Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999865279 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960721)
  • known disease mutation: rs2084 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:13010285C>TN/A show variant in all transcripts   IGV
HGNC symbol GCDH
Ensembl transcript ID ENST00000222214
Genbank transcript ID NM_000159
UniProt peptide Q92947
alteration type single base exchange
alteration region CDS
DNA changes c.1247C>T
cDNA.1458C>T
g.8446C>T
AA changes T416I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 416
frameshift no
known variant Reference ID: rs121434368
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs2084 (pathogenic for Glutaric aciduria, type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.6291
5.6051
(flanking)-0.5650.864
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 increased8450wt: 0.2395 / mu: 0.2405 (marginal change - not scored)wt: ACACATGACATTCAC
mu: ATACATGACATTCAC		 ACAT|gaca
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      416MNLEAVNTYEGTHDIHALILGRAI
mutated  not conserved    416MNLEAVNTYEGIHDIH
Ptroglodytes  all identical  ENSPTRG00000010548  416MNLEAVNTYEGTHDIH
Mmulatta  all identical  ENSMMUG00000007043  416MNLEAVNTYEGTHDIH
Fcatus  all identical  ENSFCAG00000000477  416MNLESVNTYEGTHDIH
Mmusculus  all identical  ENSMUSG00000003809  416MNLEAVNTYEGTHDIHALILGRA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008257  422GTHDIHALILGRA
Drerio  not conserved  ENSDARG00000038361  386LNLEAVNTYEGQRE
Dmelanogaster  all identical  FBgn0031824  399INLESVNTYEGTHDIHALILGRA
Celegans  all identical  F54D5.7  390ETVNTYEGTHDVHALILGRA
Xtropicalis  all identical  ENSXETG00000007932  418MNLESVNTYEGTHDVHALILGRA
protein features
start (aa)end (aa)featuredetails 
416418NP_BINDFAD.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 1528 / 1528
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 212 / 212
chromosome 19
strand 1
last intron/exon boundary 1455
theoretical NMD boundary in CDS 1193
length of CDS 1317
coding sequence (CDS) position 1247
cDNA position
(for ins/del: last normal base / first normal base)		 1458
gDNA position
(for ins/del: last normal base / first normal base)		 8446
chromosomal position
(for ins/del: last normal base / first normal base)		 13010285
original gDNA sequence snippet GTATTAATCTTGTCCAGGTACACATGACATTCACGCCCTGA
altered gDNA sequence snippet GTATTAATCTTGTCCAGGTATACATGACATTCACGCCCTGA
original cDNA sequence snippet CGTGAACACCTACGAAGGTACACATGACATTCACGCCCTGA
altered cDNA sequence snippet CGTGAACACCTACGAAGGTATACATGACATTCACGCCCTGA
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 NNARYGIAWG
VLGASEFCLH TARQYALDRM QFGVPLARNQ LIQKKLADML TEITLGLHAC LQLGRLKDQD
KAAPEMVSLL KRNNCGKALD IARQARDMLG GNGISDEYHV IRHAMNLEAV NTYEGIHDIH
ALILGRAITG IQAFTASK*
speed 0.71 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