Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999994335 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CD1111267)
  • known disease mutation at this position (HGMD CM960713)
  • known disease mutation: rs2083 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:13007748G>AN/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.877G>A
cDNA.1022G>A
g.5909G>A
AA changes A293T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 293
frameshift no
known variant Reference ID: rs121434371
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC01212

known disease mutation: rs2083 (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 CD1111267)

known disease mutation at this position, please check HGMD for details (HGMD ID CD1111267)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960713)

known disease mutation at this position, please check HGMD for details (HGMD ID CD1111267)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960713)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960713)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8360.519
5.5731
(flanking)5.5731
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 increased5903wt: 0.3521 / mu: 0.4392 (marginal change - not scored)wt: AGGGTCCCTTCGGCTGCCTGAACAACGCCCGGTACGGCATC
mu: AGGGTCCCTTCGGCTGCCTGAACAACACCCGGTACGGCATC		 ctga|ACAA
Donor marginally increased5912wt: 0.9048 / mu: 0.9603 (marginal change - not scored)wt: ACGCCCGGTACGGCA
mu: ACACCCGGTACGGCA		 GCCC|ggta
distance from splice site 25
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      293SLGGPFGCLNNARYGIAWGVLGAS
mutated  not conserved    293SLGGPFGCLNNTRYGIAWG
Ptroglodytes  all identical  ENSPTRG00000010548  293SLGGPFGCLNNARYGIAWG
Mmulatta  all identical  ENSMMUG00000007043  293SLGGPFGCLNNARYGIAWG
Fcatus  all identical  ENSFCAG00000000477  293GLSGPFGCLNNARFGITWG
Mmusculus  all identical  ENSMUSG00000003809  293SLAGPFGCLNTARYGI
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008257  296GLAGPFGCLNNARYGI
Drerio  all identical  ENSDARG00000038361  263GLAGPFGCLNNARYGIAWGALGA
Dmelanogaster  all identical  FBgn0031824  276GFSGPFSCLNNARYGIAWGALGA
Celegans  all identical  F54D5.7  267GCLNNARLGIAWGALGA
Xtropicalis  all identical  ENSXETG00000007932  295GLGGPFGCLNNARYGI
protein features
start (aa)end (aa)featuredetails 
284318HELIXlost
287294REGIONSubstrate binding.lost
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 877
cDNA position
(for ins/del: last normal base / first normal base)		 1022
gDNA position
(for ins/del: last normal base / first normal base)		 5909
chromosomal position
(for ins/del: last normal base / first normal base)		 13007748
original gDNA sequence snippet CCTTCGGCTGCCTGAACAACGCCCGGTACGGCATCGCGTGG
altered gDNA sequence snippet CCTTCGGCTGCCTGAACAACACCCGGTACGGCATCGCGTGG
original cDNA sequence snippet CCTTCGGCTGCCTGAACAACGCCCGGTACGGCATCGCGTGG
altered cDNA sequence snippet CCTTCGGCTGCCTGAACAACACCCGGTACGGCATCGCGTGG
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 LFVVWARCED GCIRGFLLEK
GMRGLSAPRI QGKFSLRASA TGMIIMDGVE VPEENVLPGA SSLGGPFGCL NNTRYGIAWG
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