSFP
protein features
start (aa)end (aa)featuredetails 
390396STRANDlost
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 5
strand -1
last intron/exon boundary 1713
theoretical NMD boundary in CDS 1163
length of CDS 1242
coding sequence (CDS) position 1178
cDNA position
(for ins/del: last normal base / first normal base)		 1677
gDNA position
(for ins/del: last normal base / first normal base)		 146697
chromosomal position
(for ins/del: last normal base / first normal base)		 78135214
original gDNA sequence snippet CCCCAGAATTGAGCTGCTGCATAATATTGACCCGAACTTCG
altered gDNA sequence snippet CCCCAGAATTGAGCTGCTGCCTAATATTGACCCGAACTTCG
original cDNA sequence snippet CCCCAGAATTGAGCTGCTGCATAATATTGACCCGAACTTCG
altered cDNA sequence snippet CCCCAGAATTGAGCTGCTGCCTAATATTGACCCGAACTTCG
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 DSSPYWPECS LLL*
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 LLPNIDPNFV DSSPYWPECS LLL*
speed 0.93 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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999996545142112 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM1513714)
  • known disease mutation at this position (HGMD CM960082)
  • known disease mutation: rs886 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:78135214T>GN/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.1178A>C
cDNA.1715A>C
g.146697A>C
AA changes H393P Score: 77 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 393
frameshift no
known variant Reference ID: rs118203944
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC033

known disease mutation: rs886 (pathogenic for Mucopolysaccharidosis type 6|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960082)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960082)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1513714)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960082)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1513714)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960082)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2280.991
1.7881
(flanking)3.8121
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 36
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      393EGSPSPRIELLHNIDPNFVDSSPC
mutated  not conserved    393EGSPSPRIELLPNIDPNFVDSSP
Ptroglodytes  all identical  ENSPTRG00000017019  395EGSPSPRIELLHNIDPNFVDSSP
Mmulatta  all identical  ENSMMUG00000006792  394EGSPSPRVELLHNIDPNFVDSSP
Fcatus  all identical  ENSFCAG00000011879  395EGSPSPRKELLHNIDPNFVDISP
Mmusculus  all identical  ENSMUSG00000042082  394EGHPSPRVELLHNIDQDFFDGLP
Ggallus  all identical  ENSGALG00000004438  386EGRPSPRVELLHNIDPMFVDDYP
Trubripes  all identical  ENSTRUG00000003412  373KGFASPRLELLHNIDPLYN
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000000542  387EGSPSPRVELLHNIDPLFEDSFP
protein features
start (aa)end (aa)featuredetails 
390396STRANDlost
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 5
strand -1
last intron/exon boundary 1874
theoretical NMD boundary in CDS 1286
length of CDS 1602
coding sequence (CDS) position 1178
cDNA position
(for ins/del: last normal base / first normal base)		 1715
gDNA position
(for ins/del: last normal base / first normal base)		 146697
chromosomal position
(for ins/del: last normal base / first normal base)		 78135214
original gDNA sequence snippet CCCCAGAATTGAGCTGCTGCATAATATTGACCCGAACTTCG
altered gDNA sequence snippet CCCCAGAATTGAGCTGCTGCCTAATATTGACCCGAACTTCG
original cDNA sequence snippet CCCCAGAATTGAGCTGCTGCATAATATTGACCCGAACTTCG
altered cDNA sequence snippet CCCCAGAATTGAGCTGCTGCCTAATATTGACCCGAACTTCG
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 LLPNIDPNFV DSSPCPRNSM APAKDDSSLP
EYSAFNTSVH AAIRHGNWKL LTGYPGCGYW FPPPSQYNVS EIPSSDPPTK TLWLFDIDRD
PEERHDLSRE YPHIVTKLLS RLQFYHKHSV PVYFPAQDPR CDPKATGVWG PWM*
speed 0.75 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

Problems