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The-Sequence-Ontology / SO-Ontologies

Collect of SO Ontologies
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NTR: switch_of_function_variant #642

Open drobbarfield opened 1 year ago

drobbarfield commented 1 year ago

What is this request referring to? Switch-of-function variant

What is the name you would like SO to give the term? switch_of_function_variant

What is the definition that you would like for this term? The alteration causes the protein to acquire a new function, such as the neomorphic ability of the IDH1 R132H-mutant protein to produce D-2-hydroxyglutarate. https://faq.oncokb.org/data-curation#what-does-switch-of-function-mean

Synonyms NA

Parent Term It could be put under gain_of_function_variant (SO:0002053).

Relevant Publications https://faq.oncokb.org/data-curation#what-does-switch-of-function-mean https://pubmed.ncbi.nlm.nih.gov/28890946/

egchristensen commented 6 months ago

Would it be correct to instead add switch_of_function_variant as a synonym of gain_of_function_variant or is there something that differentiates the two? Does switch_of_function_variant apply specifically to protein products or could it also be used to describe changes in the function of other gene products?

drobbarfield commented 6 months ago

Hi Evan, thanks for following up.

Researching this again, gain_of_function variant may not be the appropriate parent term or synonym as switch of function is more of an intermediate term that can involve both gain and loss of function.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3177186/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919555/

functionally_abnormal (SO:0002218) appears to be more appropriate so that gain_of_function_variant and loss_of_function_variant are siblings.

I have only seen the term applied to the protein product.