Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999938592 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950135)
  • known disease mutation: rs2377 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:41928548G>AN/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.868G>A
cDNA.1236G>A
g.25184G>A
AA changes G290R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 290
frameshift no
known variant Reference ID: rs137852871
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC033

known disease mutation: rs2377 (pathogenic for Maple syrup urine disease|Maple syrup urine disease type 1A|MAPLE SYRUP URINE DISEASE, INTERMEDIATE, TYPE IA|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950135)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950135)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950135)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.1040.039
5.9131
(flanking)5.9131
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased25184wt: 0.52 / mu: 0.98wt: GCCCCGGGTATGGCA
mu: GCCCCAGGTATGGCA		 CCCG|ggta
Donor gained251800.43mu: CGAGGCCCCAGGTAT AGGC|ccca
distance from splice site 15
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      290YRGDGIAARGPGYGIMSIRVDGND
mutated  not conserved    290YRGDGIAARGPRYGIMSIRVDG
Ptroglodytes  all identical  ENSPTRG00000011025  290YRGDGIAARGPGYGIMSIRVDG
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000060376  291YRGDGIAARGPGYGIMSIRVD
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000009706  291DGIAARGPGYGMLSIRVDGN
Drerio  all identical  ENSDARG00000040555  291YRGDGIAARGPGYGLMSIRVDGN
Dmelanogaster  all identical  FBgn0037709  283GPMGYGITTIRVDGT
Celegans  not conserved  Y39E4A.3  275YGGDGIAGKGPAYGLHTIR
Xtropicalis  all identical  ENSXETG00000018753  253RGDGIAARGPGYGIMSIRVDGN
protein features
start (aa)end (aa)featuredetails 
289291HELIXlost
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 868
cDNA position
(for ins/del: last normal base / first normal base)		 1236
gDNA position
(for ins/del: last normal base / first normal base)		 25184
chromosomal position
(for ins/del: last normal base / first normal base)		 41928548
original gDNA sequence snippet CCACAGCAGCACGAGGCCCCGGGTATGGCATCATGTCAATC
altered gDNA sequence snippet CCACAGCAGCACGAGGCCCCAGGTATGGCATCATGTCAATC
original cDNA sequence snippet GCATTGCAGCACGAGGCCCCGGGTATGGCATCATGTCAATC
altered cDNA sequence snippet GCATTGCAGCACGAGGCCCCAGGTATGGCATCATGTCAATC
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 GDGIAARGPR YGIMSIRVDG
NDVFAVYNAT KEARRRAVAE NQPFLIEAMT YRIGHHSTSD DSSAYRSVDE VNYWDKQDHP
ISRLRHYLLS QGWWDEEQEK AWRKQSRRKV MEAFEQAERK PKPNPNLLFS DVYQEMPAQL
RKQQESLARH LQTYGEHYPL DHFDK*
speed 0.56 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