Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999946452 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960719)
  • known disease mutation: rs2085 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:13008638C>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.1204C>T
cDNA.1415C>T
g.6799C>T
AA changes R402W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 402
frameshift no
known variant Reference ID: rs121434369
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC02727

known disease mutation: rs2085 (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 CM960719)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960719)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960719)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.2071
3.7981
(flanking)5.6691
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 increased6804wt: 0.9900 / mu: 0.9929 (marginal change - not scored)wt: CGGCACGCCATGAAC
mu: TGGCACGCCATGAAC		 GCAC|gcca
Donor increased6792wt: 0.25 / mu: 0.56wt: TATCACGTGATCCGG
mu: TATCACGTGATCTGG		 TCAC|gtga
distance from splice site 40
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      402GNGISDEYHVIRHAMNLEAVNTYE
mutated  not conserved    402GNGISDEYHVIWHAMNLEAVNTY
Ptroglodytes  all identical  ENSPTRG00000010548  402GNGISDEYHVIRHAMNLEAVNTY
Mmulatta  all identical  ENSMMUG00000007043  402GNGISDEYHVIRHAMNLEAVNTY
Fcatus  all identical  ENSFCAG00000000477  402GNGISDEYHVIRHVMNLESVNTY
Mmusculus  all identical  ENSMUSG00000003809  402GNGISDEYHVIRHAMNLEAVNTY
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008257  405GNGISDEYHIIRHVMNLEAVNTY
Drerio  all identical  ENSDARG00000038361  372GNGIADEYHIIRHVLNLEAVNTY
Dmelanogaster  all identical  FBgn0031824  385GISDEYHVIRHVINLESVNTY
Celegans  all identical  F54D5.7  376GNGIVDEYHIMRHMVNL
Xtropicalis  all identical  ENSXETG00000007932  404GNGISDEYHIIRHVMNLESVNTY
protein features
start (aa)end (aa)featuredetails 
400410HELIXlost
413415STRANDmight get lost (downstream of altered splice site)
414414ACT_SITEProton acceptor (Probable).might get lost (downstream of altered splice site)
414414MUTAGENE->D: Reduced catalytic activity.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 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 1204
cDNA position
(for ins/del: last normal base / first normal base)		 1415
gDNA position
(for ins/del: last normal base / first normal base)		 6799
chromosomal position
(for ins/del: last normal base / first normal base)		 13008638
original gDNA sequence snippet CTGACGAGTATCACGTGATCCGGCACGCCATGAACCTGGAG
altered gDNA sequence snippet CTGACGAGTATCACGTGATCTGGCACGCCATGAACCTGGAG
original cDNA sequence snippet CTGACGAGTATCACGTGATCCGGCACGCCATGAACCTGGAG
altered cDNA sequence snippet CTGACGAGTATCACGTGATCTGGCACGCCATGAACCTGGAG
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 IWHAMNLEAV NTYEGTHDIH
ALILGRAITG IQAFTASK*
speed 0.55 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