Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999955048 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CD1111267)
  • known disease mutation at this position (HGMD CM960713)
  • known disease mutation: rs2083 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:13007748G>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.745G>A
cDNA.1003G>A
g.5909G>A
AA changes A249T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 249
frameshift no
known variant Reference ID: rs121434371
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC01212

known disease mutation: rs2083 (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 CD1111267)

known disease mutation at this position, please check HGMD for details (HGMD ID CD1111267)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960713)

known disease mutation at this position, please check HGMD for details (HGMD ID CD1111267)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960713)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960713)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8360.519
5.5731
(flanking)5.5731
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased5903wt: 0.3521 / mu: 0.4392 (marginal change - not scored)wt: AGGGTCCCTTCGGCTGCCTGAACAACGCCCGGTACGGCATC
mu: AGGGTCCCTTCGGCTGCCTGAACAACACCCGGTACGGCATC		 ctga|ACAA
Donor marginally increased5912wt: 0.9048 / mu: 0.9603 (marginal change - not scored)wt: ACGCCCGGTACGGCA
mu: ACACCCGGTACGGCA		 GCCC|ggta
distance from splice site 25
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      249SLGGPFGCLNNARYGIAWGVLGAS
mutated  not conserved    249GPFGCLNNTRYGIAWGVLGA
Ptroglodytes  all identical  ENSPTRG00000010548  293LNNARYGIAWGVLGA
Mmulatta  all identical  ENSMMUG00000007043  293LNNARYGIAWGVLGA
Fcatus  all identical  ENSFCAG00000000477  293ARFGITWGVLGA
Mmusculus  all identical  ENSMUSG00000003809  293LNTARYGITWGVLGA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008257  296LNNARYGIAWGALGA
Drerio  all identical  ENSDARG00000038361  263LNNARYGIAWGALGA
Dmelanogaster  all identical  FBgn0031824  276SCLNNARYGIAWGALGA
Celegans  all identical  F54D5.7  267GLQGPFGCLNNARLGIAWGAL
Xtropicalis  all identical  ENSXETG00000007932  295LNNARYGISWGALGA
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 745
cDNA position
(for ins/del: last normal base / first normal base)		 1003
gDNA position
(for ins/del: last normal base / first normal base)		 5909
chromosomal position
(for ins/del: last normal base / first normal base)		 13007748
original gDNA sequence snippet CCTTCGGCTGCCTGAACAACGCCCGGTACGGCATCGCGTGG
altered gDNA sequence snippet CCTTCGGCTGCCTGAACAACACCCGGTACGGCATCGCGTGG
original cDNA sequence snippet CCTTCGGCTGCCTGAACAACGCCCGGTACGGCATCGCGTGG
altered cDNA sequence snippet CCTTCGGCTGCCTGAACAACACCCGGTACGGCATCGCGTGG
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
GPFGCLNNTR YGIAWGVLGA SEFCLHTARQ YALDRMQFGV PLARNQLIQK KLADMLTEIT
LGLHACLQLG RLKDQDKAAP EMVSLLKRNN CGKALDIARQ ARDMLGGNGI SDEYHVIRHA
MNLEAVNTYE GTHDIHALIL GRAITGIQAF TASK*
speed 1.13 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