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Mondo Disease Ontology
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[Obsolete] Antithrombin II deficiency #4476

Closed kristyleelowdermilk closed 2 years ago

kristyleelowdermilk commented 2 years ago

Mondo term (ID and Label) Antithrombin II deficiency MONDO:0020670

Reason for deprecation There is no antithrombin I or II deficiency, so this should be referred to as antithrombin deficiency (PMID: 19141163, 31697819, 28317092, 30005274); https://medlineplus.gov/genetics/condition/hereditary-antithrombin-deficiency/; https://rarediseases.info.nih.gov/diseases/6148/hereditary-antithrombin-deficiency); https://rarediseases.org/rare-diseases/antithrombin-deficiency/. However, there are type I (quantitative) and type II (qualitative) defects within antithrombin deficiency. They are caused by different variants within the SERPINC1 gene, and should all be considered antithrombin deficiency.

Suggested term to consider Antithrombin deficiency

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nicolevasilevsky commented 2 years ago

@galyea-gard this term is in GARD, are you considering obsoleting this term or is still in use? https://rarediseases.info.nih.gov/diseases/10182/antithrombin-deficiency-type-2 Thanks!

kristyleelowdermilk commented 2 years ago

Hi again,

So to provide you with a little more clarity, within antithrombin deficiency there are SERPINC1 variants that cause a type 1 deficiency and a type 2 deficiency. Type 1 deficiency variants cause a quantitative defect and the type 2 variants cause a qualitative defect. The distinction can be important because folks with a type 2 defect may not have lower levels of the antithrombin protein on the routine assays since those assays are designed to detect a quantitative defect. Additional studies may be needed to confirm type 2 cases. However, both of these subtypes are caused by variants in the SERPINC1 gene and are all considered antithrombin deficiency. There is no antithrombin I or antithrombin II protein, so that’s why my experts wanted to go ahead and try to expunge this dated term of antithrombin III; however, we could certainly do our work by having one of the two terms: “antithrombin deficiency” or “hereditary antithrombin deficiency”. Both of those terms are used interchangeably throughout the literature.

Thanks again for your help with this. Please let me know if I could answer any additional questions or concerns!!

Kristy

Kristy Lee, MS, CGC Genetic Counselor Associate Professor

From: Nicole Vasilevsky @.> Sent: Wednesday, February 16, 2022 8:59 PM To: monarch-initiative/mondo @.> Cc: Lee, Kristy @.>; Author @.> Subject: Re: [monarch-initiative/mondo] [Obsolete] (Issue #4476)

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@galyea-gardhttps://github.com/galyea-gard this term is in GARD, are you considering obsoleting this term or is still in use? https://rarediseases.info.nih.gov/diseases/10182/antithrombin-deficiency-type-2 Thanks!

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nicolevasilevsky commented 2 years ago

Hi @kristyleelowdermilk Thanks so much for the info and clarification, this makes much more sense to me now. :) I also spoke with our medical expert on our team (Peter Robinson) and he confirmed that this term should be obsoleted and we should consider: MONDO_0012876 'heparin cofactor 2 deficiency'.

We'll mark this for obsoletion and leave it open for 2 months for further comment and we'll obsolete it on or after May 01.

Thanks for your recommendation and feedback. I'll comment separately on the other ticket.

nicolevasilevsky commented 2 years ago

I closed the wrong ticket! Reopening

galyea-gard commented 2 years ago

Hi Nicole! The review process is still ongoing and I cannot say with certainty what changes may be made but I believe this one will be retired. (as it does not meet the current criteria for having a separate page). We will know more when the process is over. Sorry not to be more helpful. Thank you! Gioconda.

From: Nicole Vasilevsky @.> Sent: Wednesday, February 16, 2022 8:59 PM To: monarch-initiative/mondo @.> Cc: Alyea, Gioconda (NIH/NCATS) [C] @.>; Mention @.> Subject: [EXTERNAL] Re: [monarch-initiative/mondo] [Obsolete] (Issue #4476)

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@galyea-gardhttps://github.com/galyea-gard this term is in GARD, are you considering obsoleting this term or is still in use? https://rarediseases.info.nih.gov/diseases/10182/antithrombin-deficiency-type-2 Thanks!

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