Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999914737497853 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960718)
  • known disease mutation: rs2088 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:13008632G>AN/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.1198G>A
cDNA.1275G>A
g.6793G>A
AA changes V400M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 400
frameshift no
known variant Reference ID: rs121434372
databasehomozygous (A/A)heterozygousallele carriers
1000G011
ExAC099

known disease mutation: rs2088 (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 CM960718)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960718)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960718)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0110.988
2.6081
(flanking)4.6821
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 46
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      400LGGNGISDEYHVIRHAMNLEAVNT
mutated  all conserved    400LGGNGISDEYHMIRHAMNLEAVN
Ptroglodytes  all identical  ENSPTRG00000010548  400LGGNGISDEYHVIRHAMNLEAVN
Mmulatta  all identical  ENSMMUG00000007043  400LGGNGISDEYHVIRHAMNLEAVN
Fcatus  all identical  ENSFCAG00000000477  400LGGNGISDEYHVIRHVMNLESVN
Mmusculus  all identical  ENSMUSG00000003809  400LGGNGISDEYHVIRHAMNLEAVN
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000008257  403LGGNGISDEYHIIRHVMNLEAVN
Drerio  all conserved  ENSDARG00000038361  370GNGIADEYHIIRHVLNLEAVN
Dmelanogaster  all identical  FBgn0031824  383GISDEYHVIRHVINLESVN
Celegans  all conserved  F54D5.7  374LGGNGIVDEYHIMRHMVNL
Xtropicalis  all conserved  ENSXETG00000007932  402LGGNGISDEYHIIRHVMNLESVN
protein features
start (aa)end (aa)featuredetails 
400410HELIXlost
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 1198
cDNA position
(for ins/del: last normal base / first normal base)		 1275
gDNA position
(for ins/del: last normal base / first normal base)		 6793
chromosomal position
(for ins/del: last normal base / first normal base)		 13008632
original gDNA sequence snippet GGATTTCTGACGAGTATCACGTGATCCGGCACGCCATGAAC
altered gDNA sequence snippet GGATTTCTGACGAGTATCACATGATCCGGCACGCCATGAAC
original cDNA sequence snippet GGATTTCTGACGAGTATCACGTGATCCGGCACGCCATGAAC
altered cDNA sequence snippet GGATTTCTGACGAGTATCACATGATCCGGCACGCCATGAAC
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 NNARYGIAWG
VLGASEFCLH TARQYALDRM QFGVPLARNQ LIQKKLADML TEITLGLHAC LQLGRLKDQD
KAAPEMVSLL KRNNCGKALD IARQARDMLG GNGISDEYHM IRHAMNLEAV NTYEVVQMCS
LKRRWNSL*
speed 0.97 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