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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000295240
Querying Taster for transcript #2: ENST00000392663
Querying Taster for transcript #3: ENST00000554017
Querying Taster for transcript #4: ENST00000513963
MT speed 0 s - this script 4.295833 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BBS5disease_causing_automatic0.999999999995871simple_aaeaffected0G72Ssingle base exchangers121908581show file
BBS5disease_causing_automatic0.999999999995871simple_aaeaffected0G72Ssingle base exchangers121908581show file
BBS5disease_causing_automatic0.999999999995871simple_aaeaffected0G72Ssingle base exchangers121908581show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999995871 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM080097)
  • known disease mutation: rs6161 (pathogenic)
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:170344321G>AN/A show variant in all transcripts   IGV
HGNC symbol BBS5
Ensembl transcript ID ENST00000392663
Genbank transcript ID N/A
UniProt peptide Q8N3I7
alteration type single base exchange
alteration region CDS
DNA changes c.214G>A
cDNA.285G>A
g.8634G>A
AA changes G72S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 72
frameshift no
known variant Reference ID: rs121908581
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs6161 (pathogenic for Bardet-Biedl syndrome 5|Bardet-Biedl syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM080097)

known disease mutation at this position, please check HGMD for details (HGMD ID CM080097)
known disease mutation at this position, please check HGMD for details (HGMD ID CM080097)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5180.652
6.1691
(flanking)4.2091
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased8635wt: 0.2228 / mu: 0.2434 (marginal change - not scored)wt: CTTTTGGATTTTAGCTGTCGGTTACAATTGCATATTGAATA
mu: CTTTTGGATTTTAGCTGTCAGTTACAATTGCATATTGAATA		 tcgg|TTAC
Acc marginally decreased8628wt: 0.7540 / mu: 0.7022 (marginal change - not scored)wt: TTCTTTGCTTTTGGATTTTAGCTGTCGGTTACAATTGCATA
mu: TTCTTTGCTTTTGGATTTTAGCTGTCAGTTACAATTGCATA		 ttag|CTGT
Acc marginally increased8634wt: 0.4570 / mu: 0.5294 (marginal change - not scored)wt: GCTTTTGGATTTTAGCTGTCGGTTACAATTGCATATTGAAT
mu: GCTTTTGGATTTTAGCTGTCAGTTACAATTGCATATTGAAT		 gtcg|GTTA
Donor increased8634wt: 0.27 / mu: 0.93wt: CTGTCGGTTACAATT
mu: CTGTCAGTTACAATT		 GTCG|gtta
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      72SLALSRVNVSVGYNCILNITTRTA
mutated  not conserved    72SLALSRVNVSVSYNCILNITTRT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000020506  72SLALSRVNVSVGYNCILNITTRT
Fcatus  all identical  ENSFCAG00000010291  72XXXXXXXXXXIGYNCILNITTRT
Mmusculus  all identical  ENSMUSG00000063145  72SLALPRVNLSIGYNCILNITTRT
Ggallus  all identical  ENSGALG00000009846  73LSLPRVNLSVGYNCIINITTRT
Trubripes  all identical  ENSTRUG00000017898  73LALPRVNLSVGYNSIINITTRT
Drerio  all identical  ENSDARG00000039827  73LALPRVNLSVGYNCIINITTRT
Dmelanogaster  all identical  FBgn0037280  84VHKKYNLSIGYARIGNTNTRV
Celegans  all identical  R01H10.6  74INITIGWNAITGVQSKQ
Xtropicalis  all identical  ENSXETG00000018935  58SLALPRVNLAVGYN
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 963 / 963
position (AA) of stopcodon in wt / mu AA sequence 321 / 321
position of stopcodon in wt / mu cDNA 1034 / 1034
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 72 / 72
chromosome 2
strand 1
last intron/exon boundary 933
theoretical NMD boundary in CDS 811
length of CDS 963
coding sequence (CDS) position 214
cDNA position
(for ins/del: last normal base / first normal base)		 285
gDNA position
(for ins/del: last normal base / first normal base)		 8634
chromosomal position
(for ins/del: last normal base / first normal base)		 170344321
original gDNA sequence snippet GCTTTTGGATTTTAGCTGTCGGTTACAATTGCATATTGAAT
altered gDNA sequence snippet GCTTTTGGATTTTAGCTGTCAGTTACAATTGCATATTGAAT
original cDNA sequence snippet CAAGAGTCAATGTTTCTGTCGGTTACAATTGCATATTGAAT
altered cDNA sequence snippet CAAGAGTCAATGTTTCTGTCAGTTACAATTGCATATTGAAT
wildtype AA sequence MSVLDALWED RDVRFDLSAQ QMKTRPGEVL IDCLDSIEDT KGNNGDRGRL LVTNLRILWH
SLALSRVNVS VGYNCILNIT TRTANSKLRG QTEALYILTK CNSTRFEFIF TNLVPGSPRL
FTSVMAVHRA YETSKMYRDF KLRSALIQNK QLRLLPQEHV YDKINGVWNL SSDQGNLGTF
FITNVRIVWH ANMNDSFNVS IPYLQISGGY VLGFKIDPVE KLQESVKEIN SLHKVYSASP
IFGVDYEMEE KPQPLEALTV EQIQDDVEID SDGHTDAFVA YFADGNKQQD REPVFSEELG
LAIEKLKDGF TLQGLWEVMS *
mutated AA sequence MSVLDALWED RDVRFDLSAQ QMKTRPGEVL IDCLDSIEDT KGNNGDRGRL LVTNLRILWH
SLALSRVNVS VSYNCILNIT TRTANSKLRG QTEALYILTK CNSTRFEFIF TNLVPGSPRL
FTSVMAVHRA YETSKMYRDF KLRSALIQNK QLRLLPQEHV YDKINGVWNL SSDQGNLGTF
FITNVRIVWH ANMNDSFNVS IPYLQISGGY VLGFKIDPVE KLQESVKEIN SLHKVYSASP
IFGVDYEMEE KPQPLEALTV EQIQDDVEID SDGHTDAFVA YFADGNKQQD REPVFSEELG
LAIEKLKDGF TLQGLWEVMS *
speed 1.32 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: 0.999999999995871 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM080097)
  • known disease mutation: rs6161 (pathogenic)
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:170344321G>AN/A show variant in all transcripts   IGV
HGNC symbol BBS5
Ensembl transcript ID ENST00000554017
Genbank transcript ID N/A
UniProt peptide Q8N3I7
alteration type single base exchange
alteration region CDS
DNA changes c.214G>A
cDNA.288G>A
g.8634G>A
AA changes G72S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 72
frameshift no
known variant Reference ID: rs121908581
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs6161 (pathogenic for Bardet-Biedl syndrome 5|Bardet-Biedl syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM080097)

known disease mutation at this position, please check HGMD for details (HGMD ID CM080097)
known disease mutation at this position, please check HGMD for details (HGMD ID CM080097)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5180.652
6.1691
(flanking)4.2091
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased8635wt: 0.2228 / mu: 0.2434 (marginal change - not scored)wt: CTTTTGGATTTTAGCTGTCGGTTACAATTGCATATTGAATA
mu: CTTTTGGATTTTAGCTGTCAGTTACAATTGCATATTGAATA		 tcgg|TTAC
Acc marginally decreased8628wt: 0.7540 / mu: 0.7022 (marginal change - not scored)wt: TTCTTTGCTTTTGGATTTTAGCTGTCGGTTACAATTGCATA
mu: TTCTTTGCTTTTGGATTTTAGCTGTCAGTTACAATTGCATA		 ttag|CTGT
Acc marginally increased8634wt: 0.4570 / mu: 0.5294 (marginal change - not scored)wt: GCTTTTGGATTTTAGCTGTCGGTTACAATTGCATATTGAAT
mu: GCTTTTGGATTTTAGCTGTCAGTTACAATTGCATATTGAAT		 gtcg|GTTA
Donor increased8634wt: 0.27 / mu: 0.93wt: CTGTCGGTTACAATT
mu: CTGTCAGTTACAATT		 GTCG|gtta
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      72SLALSRVNVSVGYNCILNITTRTA
mutated  not conserved    72SLALSRVNVSVSYNCILNITTRT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000020506  72SLALSRVNVSVGYNCILNITTRT
Fcatus  all identical  ENSFCAG00000010291  72XXXXXXXXXXIGYNCILNITTRT
Mmusculus  all identical  ENSMUSG00000063145  72SLALPRVNLSIGYNCILNITTRT
Ggallus  all identical  ENSGALG00000009846  73LSLPRVNLSVGYNCIINITTRT
Trubripes  all identical  ENSTRUG00000017898  73LALPRVNLSVGYNSIINITTRT
Drerio  all identical  ENSDARG00000039827  73LALPRVNLSVGYNCIINITTRT
Dmelanogaster  all identical  FBgn0037280  84VHKKYNLSIGYARIGNTNTRV
Celegans  all identical  R01H10.6  74INITIGWNAITGVQSKQ
Xtropicalis  all identical  ENSXETG00000018935  58SLALPRVNLAVGYN
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1635 / 1635
position (AA) of stopcodon in wt / mu AA sequence 545 / 545
position of stopcodon in wt / mu cDNA 1709 / 1709
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 75 / 75
chromosome 2
strand 1
last intron/exon boundary 1598
theoretical NMD boundary in CDS 1473
length of CDS 1635
coding sequence (CDS) position 214
cDNA position
(for ins/del: last normal base / first normal base)		 288
gDNA position
(for ins/del: last normal base / first normal base)		 8634
chromosomal position
(for ins/del: last normal base / first normal base)		 170344321
original gDNA sequence snippet GCTTTTGGATTTTAGCTGTCGGTTACAATTGCATATTGAAT
altered gDNA sequence snippet GCTTTTGGATTTTAGCTGTCAGTTACAATTGCATATTGAAT
original cDNA sequence snippet CAAGAGTCAATGTTTCTGTCGGTTACAATTGCATATTGAAT
altered cDNA sequence snippet CAAGAGTCAATGTTTCTGTCAGTTACAATTGCATATTGAAT
wildtype AA sequence MSVLDALWED RDVRFDLSAQ QMKTRPGEVL IDCLDSIEDT KGNNGDRGRL LVTNLRILWH
SLALSRVNVS VGYNCILNIT TRTANSKLRG QTEALYILTK CNSTRFEFIF TNLVPGSPRL
FTSVMAVHRA YETSKMYRDF KLRSALIQNK QLRLLPQEHV YDKINGVWNL SSDQGNLGTF
FITNVRIVWH ANMNDSFNVS IPYLQIRSIK IRDSKFGLAL VIESSQQSGG YVLGFKIDPV
EKLQESVKEI NSLHKVYSAS PIFGVDYEME EKPQPLEALT VEQIQDDVEI DSDGHTDAFV
AYFADGNKLD SIASEWVGLP PLPSARCLFG LGEVDDKIYV VAGKDLQTEA SLDSVLCYDP
VAAKWNEVKK LPIKVYGHNV ISHKGMIYCL GGKTDDKKCT NRVFIFNPKK GDWKDLAPMK
IPRSMFGVAV HKGKIVIAGG VTEDGLSASV EAFDLTTNKW DVMTEFPQER SSISLVSLAG
SLYAIGGFAM IQLESKEFAP TEVNDIWKYE DDKKEWAGML KEIRYASGAS CLATRLNLFK
LSKL*
mutated AA sequence MSVLDALWED RDVRFDLSAQ QMKTRPGEVL IDCLDSIEDT KGNNGDRGRL LVTNLRILWH
SLALSRVNVS VSYNCILNIT TRTANSKLRG QTEALYILTK CNSTRFEFIF TNLVPGSPRL
FTSVMAVHRA YETSKMYRDF KLRSALIQNK QLRLLPQEHV YDKINGVWNL SSDQGNLGTF
FITNVRIVWH ANMNDSFNVS IPYLQIRSIK IRDSKFGLAL VIESSQQSGG YVLGFKIDPV
EKLQESVKEI NSLHKVYSAS PIFGVDYEME EKPQPLEALT VEQIQDDVEI DSDGHTDAFV
AYFADGNKLD SIASEWVGLP PLPSARCLFG LGEVDDKIYV VAGKDLQTEA SLDSVLCYDP
VAAKWNEVKK LPIKVYGHNV ISHKGMIYCL GGKTDDKKCT NRVFIFNPKK GDWKDLAPMK
IPRSMFGVAV HKGKIVIAGG VTEDGLSASV EAFDLTTNKW DVMTEFPQER SSISLVSLAG
SLYAIGGFAM IQLESKEFAP TEVNDIWKYE DDKKEWAGML KEIRYASGAS CLATRLNLFK
LSKL*
speed 1.00 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: 0.999999999995871 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM080097)
  • known disease mutation: rs6161 (pathogenic)
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:170344321G>AN/A show variant in all transcripts   IGV
HGNC symbol BBS5
Ensembl transcript ID ENST00000295240
Genbank transcript ID NM_152384
UniProt peptide Q8N3I7
alteration type single base exchange
alteration region CDS
DNA changes c.214G>A
cDNA.590G>A
g.8634G>A
AA changes G72S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 72
frameshift no
known variant Reference ID: rs121908581
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs6161 (pathogenic for Bardet-Biedl syndrome 5|Bardet-Biedl syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM080097)

known disease mutation at this position, please check HGMD for details (HGMD ID CM080097)
known disease mutation at this position, please check HGMD for details (HGMD ID CM080097)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5180.652
6.1691
(flanking)4.2091
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased8635wt: 0.2228 / mu: 0.2434 (marginal change - not scored)wt: CTTTTGGATTTTAGCTGTCGGTTACAATTGCATATTGAATA
mu: CTTTTGGATTTTAGCTGTCAGTTACAATTGCATATTGAATA		 tcgg|TTAC
Acc marginally decreased8628wt: 0.7540 / mu: 0.7022 (marginal change - not scored)wt: TTCTTTGCTTTTGGATTTTAGCTGTCGGTTACAATTGCATA
mu: TTCTTTGCTTTTGGATTTTAGCTGTCAGTTACAATTGCATA		 ttag|CTGT
Acc marginally increased8634wt: 0.4570 / mu: 0.5294 (marginal change - not scored)wt: GCTTTTGGATTTTAGCTGTCGGTTACAATTGCATATTGAAT
mu: GCTTTTGGATTTTAGCTGTCAGTTACAATTGCATATTGAAT		 gtcg|GTTA
Donor increased8634wt: 0.27 / mu: 0.93wt: CTGTCGGTTACAATT
mu: CTGTCAGTTACAATT		 GTCG|gtta
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      72SLALSRVNVSVGYNCILNITTRTA
mutated  not conserved    72SLALSRVNVSVSYNCILNITTRT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000020506  72SLALSRVNVSVGYNCILNITTRT
Fcatus  all identical  ENSFCAG00000010291  72XXXXXXXXXXIGYNCILNITTRT
Mmusculus  all identical  ENSMUSG00000063145  72SLALPRVNLSIGYNCILNITTRT
Ggallus  all identical  ENSGALG00000009846  73LSLPRVNLSVGYNCIINITTRT
Trubripes  all identical  ENSTRUG00000017898  73LALPRVNLSVGYNSIINITTRT
Drerio  all identical  ENSDARG00000039827  73LALPRVNLSVGYNCIINITTRT
Dmelanogaster  all identical  FBgn0037280  84VHKKYNLSIGYARIGNTNTRV
Celegans  all identical  R01H10.6  74INITIGWNAITGVQSKQ
Xtropicalis  all identical  ENSXETG00000018935  58SLALPRVNLAVGYN
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1026 / 1026
position (AA) of stopcodon in wt / mu AA sequence 342 / 342
position of stopcodon in wt / mu cDNA 1402 / 1402
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 377 / 377
chromosome 2
strand 1
last intron/exon boundary 1301
theoretical NMD boundary in CDS 874
length of CDS 1026
coding sequence (CDS) position 214
cDNA position
(for ins/del: last normal base / first normal base)		 590
gDNA position
(for ins/del: last normal base / first normal base)		 8634
chromosomal position
(for ins/del: last normal base / first normal base)		 170344321
original gDNA sequence snippet GCTTTTGGATTTTAGCTGTCGGTTACAATTGCATATTGAAT
altered gDNA sequence snippet GCTTTTGGATTTTAGCTGTCAGTTACAATTGCATATTGAAT
original cDNA sequence snippet CAAGAGTCAATGTTTCTGTCGGTTACAATTGCATATTGAAT
altered cDNA sequence snippet CAAGAGTCAATGTTTCTGTCAGTTACAATTGCATATTGAAT
wildtype AA sequence MSVLDALWED RDVRFDLSAQ QMKTRPGEVL IDCLDSIEDT KGNNGDRGRL LVTNLRILWH
SLALSRVNVS VGYNCILNIT TRTANSKLRG QTEALYILTK CNSTRFEFIF TNLVPGSPRL
FTSVMAVHRA YETSKMYRDF KLRSALIQNK QLRLLPQEHV YDKINGVWNL SSDQGNLGTF
FITNVRIVWH ANMNDSFNVS IPYLQIRSIK IRDSKFGLAL VIESSQQSGG YVLGFKIDPV
EKLQESVKEI NSLHKVYSAS PIFGVDYEME EKPQPLEALT VEQIQDDVEI DSDGHTDAFV
AYFADGNKQQ DREPVFSEEL GLAIEKLKDG FTLQGLWEVM S*
mutated AA sequence MSVLDALWED RDVRFDLSAQ QMKTRPGEVL IDCLDSIEDT KGNNGDRGRL LVTNLRILWH
SLALSRVNVS VSYNCILNIT TRTANSKLRG QTEALYILTK CNSTRFEFIF TNLVPGSPRL
FTSVMAVHRA YETSKMYRDF KLRSALIQNK QLRLLPQEHV YDKINGVWNL SSDQGNLGTF
FITNVRIVWH ANMNDSFNVS IPYLQIRSIK IRDSKFGLAL VIESSQQSGG YVLGFKIDPV
EKLQESVKEI NSLHKVYSAS PIFGVDYEME EKPQPLEALT VEQIQDDVEI DSDGHTDAFV
AYFADGNKQQ DREPVFSEEL GLAIEKLKDG FTLQGLWEVM S*
speed 1.24 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

data problem

back to results table