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: ENST00000540732
Querying Taster for transcript #2: ENST00000269980
Querying Taster for transcript #3: ENST00000457836
MT speed 3.35 s - this script 6.955705 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BCKDHAdisease_causing_automatic0.999999998469745simple_aaeaffected0T288Rsingle base exchangers137852875show file
BCKDHAdisease_causing_automatic0.999999999748912simple_aaeaffected0T310Rsingle base exchangers137852875show file

some transcripts had annotation problems and are not shown

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999998469745 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM984180)
  • known disease mutation: rs2381 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:41928609C>GN/A show variant in all transcripts   IGV
HGNC symbol BCKDHA
Ensembl transcript ID ENST00000457836
Genbank transcript ID N/A
UniProt peptide P12694
alteration type single base exchange
alteration region CDS
DNA changes c.863C>G
cDNA.868C>G
g.25245C>G
AA changes T288R Score: 71 explain score(s)
position(s) of altered AA
if AA alteration in CDS
288
frameshift no
known variant Reference ID: rs137852875
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2381 (pathogenic for Maple syrup urine disease type 1A|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM984180)

known disease mutation at this position, please check HGMD for details (HGMD ID CM984180)
known disease mutation at this position, please check HGMD for details (HGMD ID CM984180)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.8821
5.9131
(flanking)-0.3070.95
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 increased25235wt: 0.2671 / mu: 0.3013 (marginal change - not scored)wt: GTAATGATGTGTTTGCCGTATACAACGCCACAAAGGAGGCC
mu: GTAATGATGTGTTTGCCGTATACAACGCCAGAAAGGAGGCC
 gtat|ACAA
Donor increased25244wt: 0.46 / mu: 0.97wt: ACGCCACAAAGGAGG
mu: ACGCCAGAAAGGAGG
 GCCA|caaa
distance from splice site 67
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      288DGNDVFAVYNATKEARRRAVAENQ
mutated  not conserved    288DGNDVFAVYNARKEARRRAVAEN
Ptroglodytes  all identical  ENSPTRG00000011025  310NDVFAVYNATKEARRRAVAEN
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000060376  311GNDVFAVYNATKEARRRAVAEN
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000009706  311DGNDVFAVYNATKEARRRAVAEN
Drerio  all identical  ENSDARG00000040555  311DGNDVFAVYNATKEARRRAVAEN
Dmelanogaster  not conserved  FBgn0037709  303DGTDVFAVYNAMKAAREYVLKEN
Celegans  all identical  Y39E4A.3  295DGNDLLAVYNATKEARRVALT-N
Xtropicalis  all identical  ENSXETG00000018753  273DGNDVFAVYNATKEARRRAVAEN
protein features
start (aa)end (aa)featuredetails 
285287HELIXmight get lost (downstream of altered splice site)
289291HELIXmight get lost (downstream of altered splice site)
294299STRANDmight get lost (downstream of altered splice site)
303320HELIXmight get lost (downstream of altered splice site)
324329STRANDmight get lost (downstream of altered splice site)
337337MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
342344HELIXmight get lost (downstream of altered splice site)
345345MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
347347MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
351357HELIXmight get lost (downstream of altered splice site)
360368HELIXmight get lost (downstream of altered splice site)
369372TURNmight get lost (downstream of altered splice site)
376399HELIXmight get lost (downstream of altered splice site)
405408HELIXmight get lost (downstream of altered splice site)
409411TURNmight get lost (downstream of altered splice site)
412415STRANDmight get lost (downstream of altered splice site)
418434HELIXmight get lost (downstream of altered splice site)
435437HELIXmight get lost (downstream of altered splice site)
440442HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1347 / 1347
position (AA) of stopcodon in wt / mu AA sequence 449 / 449
position of stopcodon in wt / mu cDNA 1352 / 1352
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 6 / 6
chromosome 19
strand 1
last intron/exon boundary 1182
theoretical NMD boundary in CDS 1126
length of CDS 1347
coding sequence (CDS) position 863
cDNA position
(for ins/del: last normal base / first normal base)
868
gDNA position
(for ins/del: last normal base / first normal base)
25245
chromosomal position
(for ins/del: last normal base / first normal base)
41928609
original gDNA sequence snippet GTTTGCCGTATACAACGCCACAAAGGAGGCCCGACGGCGGG
altered gDNA sequence snippet GTTTGCCGTATACAACGCCAGAAAGGAGGCCCGACGGCGGG
original cDNA sequence snippet GTTTGCCGTATACAACGCCACAAAGGAGGCCCGACGGCGGG
altered cDNA sequence snippet GTTTGCCGTATACAACGCCAGAAAGGAGGCCCGACGGCGGG
wildtype AA sequence MAVAIAAARV WRLNRGLSQQ QQFSSLDDKP QFPGASAEFI DKLEFIQPNV ISGIPIYRVM
DRQGQIINPS EDPHLPKEKV LKLYKSMTLL NTMDRILYES QRQGRISFYM TNYGEEGTHV
GSAAALDNTD LVFGQYREAG VLMYRDYPLE LFMAQCYGNI SDLGKGRQMP VHYGCKERHF
VTISSPLATQ IPQAVGAAYA AKRANANRVV ICYFGEGAAS EGDAHAGFNF AATLECPIIF
FCRNNGYAIS TPTSEQYRGD GIAARGPGYG IMSIRVDGND VFAVYNATKE ARRRAVAENQ
PFLIEAMTYS SSPILPPDPH SREPTLTWGP LPLCRIGHHS TSDDSSAYRS VDEVNYWDKQ
DHPISRLRHY LLSQGWWDEE QEKAWRKQSR RKVMEAFEQA ERKPKPNPNL LFSDVYQEMP
AQLRKQQESL ARHLQTYGEH YPLDHFDK*
mutated AA sequence MAVAIAAARV WRLNRGLSQQ QQFSSLDDKP QFPGASAEFI DKLEFIQPNV ISGIPIYRVM
DRQGQIINPS EDPHLPKEKV LKLYKSMTLL NTMDRILYES QRQGRISFYM TNYGEEGTHV
GSAAALDNTD LVFGQYREAG VLMYRDYPLE LFMAQCYGNI SDLGKGRQMP VHYGCKERHF
VTISSPLATQ IPQAVGAAYA AKRANANRVV ICYFGEGAAS EGDAHAGFNF AATLECPIIF
FCRNNGYAIS TPTSEQYRGD GIAARGPGYG IMSIRVDGND VFAVYNARKE ARRRAVAENQ
PFLIEAMTYS SSPILPPDPH SREPTLTWGP LPLCRIGHHS TSDDSSAYRS VDEVNYWDKQ
DHPISRLRHY LLSQGWWDEE QEKAWRKQSR RKVMEAFEQA ERKPKPNPNL LFSDVYQEMP
AQLRKQQESL ARHLQTYGEH YPLDHFDK*
speed 1.65 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: 0.999999999748912 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM984180)
  • known disease mutation: rs2381 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:41928609C>GN/A show variant in all transcripts   IGV
HGNC symbol BCKDHA
Ensembl transcript ID ENST00000269980
Genbank transcript ID NM_000709
UniProt peptide P12694
alteration type single base exchange
alteration region CDS
DNA changes c.929C>G
cDNA.1297C>G
g.25245C>G
AA changes T310R Score: 71 explain score(s)
position(s) of altered AA
if AA alteration in CDS
310
frameshift no
known variant Reference ID: rs137852875
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2381 (pathogenic for Maple syrup urine disease type 1A|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM984180)

known disease mutation at this position, please check HGMD for details (HGMD ID CM984180)
known disease mutation at this position, please check HGMD for details (HGMD ID CM984180)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.8821
5.9131
(flanking)-0.3070.95
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 increased25235wt: 0.2671 / mu: 0.3013 (marginal change - not scored)wt: GTAATGATGTGTTTGCCGTATACAACGCCACAAAGGAGGCC
mu: GTAATGATGTGTTTGCCGTATACAACGCCAGAAAGGAGGCC
 gtat|ACAA
Donor increased25244wt: 0.46 / mu: 0.97wt: ACGCCACAAAGGAGG
mu: ACGCCAGAAAGGAGG
 GCCA|caaa
distance from splice site 67
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      310DGNDVFAVYNATKEARRRAVAENQ
mutated  not conserved    310NDVFAVYNARKEARRRAVAEN
Ptroglodytes  all identical  ENSPTRG00000011025  310NDVFAVYNATKEARRRAVAEN
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000060376  311GNDVFAVYNATKEARRRAVAEN
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000009706  311DGNDVFAVYNATKEARRRAVAEN
Drerio  all identical  ENSDARG00000040555  311DGNDVFAVYNATKEARRRAVAEN
Dmelanogaster  not conserved  FBgn0037709  303DGTDVFAVYNAMKAAREYVLKEN
Celegans  all identical  Y39E4A.3  295DGNDLLAVYNATKEARRVALT-N
Xtropicalis  all identical  ENSXETG00000018753  273DGNDVFAVYNATKEARRRAVAEN
protein features
start (aa)end (aa)featuredetails 
303320HELIXlost
324329STRANDmight get lost (downstream of altered splice site)
337337MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
342344HELIXmight get lost (downstream of altered splice site)
345345MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
347347MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
351357HELIXmight get lost (downstream of altered splice site)
360368HELIXmight get lost (downstream of altered splice site)
369372TURNmight get lost (downstream of altered splice site)
376399HELIXmight get lost (downstream of altered splice site)
405408HELIXmight get lost (downstream of altered splice site)
409411TURNmight get lost (downstream of altered splice site)
412415STRANDmight get lost (downstream of altered splice site)
418434HELIXmight get lost (downstream of altered splice site)
435437HELIXmight get lost (downstream of altered splice site)
440442HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1338 / 1338
position (AA) of stopcodon in wt / mu AA sequence 446 / 446
position of stopcodon in wt / mu cDNA 1706 / 1706
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 369 / 369
chromosome 19
strand 1
last intron/exon boundary 1536
theoretical NMD boundary in CDS 1117
length of CDS 1338
coding sequence (CDS) position 929
cDNA position
(for ins/del: last normal base / first normal base)
1297
gDNA position
(for ins/del: last normal base / first normal base)
25245
chromosomal position
(for ins/del: last normal base / first normal base)
41928609
original gDNA sequence snippet GTTTGCCGTATACAACGCCACAAAGGAGGCCCGACGGCGGG
altered gDNA sequence snippet GTTTGCCGTATACAACGCCAGAAAGGAGGCCCGACGGCGGG
original cDNA sequence snippet GTTTGCCGTATACAACGCCACAAAGGAGGCCCGACGGCGGG
altered cDNA sequence snippet GTTTGCCGTATACAACGCCAGAAAGGAGGCCCGACGGCGGG
wildtype AA sequence MAVAIAAARV WRLNRGLSQA ALLLLRQPGA RGLARSHPPR QQQQFSSLDD KPQFPGASAE
FIDKLEFIQP NVISGIPIYR VMDRQGQIIN PSEDPHLPKE KVLKLYKSMT LLNTMDRILY
ESQRQGRISF YMTNYGEEGT HVGSAAALDN TDLVFGQYRE AGVLMYRDYP LELFMAQCYG
NISDLGKGRQ MPVHYGCKER HFVTISSPLA TQIPQAVGAA YAAKRANANR VVICYFGEGA
ASEGDAHAGF NFAATLECPI IFFCRNNGYA ISTPTSEQYR GDGIAARGPG YGIMSIRVDG
NDVFAVYNAT KEARRRAVAE NQPFLIEAMT YRIGHHSTSD DSSAYRSVDE VNYWDKQDHP
ISRLRHYLLS QGWWDEEQEK AWRKQSRRKV MEAFEQAERK PKPNPNLLFS DVYQEMPAQL
RKQQESLARH LQTYGEHYPL DHFDK*
mutated AA sequence MAVAIAAARV WRLNRGLSQA ALLLLRQPGA RGLARSHPPR QQQQFSSLDD KPQFPGASAE
FIDKLEFIQP NVISGIPIYR VMDRQGQIIN PSEDPHLPKE KVLKLYKSMT LLNTMDRILY
ESQRQGRISF YMTNYGEEGT HVGSAAALDN TDLVFGQYRE AGVLMYRDYP LELFMAQCYG
NISDLGKGRQ MPVHYGCKER HFVTISSPLA TQIPQAVGAA YAAKRANANR VVICYFGEGA
ASEGDAHAGF NFAATLECPI IFFCRNNGYA ISTPTSEQYR GDGIAARGPG YGIMSIRVDG
NDVFAVYNAR KEARRRAVAE NQPFLIEAMT YRIGHHSTSD DSSAYRSVDE VNYWDKQDHP
ISRLRHYLLS QGWWDEEQEK AWRKQSRRKV MEAFEQAERK PKPNPNLLFS DVYQEMPAQL
RKQQESLARH LQTYGEHYPL DHFDK*
speed 1.70 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