VariO annotation examples

Examples of use of VariO terms for annotation of variations and their effects

Missense variation

Missense variation g>a in sequence EMBL: U78027: at position 62789 leading to G302E substitution (BTKBase entry A0165) causing X-linked agammaglobulinemia (Hageman T. et al. Hum Mut. 1995).


The effects of the variant were investigated in expressed SH2 domain of the protein and found to affect protein structure accoding CD spectroscopy, binding to substrate according to pY-Sepharose binding (Mattsson et al. J. Immunol 2000).

Annotation of the substitution on DNA level:
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0130 DNA variation of genetic origin
VariO:0135 DNA chain variation
VariO:0136 DNA substitution
VariO:0313 transition
VariO:0315 purine transition

Annotation of the missense variation on RNA level:
VariO:0297 variation affecting RNA
VariO:0306 RNA variation type
VariO:0307 RNA variation of genetic origin
VariO:0312 RNA nucleotide substitution
VariO:0308 missense variation

Annotations on protein level:
Variation type
VariO:0002 variation affecting protein
VariO:0012 protein variation type
VariO:0013 protein variation of genetic origin
VariO:0021 amino acid substitution

Function
VariO:0003 variation affecting protein function
VariO:0007 effect on protein recognition

Structure
VariO:0060 variation affecting protein structure
VariO:0064 effect on protein 3D structure
VariO:0070 effect on protein tertiary structure
VariO:0073 effect on protein fold
VariO:0074 protein conformational change

Property
Disease-causing variation
VariO:0032 variation affecting protein property
VariO:0035 effect on protein solubility; VariO:0290 decreased
VariO:0052 effect on protein abundance; VariO:0290 decreased
VariO:0058 effect on protein interaction
VariO:0236 interaction
VariO:0258 structural level of interaction
VariO:0259 intermolecular interaction; VariO:0290 decreased
VariO: 0262 interactor
VariO:0272 biopolymer
VariO:0275 peptide

Splice site variation

X-linked agammaglobulinemia causing g>a substitution in exon-intron boundary. Insertion of 106 nucleotides from intron leads to frameshift alteration and premature stop. Expressed protein is not detectable in Western blot (Noordzij, J. G., et al. J. Clin. Immunol. 22:306-318 2002)

Annotation of substitution at DNA level
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0130 DNA variation of genetic origin
VariO:0135 DNA chain variation
VariO:0142 DNA substitution
VariO:0313 transition
VariO:0315 purine transition

Annotation of insertion at RNA level
Variation type
VariO:0297 variation affecting RNA
VariO:0306 RNA variation type
VariO:0307 RNA variation of genetic origin
VariO:0326 RNA insertion
VariO:0327 out-of-frame insertion

Effect on RNA structure
VariO:0338 variation affecting RNA structure
VariO:0349 affected RNA level
VariO:0351 protein coding RNA sequence
VariO:0352 coding RNA sequence
VariO:0354 effect on RNA maturation
VariO:0362 effect on RNA splicing
VariO:0365 variation affecting cis splice site
VariO:0367 variation at five prime splice site
VariO:0368 variation at canonical five prime splice site

Annotation at protein level
Variation type
VariO:0002 variation affecting protein
VariO:0012 protein variation type
VariO:0013 protein variation of genetic origin
VariO:0018 amino acid insertion
VariO:0019 amphigoric amino acid insertion

Effect on protein property
VariO:0032 variation affecting protein property
VariO:0047 association of protein variation to pathogenicity; VariO:0294 disease causing
VariO:0052 effect on protein abundance; VariO:0292 missing