Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99988024477924 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920303)
  • known disease mutation: rs2081 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:13007754T>CN/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.751T>C
cDNA.1009T>C
g.5915T>C
AA changes Y251H Score: 83 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 251
frameshift no
known variant Reference ID: rs121434366
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs2081 (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 CM920303)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920303)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920303)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.6440.138
4.6030.75
(flanking)0.380.725
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 increased5912wt: 0.9048 / mu: 0.9599 (marginal change - not scored)wt: ACGCCCGGTACGGCA
mu: ACGCCCGGCACGGCA		 GCCC|ggta
distance from splice site 31
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      251GGPFGCLNNARYGIAWGVLGASEF
mutated  all conserved    251GPFGCLNNARHGIAWGVLGASE
Ptroglodytes  all identical  ENSPTRG00000010548  295LNNARYGIAWGVLGASE
Mmulatta  all identical  ENSMMUG00000007043  295LNNARYGIAWGVLGASE
Fcatus  all conserved  ENSFCAG00000000477  295ARFGITWGVLGAAE
Mmusculus  all identical  ENSMUSG00000003809  295LNTARYGITWGVLGAAE
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008257  298LNNARYGIAWGALGAAE
Drerio  all identical  ENSDARG00000038361  265LNNARYGIAWGALGAAE
Dmelanogaster  all identical  FBgn0031824  278SCLNNARYGIAWGALGAAE
Celegans  not conserved  F54D5.7  269QGPFGCLNNARLGIAWGAL
Xtropicalis  all identical  ENSXETG00000007932  297LNNARYGISWGALGAAE
protein features no protein features affected
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 751
cDNA position
(for ins/del: last normal base / first normal base)		 1009
gDNA position
(for ins/del: last normal base / first normal base)		 5915
chromosomal position
(for ins/del: last normal base / first normal base)		 13007754
original gDNA sequence snippet GCTGCCTGAACAACGCCCGGTACGGCATCGCGTGGGGCGTG
altered gDNA sequence snippet GCTGCCTGAACAACGCCCGGCACGGCATCGCGTGGGGCGTG
original cDNA sequence snippet GCTGCCTGAACAACGCCCGGTACGGCATCGCGTGGGGCGTG
altered cDNA sequence snippet GCTGCCTGAACAACGCCCGGCACGGCATCGCGTGGGGCGTG
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 HGIAWGVLGA SEFCLHTARQ YALDRMQFGV PLARNQLIQK KLADMLTEIT
LGLHACLQLG RLKDQDKAAP EMVSLLKRNN CGKALDIARQ ARDMLGGNGI SDEYHVIRHA
MNLEAVNTYE GTHDIHALIL GRAITGIQAF TASK*
speed 0.78 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