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 ENST00000422947
Genbank transcript ID N/A
UniProt peptide Q92947
alteration type single base exchange
alteration region CDS
DNA changes c.1066G>A
cDNA.1324G>A
g.6793G>A
AA changes V356M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 356
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      356LGGNGISDEYHVIRHAMNLEAVNT
mutated  all conserved    356LGGNGISDEYHMIRHA
Ptroglodytes  all identical  ENSPTRG00000010548  400LGGNGISDEYHVIRHAMNLEA
Mmulatta  all identical  ENSMMUG00000007043  400LGGNGISDEYHVIRHAMNLEA
Fcatus  all identical  ENSFCAG00000000477  400LGGNGISDEYHVIRHVMNLESVN
Mmusculus  all identical  ENSMUSG00000003809  400LGGNGISDEYHVIRHAMNLEA
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000008257  403LGGNGISDEYHIIRHVMN
Drerio  all conserved  ENSDARG00000038361  370LGGNGIADEYHIIRHVLNLEA
Dmelanogaster  all identical  FBgn0031824  383LGANGISDEYHVIRHVINL
Celegans  all conserved  F54D5.7  374LGGNGIVDEYHIMRHMVNLETVN
Xtropicalis  all conserved  ENSXETG00000007932  402LGGNGISDEYHIIRHVMNLES
protein features
start (aa)end (aa)featuredetails 
330358HELIXlost
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 1066
cDNA position
(for ins/del: last normal base / first normal base)		 1324
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 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 SDEYHMIRHA
MNLEAVNTYE GTHDIHALIL GRAITGIQAF TASK*
speed 0.94 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