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: ENST00000369760
Querying Taster for transcript #2: ENST00000320393
Querying Taster for transcript #3: ENST00000356489
Querying Taster for transcript #4: ENST00000545529
MT speed 0 s - this script 4.455432 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BCKDHBdisease_causing_automatic0.999999978907018simple_aaeaffected0R183Psingle base exchangers79761867show file
BCKDHBdisease_causing_automatic0.999999978907018simple_aaeaffected0R183Psingle base exchangers79761867show file
BCKDHBdisease_causing_automatic0.999999997154057simple_aaeaffected0R183Psingle base exchangers79761867show file
BCKDHBdisease_causing_automatic0.999999997154057simple_aaeaffected0R183Psingle base exchangers79761867show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999978907018 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM014511)
  • known disease mutation at this position (HGMD CM124309)
  • known disease mutation: rs11937 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:80878662G>CN/A show variant in all transcripts   IGV
HGNC symbol BCKDHB
Ensembl transcript ID ENST00000320393
Genbank transcript ID NM_183050
UniProt peptide P21953
alteration type single base exchange
alteration region CDS
DNA changes c.548G>C
cDNA.595G>C
g.62299G>C
AA changes R183P Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 183
frameshift no
known variant Reference ID: rs79761867
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC02424

known disease mutation: rs11937 (pathogenic for Maple syrup urine disease|Maple syrup urine disease type 1B|MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IB|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM014511)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014511)
known disease mutation at this position, please check HGMD for details (HGMD ID CM124309)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014511)
known disease mutation at this position, please check HGMD for details (HGMD ID CM124309)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014511)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9170.999
5.3431
(flanking)0.4260.998
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 increased62308wt: 0.9179 / mu: 0.9669 (marginal change - not scored)wt: CCTCACTATCCGGTCCCCTTGGGGCTGTGTTGGTCATGGGG
mu: CCTCACTATCCCGTCCCCTTGGGGCTGTGTTGGTCATGGGG		 cttg|GGGC
Acc increased62307wt: 0.22 / mu: 0.68wt: GCCTCACTATCCGGTCCCCTTGGGGCTGTGTTGGTCATGGG
mu: GCCTCACTATCCCGTCCCCTTGGGGCTGTGTTGGTCATGGG		 cctt|GGGG
Acc marginally increased62309wt: 0.9732 / mu: 0.9857 (marginal change - not scored)wt: CTCACTATCCGGTCCCCTTGGGGCTGTGTTGGTCATGGGGC
mu: CTCACTATCCCGTCCCCTTGGGGCTGTGTTGGTCATGGGGC		 ttgg|GGCT
Acc gained623060.46mu: AGCCTCACTATCCCGTCCCCTTGGGGCTGTGTTGGTCATGG ccct|TGGG
distance from splice site 71
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      183GDLFNCGSLTIRSPWGCVGHGALY
mutated  not conserved    183TIPSPWGCVGHGAL
Ptroglodytes  all identical  ENSPTRG00000018372  183TIRSPWGCVGHGAL
Mmulatta  all conserved  ENSMMUG00000004829  191NIFNNWLFKIKSSL----LGYI
Fcatus  all identical  ENSFCAG00000010609  183TIRAPWGCVGHGAL
Mmusculus  all identical  ENSMUSG00000032263  113GDLFNCGSLTIRAPWGCVG
Ggallus  all identical  ENSGALG00000015866  183GDLFNCGNLTIRAPWGCVGHG
Trubripes  all identical  ENSTRUG00000002294  183GNLFDCGKLTIRAPWGCVGHGSL
Drerio  no alignment  ENSDARG00000086611  n/a
Dmelanogaster  all identical  FBgn0039993  155GGLFDCGSLTFRVPCGAVGHGAL
Celegans  all identical  F27D4.5  157GNQFDCGKLTVRTTWGAVGHGAL
Xtropicalis  all identical  ENSXETG00000011773  172GDLFNCGSLTIRAPWGCVGHGAL
protein features
start (aa)end (aa)featuredetails 
180187STRANDlost
193195HELIXmight get lost (downstream of altered splice site)
201205HELIXmight get lost (downstream of altered splice site)
211213STRANDmight get lost (downstream of altered splice site)
218230HELIXmight get lost (downstream of altered splice site)
231233STRANDmight get lost (downstream of altered splice site)
235240STRANDmight get lost (downstream of altered splice site)
241241MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
241243HELIXmight get lost (downstream of altered splice site)
244246TURNmight get lost (downstream of altered splice site)
249254STRANDmight get lost (downstream of altered splice site)
264267STRANDmight get lost (downstream of altered splice site)
270276STRANDmight get lost (downstream of altered splice site)
280295HELIXmight get lost (downstream of altered splice site)
299303STRANDmight get lost (downstream of altered splice site)
306309STRANDmight get lost (downstream of altered splice site)
312322HELIXmight get lost (downstream of altered splice site)
322322CONFLICTT -> S (in Ref. 8; CAA36685).might get lost (downstream of altered splice site)
325333STRANDmight get lost (downstream of altered splice site)
337349HELIXmight get lost (downstream of altered splice site)
350352HELIXmight get lost (downstream of altered splice site)
358362STRANDmight get lost (downstream of altered splice site)
372375HELIXmight get lost (downstream of altered splice site)
379390HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1179 / 1179
position (AA) of stopcodon in wt / mu AA sequence 393 / 393
position of stopcodon in wt / mu cDNA 1226 / 1226
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 48 / 48
chromosome 6
strand 1
last intron/exon boundary 1086
theoretical NMD boundary in CDS 988
length of CDS 1179
coding sequence (CDS) position 548
cDNA position
(for ins/del: last normal base / first normal base)		 595
gDNA position
(for ins/del: last normal base / first normal base)		 62299
chromosomal position
(for ins/del: last normal base / first normal base)		 80878662
original gDNA sequence snippet CTGTGGAAGCCTCACTATCCGGTCCCCTTGGGGCTGTGTTG
altered gDNA sequence snippet CTGTGGAAGCCTCACTATCCCGTCCCCTTGGGGCTGTGTTG
original cDNA sequence snippet CTGTGGAAGCCTCACTATCCGGTCCCCTTGGGGCTGTGTTG
altered cDNA sequence snippet CTGTGGAAGCCTCACTATCCCGTCCCCTTGGGGCTGTGTTG
wildtype AA sequence MAVVAAAAGW LLRLRAAGAE GHWRRLPGAG LARGFLHPAA TVEDAAQRRQ VAHFTFQPDP
EPREYGQTQK MNLFQSVTSA LDNSLAKDPT AVIFGEDVAF GGVFRCTVGL RDKYGKDRVF
NTPLCEQGIV GFGIGIAVTG ATAIAEIQFA DYIFPAFDQI VNEAAKYRYR SGDLFNCGSL
TIRSPWGCVG HGALYHSQSP EAFFAHCPGI KVVIPRSPFQ AKGLLLSCIE DKNPCIFFEP
KILYRAAAEE VPIEPYNIPL SQAEVIQEGS DVTLVAWGTQ VHVIREVASM AKEKLGVSCE
VIDLRTIIPW DVDTICKSVI KTGRLLISHE APLTGGFASE ISSTVQEECF LNLEAPISRV
CGYDTPFPHI FEPFYIPDKW KCYDALRKMI NY*
mutated AA sequence MAVVAAAAGW LLRLRAAGAE GHWRRLPGAG LARGFLHPAA TVEDAAQRRQ VAHFTFQPDP
EPREYGQTQK MNLFQSVTSA LDNSLAKDPT AVIFGEDVAF GGVFRCTVGL RDKYGKDRVF
NTPLCEQGIV GFGIGIAVTG ATAIAEIQFA DYIFPAFDQI VNEAAKYRYR SGDLFNCGSL
TIPSPWGCVG HGALYHSQSP EAFFAHCPGI KVVIPRSPFQ AKGLLLSCIE DKNPCIFFEP
KILYRAAAEE VPIEPYNIPL SQAEVIQEGS DVTLVAWGTQ VHVIREVASM AKEKLGVSCE
VIDLRTIIPW DVDTICKSVI KTGRLLISHE APLTGGFASE ISSTVQEECF LNLEAPISRV
CGYDTPFPHI FEPFYIPDKW KCYDALRKMI NY*
speed 0.85 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: 0.999999978907018 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM014511)
  • known disease mutation at this position (HGMD CM124309)
  • known disease mutation: rs11937 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:80878662G>CN/A show variant in all transcripts   IGV
HGNC symbol BCKDHB
Ensembl transcript ID ENST00000356489
Genbank transcript ID NM_000056
UniProt peptide P21953
alteration type single base exchange
alteration region CDS
DNA changes c.548G>C
cDNA.595G>C
g.62299G>C
AA changes R183P Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 183
frameshift no
known variant Reference ID: rs79761867
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC02424

known disease mutation: rs11937 (pathogenic for Maple syrup urine disease|Maple syrup urine disease type 1B|MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IB|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM014511)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014511)
known disease mutation at this position, please check HGMD for details (HGMD ID CM124309)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014511)
known disease mutation at this position, please check HGMD for details (HGMD ID CM124309)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014511)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9170.999
5.3431
(flanking)0.4260.998
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 increased62308wt: 0.9179 / mu: 0.9669 (marginal change - not scored)wt: CCTCACTATCCGGTCCCCTTGGGGCTGTGTTGGTCATGGGG
mu: CCTCACTATCCCGTCCCCTTGGGGCTGTGTTGGTCATGGGG		 cttg|GGGC
Acc increased62307wt: 0.22 / mu: 0.68wt: GCCTCACTATCCGGTCCCCTTGGGGCTGTGTTGGTCATGGG
mu: GCCTCACTATCCCGTCCCCTTGGGGCTGTGTTGGTCATGGG		 cctt|GGGG
Acc marginally increased62309wt: 0.9732 / mu: 0.9857 (marginal change - not scored)wt: CTCACTATCCGGTCCCCTTGGGGCTGTGTTGGTCATGGGGC
mu: CTCACTATCCCGTCCCCTTGGGGCTGTGTTGGTCATGGGGC		 ttgg|GGCT
Acc gained623060.46mu: AGCCTCACTATCCCGTCCCCTTGGGGCTGTGTTGGTCATGG ccct|TGGG
distance from splice site 71
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      183GDLFNCGSLTIRSPWGCVGHGALY
mutated  not conserved    183TIPSPWGCVGHGAL
Ptroglodytes  all identical  ENSPTRG00000018372  183TIRSPWGCVGHGAL
Mmulatta  all conserved  ENSMMUG00000004829  191NIFNNWLFKIKSSL----LGYI
Fcatus  all identical  ENSFCAG00000010609  183TIRAPWGCVGHGAL
Mmusculus  all identical  ENSMUSG00000032263  113GDLFNCGSLTIRAPWGCVG
Ggallus  all identical  ENSGALG00000015866  183GDLFNCGNLTIRAPWGCVGHG
Trubripes  all identical  ENSTRUG00000002294  183GNLFDCGKLTIRAPWGCVGHGSL
Drerio  no alignment  ENSDARG00000086611  n/a
Dmelanogaster  all identical  FBgn0039993  155GGLFDCGSLTFRVPCGAVGHGAL
Celegans  all identical  F27D4.5  157GNQFDCGKLTVRTTWGAVGHGAL
Xtropicalis  all identical  ENSXETG00000011773  172GDLFNCGSLTIRAPWGCVGHGAL
protein features
start (aa)end (aa)featuredetails 
180187STRANDlost
193195HELIXmight get lost (downstream of altered splice site)
201205HELIXmight get lost (downstream of altered splice site)
211213STRANDmight get lost (downstream of altered splice site)
218230HELIXmight get lost (downstream of altered splice site)
231233STRANDmight get lost (downstream of altered splice site)
235240STRANDmight get lost (downstream of altered splice site)
241241MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
241243HELIXmight get lost (downstream of altered splice site)
244246TURNmight get lost (downstream of altered splice site)
249254STRANDmight get lost (downstream of altered splice site)
264267STRANDmight get lost (downstream of altered splice site)
270276STRANDmight get lost (downstream of altered splice site)
280295HELIXmight get lost (downstream of altered splice site)
299303STRANDmight get lost (downstream of altered splice site)
306309STRANDmight get lost (downstream of altered splice site)
312322HELIXmight get lost (downstream of altered splice site)
322322CONFLICTT -> S (in Ref. 8; CAA36685).might get lost (downstream of altered splice site)
325333STRANDmight get lost (downstream of altered splice site)
337349HELIXmight get lost (downstream of altered splice site)
350352HELIXmight get lost (downstream of altered splice site)
358362STRANDmight get lost (downstream of altered splice site)
372375HELIXmight get lost (downstream of altered splice site)
379390HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1179 / 1179
position (AA) of stopcodon in wt / mu AA sequence 393 / 393
position of stopcodon in wt / mu cDNA 1226 / 1226
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 48 / 48
chromosome 6
strand 1
last intron/exon boundary 1235
theoretical NMD boundary in CDS 1137
length of CDS 1179
coding sequence (CDS) position 548
cDNA position
(for ins/del: last normal base / first normal base)		 595
gDNA position
(for ins/del: last normal base / first normal base)		 62299
chromosomal position
(for ins/del: last normal base / first normal base)		 80878662
original gDNA sequence snippet CTGTGGAAGCCTCACTATCCGGTCCCCTTGGGGCTGTGTTG
altered gDNA sequence snippet CTGTGGAAGCCTCACTATCCCGTCCCCTTGGGGCTGTGTTG
original cDNA sequence snippet CTGTGGAAGCCTCACTATCCGGTCCCCTTGGGGCTGTGTTG
altered cDNA sequence snippet CTGTGGAAGCCTCACTATCCCGTCCCCTTGGGGCTGTGTTG
wildtype AA sequence MAVVAAAAGW LLRLRAAGAE GHWRRLPGAG LARGFLHPAA TVEDAAQRRQ VAHFTFQPDP
EPREYGQTQK MNLFQSVTSA LDNSLAKDPT AVIFGEDVAF GGVFRCTVGL RDKYGKDRVF
NTPLCEQGIV GFGIGIAVTG ATAIAEIQFA DYIFPAFDQI VNEAAKYRYR SGDLFNCGSL
TIRSPWGCVG HGALYHSQSP EAFFAHCPGI KVVIPRSPFQ AKGLLLSCIE DKNPCIFFEP
KILYRAAAEE VPIEPYNIPL SQAEVIQEGS DVTLVAWGTQ VHVIREVASM AKEKLGVSCE
VIDLRTIIPW DVDTICKSVI KTGRLLISHE APLTGGFASE ISSTVQEECF LNLEAPISRV
CGYDTPFPHI FEPFYIPDKW KCYDALRKMI NY*
mutated AA sequence MAVVAAAAGW LLRLRAAGAE GHWRRLPGAG LARGFLHPAA TVEDAAQRRQ VAHFTFQPDP
EPREYGQTQK MNLFQSVTSA LDNSLAKDPT AVIFGEDVAF GGVFRCTVGL RDKYGKDRVF
NTPLCEQGIV GFGIGIAVTG ATAIAEIQFA DYIFPAFDQI VNEAAKYRYR SGDLFNCGSL
TIPSPWGCVG HGALYHSQSP EAFFAHCPGI KVVIPRSPFQ AKGLLLSCIE DKNPCIFFEP
KILYRAAAEE VPIEPYNIPL SQAEVIQEGS DVTLVAWGTQ VHVIREVASM AKEKLGVSCE
VIDLRTIIPW DVDTICKSVI KTGRLLISHE APLTGGFASE ISSTVQEECF LNLEAPISRV
CGYDTPFPHI FEPFYIPDKW KCYDALRKMI NY*
speed 0.76 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: 0.999999997154057 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM014511)
  • known disease mutation at this position (HGMD CM124309)
  • known disease mutation: rs11937 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:80878662G>CN/A show variant in all transcripts   IGV
HGNC symbol BCKDHB
Ensembl transcript ID ENST00000369760
Genbank transcript ID N/A
UniProt peptide P21953
alteration type single base exchange
alteration region CDS
DNA changes c.548G>C
cDNA.595G>C
g.62299G>C
AA changes R183P Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 183
frameshift no
known variant Reference ID: rs79761867
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC02424

known disease mutation: rs11937 (pathogenic for Maple syrup urine disease|Maple syrup urine disease type 1B|MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IB|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM014511)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014511)
known disease mutation at this position, please check HGMD for details (HGMD ID CM124309)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014511)
known disease mutation at this position, please check HGMD for details (HGMD ID CM124309)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014511)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9170.999
5.3431
(flanking)0.4260.998
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 increased62308wt: 0.9179 / mu: 0.9669 (marginal change - not scored)wt: CCTCACTATCCGGTCCCCTTGGGGCTGTGTTGGTCATGGGG
mu: CCTCACTATCCCGTCCCCTTGGGGCTGTGTTGGTCATGGGG		 cttg|GGGC
Acc increased62307wt: 0.22 / mu: 0.68wt: GCCTCACTATCCGGTCCCCTTGGGGCTGTGTTGGTCATGGG
mu: GCCTCACTATCCCGTCCCCTTGGGGCTGTGTTGGTCATGGG		 cctt|GGGG
Acc marginally increased62309wt: 0.9732 / mu: 0.9857 (marginal change - not scored)wt: CTCACTATCCGGTCCCCTTGGGGCTGTGTTGGTCATGGGGC
mu: CTCACTATCCCGTCCCCTTGGGGCTGTGTTGGTCATGGGGC		 ttgg|GGCT
Acc gained623060.46mu: AGCCTCACTATCCCGTCCCCTTGGGGCTGTGTTGGTCATGG ccct|TGGG
distance from splice site 71
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      183GDLFNCGSLTIRSPWGCVGHGALY
mutated  not conserved    183TIPSPWGCVGHGAL
Ptroglodytes  all identical  ENSPTRG00000018372  183TIRSPWGCVGHGAL
Mmulatta  no alignment  ENSMMUG00000004829  n/a
Fcatus  all identical  ENSFCAG00000010609  183TIRAPWGCVGHGAL
Mmusculus  all identical  ENSMUSG00000032263  113GDLFNCGSLTIRAPWGCVG
Ggallus  all identical  ENSGALG00000015866  183GDLFNCGNLTIRAPWGCVGHG
Trubripes  all identical  ENSTRUG00000002294  183GNLFDCGKLTIRAPWGCVGHGSL
Drerio  no alignment  ENSDARG00000086611  n/a
Dmelanogaster  all identical  FBgn0039993  155GGLFDCGSLTFRVPCGAVGHGAL
Celegans  all identical  F27D4.5  157GNQFDCGKLTVRTTWGAVGHGAL
Xtropicalis  all identical  ENSXETG00000011773  172GDLFNCGSLTIRAPWGCVGHGAL
protein features
start (aa)end (aa)featuredetails 
180187STRANDlost
193195HELIXmight get lost (downstream of altered splice site)
201205HELIXmight get lost (downstream of altered splice site)
211213STRANDmight get lost (downstream of altered splice site)
218230HELIXmight get lost (downstream of altered splice site)
231233STRANDmight get lost (downstream of altered splice site)
235240STRANDmight get lost (downstream of altered splice site)
241241MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
241243HELIXmight get lost (downstream of altered splice site)
244246TURNmight get lost (downstream of altered splice site)
249254STRANDmight get lost (downstream of altered splice site)
264267STRANDmight get lost (downstream of altered splice site)
270276STRANDmight get lost (downstream of altered splice site)
280295HELIXmight get lost (downstream of altered splice site)
299303STRANDmight get lost (downstream of altered splice site)
306309STRANDmight get lost (downstream of altered splice site)
312322HELIXmight get lost (downstream of altered splice site)
322322CONFLICTT -> S (in Ref. 8; CAA36685).might get lost (downstream of altered splice site)
325333STRANDmight get lost (downstream of altered splice site)
337349HELIXmight get lost (downstream of altered splice site)
350352HELIXmight get lost (downstream of altered splice site)
358362STRANDmight get lost (downstream of altered splice site)
372375HELIXmight get lost (downstream of altered splice site)
379390HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 657 / 657
position (AA) of stopcodon in wt / mu AA sequence 219 / 219
position of stopcodon in wt / mu cDNA 704 / 704
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 48 / 48
chromosome 6
strand 1
last intron/exon boundary 681
theoretical NMD boundary in CDS 583
length of CDS 657
coding sequence (CDS) position 548
cDNA position
(for ins/del: last normal base / first normal base)		 595
gDNA position
(for ins/del: last normal base / first normal base)		 62299
chromosomal position
(for ins/del: last normal base / first normal base)		 80878662
original gDNA sequence snippet CTGTGGAAGCCTCACTATCCGGTCCCCTTGGGGCTGTGTTG
altered gDNA sequence snippet CTGTGGAAGCCTCACTATCCCGTCCCCTTGGGGCTGTGTTG
original cDNA sequence snippet CTGTGGAAGCCTCACTATCCGGTCCCCTTGGGGCTGTGTTG
altered cDNA sequence snippet CTGTGGAAGCCTCACTATCCCGTCCCCTTGGGGCTGTGTTG
wildtype AA sequence MAVVAAAAGW LLRLRAAGAE GHWRRLPGAG LARGFLHPAA TVEDAAQRRQ VAHFTFQPDP
EPREYGQTQK MNLFQSVTSA LDNSLAKDPT AVIFGEDVAF GGVFRCTVGL RDKYGKDRVF
NTPLCEQGIV GFGIGIAVTG ATAIAEIQFA DYIFPAFDQI VNEAAKYRYR SGDLFNCGSL
TIRSPWGCVG HGALYHSQSP EAFFAHCPGI KIKVISLS*
mutated AA sequence MAVVAAAAGW LLRLRAAGAE GHWRRLPGAG LARGFLHPAA TVEDAAQRRQ VAHFTFQPDP
EPREYGQTQK MNLFQSVTSA LDNSLAKDPT AVIFGEDVAF GGVFRCTVGL RDKYGKDRVF
NTPLCEQGIV GFGIGIAVTG ATAIAEIQFA DYIFPAFDQI VNEAAKYRYR SGDLFNCGSL
TIPSPWGCVG HGALYHSQSP EAFFAHCPGI KIKVISLS*
speed 0.82 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
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Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999997154057 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM014511)
  • known disease mutation at this position (HGMD CM124309)
  • known disease mutation: rs11937 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:80878662G>CN/A show variant in all transcripts   IGV
HGNC symbol BCKDHB
Ensembl transcript ID ENST00000545529
Genbank transcript ID N/A
UniProt peptide P21953
alteration type single base exchange
alteration region CDS
DNA changes c.548G>C
cDNA.576G>C
g.62299G>C
AA changes R183P Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 183
frameshift no
known variant Reference ID: rs79761867
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC02424

known disease mutation: rs11937 (pathogenic for Maple syrup urine disease|Maple syrup urine disease type 1B|MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IB|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM014511)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014511)
known disease mutation at this position, please check HGMD for details (HGMD ID CM124309)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014511)
known disease mutation at this position, please check HGMD for details (HGMD ID CM124309)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014511)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9170.999
5.3431
(flanking)0.4260.998
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 increased62308wt: 0.9179 / mu: 0.9669 (marginal change - not scored)wt: CCTCACTATCCGGTCCCCTTGGGGCTGTGTTGGTCATGGGG
mu: CCTCACTATCCCGTCCCCTTGGGGCTGTGTTGGTCATGGGG		 cttg|GGGC
Acc increased62307wt: 0.22 / mu: 0.68wt: GCCTCACTATCCGGTCCCCTTGGGGCTGTGTTGGTCATGGG
mu: GCCTCACTATCCCGTCCCCTTGGGGCTGTGTTGGTCATGGG		 cctt|GGGG
Acc marginally increased62309wt: 0.9732 / mu: 0.9857 (marginal change - not scored)wt: CTCACTATCCGGTCCCCTTGGGGCTGTGTTGGTCATGGGGC
mu: CTCACTATCCCGTCCCCTTGGGGCTGTGTTGGTCATGGGGC		 ttgg|GGCT
Acc gained623060.46mu: AGCCTCACTATCCCGTCCCCTTGGGGCTGTGTTGGTCATGG ccct|TGGG
distance from splice site 71
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      183GDLFNCGSLTIRSPWGCVGHGALY
mutated  not conserved    183TIPSPWGCVGHGAL
Ptroglodytes  all identical  ENSPTRG00000018372  183TIRSPWGCVGHGAL
Mmulatta  no alignment  ENSMMUG00000004829  n/a
Fcatus  all identical  ENSFCAG00000010609  183TIRAPWGCVGHGAL
Mmusculus  all identical  ENSMUSG00000032263  113GDLFNCGSLTIRAPWGCVG
Ggallus  all identical  ENSGALG00000015866  183GDLFNCGNLTIRAPWGCVGHG
Trubripes  all identical  ENSTRUG00000002294  183GNLFDCGKLTIRAPWGCVGHGSL
Drerio  no alignment  ENSDARG00000086611  n/a
Dmelanogaster  all identical  FBgn0039993  155GGLFDCGSLTFRVPCGAVGHGAL
Celegans  all identical  F27D4.5  157GNQFDCGKLTVRTTWGAVGHGAL
Xtropicalis  all identical  ENSXETG00000011773  172GDLFNCGSLTIRAPWGCVGHGAL
protein features
start (aa)end (aa)featuredetails 
180187STRANDlost
193195HELIXmight get lost (downstream of altered splice site)
201205HELIXmight get lost (downstream of altered splice site)
211213STRANDmight get lost (downstream of altered splice site)
218230HELIXmight get lost (downstream of altered splice site)
231233STRANDmight get lost (downstream of altered splice site)
235240STRANDmight get lost (downstream of altered splice site)
241241MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
241243HELIXmight get lost (downstream of altered splice site)
244246TURNmight get lost (downstream of altered splice site)
249254STRANDmight get lost (downstream of altered splice site)
264267STRANDmight get lost (downstream of altered splice site)
270276STRANDmight get lost (downstream of altered splice site)
280295HELIXmight get lost (downstream of altered splice site)
299303STRANDmight get lost (downstream of altered splice site)
306309STRANDmight get lost (downstream of altered splice site)
312322HELIXmight get lost (downstream of altered splice site)
322322CONFLICTT -> S (in Ref. 8; CAA36685).might get lost (downstream of altered splice site)
325333STRANDmight get lost (downstream of altered splice site)
337349HELIXmight get lost (downstream of altered splice site)
350352HELIXmight get lost (downstream of altered splice site)
358362STRANDmight get lost (downstream of altered splice site)
372375HELIXmight get lost (downstream of altered splice site)
379390HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 657 / 657
position (AA) of stopcodon in wt / mu AA sequence 219 / 219
position of stopcodon in wt / mu cDNA 685 / 685
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 29 / 29
chromosome 6
strand 1
last intron/exon boundary 1161
theoretical NMD boundary in CDS 1082
length of CDS 657
coding sequence (CDS) position 548
cDNA position
(for ins/del: last normal base / first normal base)		 576
gDNA position
(for ins/del: last normal base / first normal base)		 62299
chromosomal position
(for ins/del: last normal base / first normal base)		 80878662
original gDNA sequence snippet CTGTGGAAGCCTCACTATCCGGTCCCCTTGGGGCTGTGTTG
altered gDNA sequence snippet CTGTGGAAGCCTCACTATCCCGTCCCCTTGGGGCTGTGTTG
original cDNA sequence snippet CTGTGGAAGCCTCACTATCCGGTCCCCTTGGGGCTGTGTTG
altered cDNA sequence snippet CTGTGGAAGCCTCACTATCCCGTCCCCTTGGGGCTGTGTTG
wildtype AA sequence MAVVAAAAGW LLRLRAAGAE GHWRRLPGAG LARGFLHPAA TVEDAAQRRQ VAHFTFQPDP
EPREYGQTQK MNLFQSVTSA LDNSLAKDPT AVIFGEDVAF GGVFRCTVGL RDKYGKDRVF
NTPLCEQGIV GFGIGIAVTG ATAIAEIQFA DYIFPAFDQI VNEAAKYRYR SGDLFNCGSL
TIRSPWGCVG HGALYHSQSP EAFFAHCPGI KIKVISLS*
mutated AA sequence MAVVAAAAGW LLRLRAAGAE GHWRRLPGAG LARGFLHPAA TVEDAAQRRQ VAHFTFQPDP
EPREYGQTQK MNLFQSVTSA LDNSLAKDPT AVIFGEDVAF GGVFRCTVGL RDKYGKDRVF
NTPLCEQGIV GFGIGIAVTG ATAIAEIQFA DYIFPAFDQI VNEAAKYRYR SGDLFNCGSL
TIPSPWGCVG HGALYHSQSP EAFFAHCPGI KIKVISLS*
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
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Problems