Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999980348319276 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920303)
  • known disease mutation: rs2081 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:13007754T>CN/A show variant in all transcripts   IGV
HGNC symbol GCDH
Ensembl transcript ID ENST00000457854
Genbank transcript ID NM_013976
UniProt peptide Q92947
alteration type single base exchange
alteration region CDS
DNA changes c.883T>C
cDNA.960T>C
g.5915T>C
AA changes Y295H Score: 83 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 295
frameshift no
known variant Reference ID: rs121434366
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs2081 (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 CM920303)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920303)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920303)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.6440.138
4.6030.75
(flanking)0.380.725
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 increased5912wt: 0.9048 / mu: 0.9599 (marginal change - not scored)wt: ACGCCCGGTACGGCA
mu: ACGCCCGGCACGGCA		 GCCC|ggta
distance from splice site 31
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      295GGPFGCLNNARYGIAWGVLGASEF
mutated  all conserved    295GGPFGCLNNARHGIAWG
Ptroglodytes  all identical  ENSPTRG00000010548  295GGPFGCLNNARYGIAWG
Mmulatta  all identical  ENSMMUG00000007043  295GGPFGCLNNARYGIAWG
Fcatus  all conserved  ENSFCAG00000000477  295SGPFGCLNNARFGITWG
Mmusculus  all identical  ENSMUSG00000003809  295AGPFGCLNTARYGI
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008257  298AGPFGCLNNARYGI
Drerio  all identical  ENSDARG00000038361  265AGPFGCLNNARYGIAWGALGAAE
Dmelanogaster  all identical  FBgn0031824  278SGPFSCLNNARYGIAWGALGAAE
Celegans  not conserved  F54D5.7  269GCLNNARLGIAWGALGAAE
Xtropicalis  all identical  ENSXETG00000007932  297GGPFGCLNNARYGI
protein features
start (aa)end (aa)featuredetails 
284318HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1287 / 1287
position (AA) of stopcodon in wt / mu AA sequence 429 / 429
position of stopcodon in wt / mu cDNA 1364 / 1364
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 78 / 78
chromosome 19
strand 1
last intron/exon boundary 1321
theoretical NMD boundary in CDS 1193
length of CDS 1287
coding sequence (CDS) position 883
cDNA position
(for ins/del: last normal base / first normal base)		 960
gDNA position
(for ins/del: last normal base / first normal base)		 5915
chromosomal position
(for ins/del: last normal base / first normal base)		 13007754
original gDNA sequence snippet GCTGCCTGAACAACGCCCGGTACGGCATCGCGTGGGGCGTG
altered gDNA sequence snippet GCTGCCTGAACAACGCCCGGCACGGCATCGCGTGGGGCGTG
original cDNA sequence snippet GCTGCCTGAACAACGCCCGGTACGGCATCGCGTGGGGCGTG
altered cDNA sequence snippet GCTGCCTGAACAACGCCCGGCACGGCATCGCGTGGGGCGTG
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 NTYEVVQMCS
LKRRWNSL*
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 NNARHGIAWG
VLGASEFCLH TARQYALDRM QFGVPLARNQ LIQKKLADML TEITLGLHAC LQLGRLKDQD
KAAPEMVSLL KRNNCGKALD IARQARDMLG GNGISDEYHV IRHAMNLEAV NTYEVVQMCS
LKRRWNSL*
speed 1.30 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