VariO protein function annotation examples

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Examples of annotation of protein function variation using the Variation Ontology VariO.

All these examples are discussed in Vihinen, M., in press. Types and effects of protein variations

The root terms for these examples are (hovering over the terms will show you the definition of the term):

VariO:0002 variation affecting protein

VariO:0003 variation affecting protein function

VariO:0008 effect on catalytic protein function

An R525Q substitution at the catalytic site inactivates the BTK kinase catalytic function.

VariO:0011 effect on protein information transfer

"Effect on protein information transfer" can be used to describe e.g. hormone effects. Insulin is a peptide hormone in which variants lead to for example neonatal diabetes due to an impaired regulation of the carbohydrate and fat metabolism.

VariO:0004 effect on protein movement

"Effect on protein movement" is used to describe changes to movement of contractile proteins such as actin and myosin. Several myopathies with muscle weakness anad muscle structrueal changes emerge due to some 200 known variants in α-actin.

VariO:0007 effect on protein recognition

"Effect on protein recognition" describes selective and non-covalent interactions of proteins e.g. for immunoglobulins and other immunologyical molecules. An insertion to the immunoglobulin gene for the common γ2 chain (Cγ2) causes IgG2 deficiency.

VariO:0005 effect on protein storage

"Effect on protein storage" describes changes to proteins acting as amino acid or metal cation stores, such as ferritin and casein. Ferritin light chain variants lead to autosomal dominant neuroferritinopathy due to iron deposition to brains.

VariO:0009 effect on transport function of protein

"Effect on transport function of protein" can be used to annotate changes that affect active transport functions of proteins such as membrane transporters. A G87R substitution in zinc transporter ZnT-2 (SLC30A2) impairs zinc transport because the protein is mislocalized and has decreased stability. The variant has ER retention.

VariO:0006 effect on structural protein

"Effect on structural protein" defines alterations in proteins providing support for cells and tissues including keratin, collagen and others. Variations in type II collagen affect the structural protein of connective tissue and result in conditions with varying severity ranging from lethal to relatively mild.