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 ENST00000422947
Genbank transcript ID N/A
UniProt peptide Q92947
alteration type single base exchange
alteration region CDS
DNA changes c.1072C>T
cDNA.1330C>T
g.6799C>T
AA changes R358W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 358
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      358GNGISDEYHVIRHAMNLEAVNTYE
mutated  not conserved    358GNGISDEYHVIWHA
Ptroglodytes  all identical  ENSPTRG00000010548  402GNGISDEYHVIRHAMNLEA
Mmulatta  all identical  ENSMMUG00000007043  402GNGISDEYHVIRHAMNLEA
Fcatus  all identical  ENSFCAG00000000477  402GNGISDEYHVIRHVMNLESVNT
Mmusculus  all identical  ENSMUSG00000003809  402GNGISDEYHVIRHAMNLEA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008257  405GNGISDEYHIIRHVMN
Drerio  all identical  ENSDARG00000038361  372GNGIADEYHIIRHVLNLEA
Dmelanogaster  all identical  FBgn0031824  385ANGISDEYHVIRHVINL
Celegans  all identical  F54D5.7  376GNGIVDEYHIMRHMVNLETVNTY
Xtropicalis  all identical  ENSXETG00000007932  404GNGISDEYHIIRHVMNLES
protein features
start (aa)end (aa)featuredetails 
330358HELIXlost
364388HELIXmight get lost (downstream of altered splice site)
387391NP_BINDFAD (By similarity).might get lost (downstream of altered splice site)
389394HELIXmight get lost (downstream of altered splice site)
396398HELIXmight get lost (downstream of altered splice site)
400410HELIXmight get lost (downstream of altered splice site)
413415STRANDmight get lost (downstream of altered splice site)
414414MUTAGENE->D: Reduced catalytic activity.might get lost (downstream of altered splice site)
414414ACT_SITEProton acceptor (Probable).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 1185 / 1185
position (AA) of stopcodon in wt / mu AA sequence 395 / 395
position of stopcodon in wt / mu cDNA 1443 / 1443
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 259 / 259
chromosome 19
strand 1
last intron/exon boundary 1370
theoretical NMD boundary in CDS 1061
length of CDS 1185
coding sequence (CDS) position 1072
cDNA position
(for ins/del: last normal base / first normal base)		 1330
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 MRSSSGTPSA PTARRDSCLA SCWPIATKSL ALLPRLECSG TILAHCKFCL PGSSDSPAST
PLVAGITGYG CAGVSSVAYG LLARELERVD SGYRSAMSVQ SSLVMHPIYA YGSEEQRQKY
LPQLAKGELL GCFGLTEPNS GSDPSSMETR AHYNSSNKSY TLNGTKTWIT NSPMADLFVV
WARCEDGCIR GFLLEKGMRG LSAPRIQGKF SLRASATGMI IMDGVEVPEE NVLPGASSLG
GPFGCLNNAR YGIAWGVLGA SEFCLHTARQ YALDRMQFGV PLARNQLIQK KLADMLTEIT
LGLHACLQLG RLKDQDKAAP EMVSLLKRNN CGKALDIARQ ARDMLGGNGI SDEYHVIRHA
MNLEAVNTYE GTHDIHALIL GRAITGIQAF TASK*
mutated AA sequence MRSSSGTPSA PTARRDSCLA SCWPIATKSL ALLPRLECSG TILAHCKFCL PGSSDSPAST
PLVAGITGYG CAGVSSVAYG LLARELERVD SGYRSAMSVQ SSLVMHPIYA YGSEEQRQKY
LPQLAKGELL GCFGLTEPNS GSDPSSMETR AHYNSSNKSY TLNGTKTWIT NSPMADLFVV
WARCEDGCIR GFLLEKGMRG LSAPRIQGKF SLRASATGMI IMDGVEVPEE NVLPGASSLG
GPFGCLNNAR YGIAWGVLGA SEFCLHTARQ YALDRMQFGV PLARNQLIQK KLADMLTEIT
LGLHACLQLG RLKDQDKAAP EMVSLLKRNN CGKALDIARQ ARDMLGGNGI SDEYHVIWHA
MNLEAVNTYE GTHDIHALIL GRAITGIQAF TASK*
speed 0.75 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