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Mondo Disease Ontology
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Severe neonatal lactic acidosis due to NFS1-ISD11 complex deficiency #7568

Open galyea123 opened 6 months ago

galyea123 commented 6 months ago

Hi! This term was obsoleted in the list MONDO provided to us (NORD) and I did not find it in MONDO. The term is active in Orphanet https://www.orpha.net/en/disease/detail/39759 and I did not find the ticket related to the reason why the term was obsoleted.

Thank you very much,

Best,
Gioconda

nicolevasilevsky commented 6 months ago

@galyea123 this term was also obsoleted as part of our mass obsoletion effort to exclude grouping classes that group together terms based on phenotypic features.

Let me know if you have further questions or if further action is needed. Thanks!

galyea123 commented 6 months ago

Hi Nicole! This term is in Orphanet classified as a disorder: Please see: https://www.orpha.net/en/disease/detail/397593 By further reviewing it I see that this is a synonym with "Combined oxidative phosphorylation deficiency 19" https://omim.org/entry/615595 which is listed in MONDO:0014269 (in MONDO it does not include the Orphanet entry, and therefore it does not list "Severe neonatal lactic acidosis due to NFS1-ISD11 complex deficiency" as its synonym. Please let me know your thoughts, Thank you! Gioconda

sabrinatoro commented 4 months ago

might be solved by https://github.com/monarch-initiative/mondo/issues/7693

kanems commented 2 months ago

I have concerns about the mapping of ORPHA:397593 to MONDO:0014269 The ORDO entry http://www.orpha.net/ORDO/Orphanet_397593 shows 2 causative genes: LYRM4 and NFS1 They also state that their mapping relative to OMIM 615595 is their term is broader to the narrower OMIM entry (BTNT). I don't think it's appropriate to include this Orpha ID as an exact match to the Mondo term with the OMIM also as an exact match, esp. given Mondo's definition is "Any combined oxidative phosphorylation deficiency in which the cause of the disease is a mutation in the LYRM4 gene."

galyea123 commented 2 months ago

Hi! To my understanding it is caused by LYRM4 gene mutations. LYRM4 gene encodes the ISD11 protein, "which forms a complex with, and stabilizes, the sulfur donor NFS1". https://pubmed.ncbi.nlm.nih.gov/23814038/ See also the article that first described this syndrome: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3888131/

Another related disease (cited in OMIM) is caused by mutations in the NFS1 gene: https://omim.org/entry/619386

Note: I sent a message to Orphanet for further clarification.

Thank you, Gioconda