Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999150751 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950136)
  • known disease mutation: rs2378 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:41930401T>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.1235T>G
cDNA.1240T>G
g.27037T>G
AA changes F412C Score: 205 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 412
frameshift no
known variant Reference ID: rs137852872
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2378 (pathogenic for Maple syrup urine disease type 1A|MAPLE SYRUP URINE DISEASE, INTERMEDIATE, TYPE IA) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950136)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950136)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950136)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.7211
4.7211
(flanking)2.1141
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased27039wt: 0.8077 / mu: 0.8766 (marginal change - not scored)wt: TCTTCTCAGACGTGT
mu: TCTGCTCAGACGTGT		 TTCT|caga
Donor gained270360.46mu: TACTCTGCTCAGACG CTCT|gctc
distance from splice site 59
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      412ERKPKPNPNLLFSDVYQEMPAQLR
mutated  not conserved    412ERKPKPNPNLLCSDVYQEMP
Ptroglodytes  all identical  ENSPTRG00000011025  409ERKPKPNPNLLFSDVYQEMPAQL
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000060376  410ERKLKPNPSLLFSDVYQEMPAQL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000009706  410EKRLKPNPELLFTDVYDEMTPTL
Drerio  all identical  ENSDARG00000040555  410ERRLKPNPDLMFTDVYDEMVP
Dmelanogaster  all identical  FBgn0037709  403EKKLKPNWREMFEGVYAEMPDHL
Celegans  all identical  Y39E4A.3  393EKRKKAHYHDLFEDVYDELPLRL
Xtropicalis  all identical  ENSXETG00000018753  372ERKHKPKVEHMFSDVYSEMPAQL
protein features
start (aa)end (aa)featuredetails 
409411TURNmight get lost (downstream of altered splice site)
412415STRANDlost
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 1235
cDNA position
(for ins/del: last normal base / first normal base)		 1240
gDNA position
(for ins/del: last normal base / first normal base)		 27037
chromosomal position
(for ins/del: last normal base / first normal base)		 41930401
original gDNA sequence snippet ACCCAACCCCAACCTACTCTTCTCAGACGTGTATCAGGAGA
altered gDNA sequence snippet ACCCAACCCCAACCTACTCTGCTCAGACGTGTATCAGGAGA
original cDNA sequence snippet ACCCAACCCCAACCTACTCTTCTCAGACGTGTATCAGGAGA
altered cDNA sequence snippet ACCCAACCCCAACCTACTCTGCTCAGACGTGTATCAGGAGA
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 VFAVYNATKE ARRRAVAENQ
PFLIEAMTYS SSPILPPDPH SREPTLTWGP LPLCRIGHHS TSDDSSAYRS VDEVNYWDKQ
DHPISRLRHY LLSQGWWDEE QEKAWRKQSR RKVMEAFEQA ERKPKPNPNL LCSDVYQEMP
AQLRKQQESL ARHLQTYGEH YPLDHFDK*
speed 1.06 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