Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999977598 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM045934)
  • known disease mutation: rs2382 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:41928214C>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.792C>G
cDNA.1160C>G
g.24850C>G
AA changes C264W Score: 215 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 264
frameshift no
known variant Reference ID: rs137852876
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2382 (pathogenic for Maple syrup urine disease type 1A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM045934)

known disease mutation at this position, please check HGMD for details (HGMD ID CM045934)
known disease mutation at this position, please check HGMD for details (HGMD ID CM045934)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.5651
0.9791
(flanking)3.7731
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased24842wt: 0.48 / mu: 0.62wt: CACTTGAGTGCCCCATCATCTTCTTCTGCCGGAACAATGGC
mu: CACTTGAGTGCCCCATCATCTTCTTCTGGCGGAACAATGGC		 atct|TCTT
Acc increased24849wt: 0.82 / mu: 0.96wt: GTGCCCCATCATCTTCTTCTGCCGGAACAATGGCTACGCCA
mu: GTGCCCCATCATCTTCTTCTGGCGGAACAATGGCTACGCCA		 tctg|CCGG
Acc marginally increased24844wt: 0.5136 / mu: 0.5513 (marginal change - not scored)wt: CTTGAGTGCCCCATCATCTTCTTCTGCCGGAACAATGGCTA
mu: CTTGAGTGCCCCATCATCTTCTTCTGGCGGAACAATGGCTA		 cttc|TTCT
distance from splice site 62
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      264AATLECPIIFFCRNNGYAISTPTS
mutated  not conserved    264AATLECPIIFFWRNNGYAISTPT
Ptroglodytes  all identical  ENSPTRG00000011025  264AATLECPIIFFCRNNGYAISTPT
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000060376  265AATLECPIIFFCRNNGYAISTPT
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000009706  265SATLECPLIFFCRNNGYAISTPT
Drerio  all identical  ENSDARG00000040555  265SATLECPLIFFCRNNGYAISTPT
Dmelanogaster  all identical  FBgn0037709  257AATLGCPAILFCRNNGFAISTPS
Celegans  all identical  Y39E4A.3  249AATLKCPIIFFCRNNGYAISTPT
Xtropicalis  all identical  ENSXETG00000018753  227SATLECPVLFFCRNNGYAISTPT
protein features
start (aa)end (aa)featuredetails 
260266STRANDlost
268270STRANDmight get lost (downstream of altered splice site)
275277HELIXmight get lost (downstream of altered splice site)
280282STRANDmight get lost (downstream of altered splice site)
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 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 792
cDNA position
(for ins/del: last normal base / first normal base)		 1160
gDNA position
(for ins/del: last normal base / first normal base)		 24850
chromosomal position
(for ins/del: last normal base / first normal base)		 41928214
original gDNA sequence snippet TGCCCCATCATCTTCTTCTGCCGGAACAATGGCTACGCCAT
altered gDNA sequence snippet TGCCCCATCATCTTCTTCTGGCGGAACAATGGCTACGCCAT
original cDNA sequence snippet TGCCCCATCATCTTCTTCTGCCGGAACAATGGCTACGCCAT
altered cDNA sequence snippet TGCCCCATCATCTTCTTCTGGCGGAACAATGGCTACGCCAT
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 IFFWRNNGYA ISTPTSEQYR GDGIAARGPG YGIMSIRVDG
NDVFAVYNAT KEARRRAVAE NQPFLIEAMT YRIGHHSTSD DSSAYRSVDE VNYWDKQDHP
ISRLRHYLLS QGWWDEEQEK AWRKQSRRKV MEAFEQAERK PKPNPNLLFS DVYQEMPAQL
RKQQESLARH LQTYGEHYPL DHFDK*
speed 1.23 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