Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.997488253598832 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960711)
  • known disease mutation: rs2089 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:13007063G>CN/A show variant in all transcripts   IGV
HGNC symbol GCDH
Ensembl transcript ID ENST00000591470
Genbank transcript ID N/A
UniProt peptide Q92947
alteration type single base exchange
alteration region CDS
DNA changes c.680G>C
cDNA.825G>C
g.5224G>C
AA changes R227P Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 227
frameshift no
known variant Reference ID: rs121434373
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC02121

known disease mutation: rs2089 (pathogenic for Glutaric aciduria, type 1|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960711)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960711)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960711)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.1830.985
0.5610.979
(flanking)0.1020.975
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased5228wt: 0.54 / mu: 0.87wt: TTTGTAGTGTGGGCTCGGTGTGAAGATGGCTGCATTCGGGG
mu: TTTGTAGTGTGGGCTCCGTGTGAAGATGGCTGCATTCGGGG		 gtgt|GAAG
Donor marginally increased5226wt: 0.9927 / mu: 0.9961 (marginal change - not scored)wt: CTCGGTGTGAAGATG
mu: CTCCGTGTGAAGATG		 CGGT|gtga
distance from splice site 45
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      227SPMADLFVVWARCEDGCIRGFLLE
mutated  not conserved    227SPMADLFVVWAPCEDGCIRGFLL
Ptroglodytes  all identical  ENSPTRG00000010548  227SPMADLFVVWARCEDGCIRGFLL
Mmulatta  all identical  ENSMMUG00000007043  227SPMADLFVVWARCEDGCIRGFLL
Fcatus  all identical  ENSFCAG00000000477  227SPVADLFVVWARCEDGRIRGFLL
Mmusculus  all identical  ENSMUSG00000003809  227SPVADLFIVWARCEDNCIRGFI
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000008257  230SPVADIAVVWAKCDDGRVRGFI
Drerio  all conserved  ENSDARG00000038361  197SPVADICVVWAKCEDGKVRGFIL
Dmelanogaster  all conserved  FBgn0031824  208APIADVIVVWAKCEDGKVRGFLV
Celegans  all identical  F54D5.7  199SPVSDVMVVWARSA
Xtropicalis  not conserved  ENSXETG00000007932  229SPIADLCVVWAICEDGKVRGFL
protein features
start (aa)end (aa)featuredetails 
220228STRANDlost
233239STRANDmight get lost (downstream of altered splice site)
254256STRANDmight get lost (downstream of altered splice site)
261272STRANDmight get lost (downstream of altered splice site)
273275HELIXmight get lost (downstream of altered splice site)
284318HELIXmight get lost (downstream of altered splice site)
287294REGIONSubstrate binding.might get lost (downstream of altered splice site)
319319BINDINGFAD (By similarity).might get lost (downstream of altered splice site)
326328HELIXmight get lost (downstream of altered splice site)
330330BINDINGFAD (By similarity).might get lost (downstream of altered splice site)
330358HELIXmight get lost (downstream of altered splice site)
364388HELIXmight get lost (downstream of altered splice site)
387391NP_BINDFAD (By similarity).might get lost (downstream of altered splice site)
389394HELIXmight get lost (downstream of altered splice site)
396398HELIXmight get lost (downstream of altered splice site)
400410HELIXmight get lost (downstream of altered splice site)
413415STRANDmight get lost (downstream of altered splice site)
414414MUTAGENE->D: Reduced catalytic activity.might get lost (downstream of altered splice site)
414414ACT_SITEProton acceptor (Probable).might get lost (downstream of altered splice site)
415415BINDINGSubstrate; via amide nitrogen.might get lost (downstream of altered splice site)
416418NP_BINDFAD.might get lost (downstream of altered splice site)
417429HELIXmight get lost (downstream of altered splice site)
434434BINDINGFAD; via carbonyl oxygen.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1317 / 1317
position (AA) of stopcodon in wt / mu AA sequence 439 / 439
position of stopcodon in wt / mu cDNA 1462 / 1462
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 146 / 146
chromosome 19
strand 1
last intron/exon boundary 1389
theoretical NMD boundary in CDS 1193
length of CDS 1317
coding sequence (CDS) position 680
cDNA position
(for ins/del: last normal base / first normal base)		 825
gDNA position
(for ins/del: last normal base / first normal base)		 5224
chromosomal position
(for ins/del: last normal base / first normal base)		 13007063
original gDNA sequence snippet TCTGTTTGTAGTGTGGGCTCGGTGTGAAGATGGCTGCATTC
altered gDNA sequence snippet TCTGTTTGTAGTGTGGGCTCCGTGTGAAGATGGCTGCATTC
original cDNA sequence snippet TCTGTTTGTAGTGTGGGCTCGGTGTGAAGATGGCTGCATTC
altered cDNA sequence snippet TCTGTTTGTAGTGTGGGCTCCGTGTGAAGATGGCTGCATTC
wildtype AA sequence MALRGVSVRL LSRGPGLHVL RTWVSSAAQT EKGGRTQSQL AKSSRPEFDW QDPLVLEEQL
TTDEILIRDT FRTYCQERLM PRILLANRNE VFHREIISEM GELGVLGPTI KGYGCAGVSS
VAYGLLAREL ERVDSGYRSA MSVQSSLVMH PIYAYGSEEQ RQKYLPQLAK GELLGCFGLT
EPNSGSDPSS METRAHYNSS NKSYTLNGTK TWITNSPMAD LFVVWARCED GCIRGFLLEK
GMRGLSAPRI QGKFSLRASA TGMIIMDGVE VPEENVLPGA SSLGGPFGCL NNARYGIAWG
VLGASEFCLH TARQYALDRM QFGVPLARNQ LIQKKLADML TEITLGLHAC LQLGRLKDQD
KAAPEMVSLL KRNNCGKALD IARQARDMLG GNGISDEYHV IRHAMNLEAV NTYEGTHDIH
ALILGRAITG IQAFTASK*
mutated AA sequence MALRGVSVRL LSRGPGLHVL RTWVSSAAQT EKGGRTQSQL AKSSRPEFDW QDPLVLEEQL
TTDEILIRDT FRTYCQERLM PRILLANRNE VFHREIISEM GELGVLGPTI KGYGCAGVSS
VAYGLLAREL ERVDSGYRSA MSVQSSLVMH PIYAYGSEEQ RQKYLPQLAK GELLGCFGLT
EPNSGSDPSS METRAHYNSS NKSYTLNGTK TWITNSPMAD LFVVWAPCED GCIRGFLLEK
GMRGLSAPRI QGKFSLRASA TGMIIMDGVE VPEENVLPGA SSLGGPFGCL NNARYGIAWG
VLGASEFCLH TARQYALDRM QFGVPLARNQ LIQKKLADML TEITLGLHAC LQLGRLKDQD
KAAPEMVSLL KRNNCGKALD IARQARDMLG GNGISDEYHV IRHAMNLEAV NTYEGTHDIH
ALILGRAITG IQAFTASK*
speed 0.94 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