New Term(s) Request: child terms for cytochrome-c oxidase deficiency disease

[vjenkinsFB]

Hi DO curators,

https://disease-ontology.org/?id=DOID:3762, cytochrome-c oxidase deficiency disease, has this definition and no children:

A mitochondrial metabolism disease that is characterized by deficiency of cytochrome c oxidase, myopathy, hepatomegaly, hypertrophic cardiomyopathy, lactic acidosis, and Leigh syndrome, and is caused by mutations related to oxidative phosphorylation.

The OMIM xref goes to https://www.omim.org/entry/220110, which is actually entry 1 in a 23 member phenotypic series, https://www.omim.org/phenotypicSeries/PS220110 Mitochondrial complex IV deficiency, nuclear-type.

Small request: could the phenotypic series xref go in this entry? Large request: could the subtypes of cytochrome-c oxidase deficiency disease be distinguised and given individual DOs? The ones that FlyBase would like to use are 1, 2, 4, 5, and 17 specifically.

Thank you!

[lschriml]

Agreed, this needs updating, we will add the PS # and the subtypes.

DOID:3762 cytochrome-c oxidase deficiency disease -- add OMIM:PS220110

  Create new 23 subtypes (mitochondrial complex IV deficiency) 

     ===========================================================  

ORDO:1561. Fatal infantile cytochrome C oxidase deficiency includes: type 2: OMIM:604377, mitochondrial complex IV deficiency nuclear type 2 type 6: OMIM:615119, mitochondrial complex IV deficiency nuclear type 6 type 9: OMIM:616500, mitochondrial complex IV deficiency nuclear type 9 type 13: OMIM:616501, mitochondrial complex IV deficiency nuclear type 13

ORPHA:70474 Leigh syndrome with cardiomyopathy OMIM:256000 Leigh disease DOID:3652 OMIM:618228 mitochondrial complex I deficiency nuclear type 6 OMIM:618252 mitochondrial complex I deficiency nuclear type 32

ORDO:70472 French Canadian Leigh disease [DOID:0111180] (OMIM:220111; ORDO:70472) ORDO: Saguenay-Lac-St. Jean (SLSJ) type congenital lactic acidosis, a French Canadian form of Leigh syndrome (see this term), is a mitochondrial disease characterized by chronic metabolic acidosis, hypotonia, facial dysmorphism and delayed development.
OMIM:220111. mitochondrial complex IV deficiency nuclear type 5 and OMIM:619065. mitochondrial complex IV deficiency nuclear type 21

ORDO:254905. Isolated cytochrome C oxidase deficiency

================================================================ https://rarediseases.org/rare-diseases/cytochrome-c-oxidase-deficiency/

     Four distinct forms of Cytochrome C Oxidase deficiency have been identified. 

The first form of this disorder is known as COX deficiency, benign infantile mitochondrial myopathy.

Affected infants exhibit many of the same symptoms as those with the more severe infantile form of the disease; however, because the COX deficiency is limited (localized) to tissues of the skeletal muscles, they typically do not have heart or kidney dysfunction.

In the second type of the disease, known as COX deficiency, infantile mitochondrial myopathy,
because the COX deficiency affects tissues of the skeletal muscles as well as several other tissues, the disorder may be characterized by a generalized weakness of skeletal muscles (myotonia), abnormalities of the heart and kidneys, and/or abnormally high levels of lactic acid in the blood (lactic acidosis). De Toni-Fanconi-Debre syndrome may also be present and may include excessive thirst, excessive urination, and excessive excretion of glucose, phosphates, amino acids, bicarbonate, calcium and water in the urine.

The third form of COX deficiency, known as Leigh’s disease (subacute necrotizing encephalomyelopathy), is thought to be a generalized (systemic) form of COX deficiency. Leigh’s disease is characterized by progressive degeneration of the brain and dysfunction of other organs of the body including the heart, kidneys, muscles, and liver. Symptoms may include loss of previously acquired motor skills, loss of appetite, vomiting, irritability, and/or seizure activity. As Leigh’s disease progresses, symptoms may also include generalized weakness; loss of muscle tone (hypotonia); and/or episodes of lactic acidosis.

In the fourth form of COX deficiency, known as COX deficiency French-Canadian type, the COX deficiency affects tissues of the skeletal muscles, connective tissue, and, in particular, the brain (Leigh’s disease) and the liver. Affected infants and children may demonstrate developmental delays, diminished muscle tone (hypotonia), crossing of the eyes (strabismus), Leigh’s disease, and/or episodes of lactic acidosis. Most cases of COX deficiency are inherited in an autosomal recessive pattern. Rarely, COX deficiency occurs as the result of a new or inherited abnormality (mutation) in a mitochondrial gene.

[allenbaron]

I'm noting that the DO has a few of these OMIM subtypes already (OMIM 1, 2, 5, 6, 9 & 13) but they are not grouped together as descendants of DOID:3762

id	label	omim	phenotype
DOID:0080357	fatal infantile cardioencephalomyopathy due to cytochrome c oxidase deficiency 1	OMIM:604377	Mitochondrial complex IV deficiency, nuclear type 2
DOID:0080358	fatal infantile cardioencephalomyopathy due to cytochrome c oxidase deficiency 2	OMIM:615119	Mitochondrial complex IV deficiency, nuclear type 6
DOID:0080359	fatal infantile cardioencephalomyopathy due to cytochrome c oxidase deficiency 3	OMIM:616500	?Mitochondrial complex IV, deficiency, nuclear type 9
DOID:0080360	fatal infantile cardioencephalomyopathy due to cytochrome c oxidase deficiency 4	OMIM:616501	Mitochondrial complex IV deficiency, nuclear type 13
DOID:0111180	French Canadian Leigh disease	OMIM:220111	Mitochondrial complex IV deficiency, nuclear type 5, (French-Canadian)
DOID:3762	cytochrome-c oxidase deficiency disease	OMIM:220110	Mitochondrial complex IV deficiency, nuclear type 1

Do we want to retain the subgroupings for the fatal infantile cardioencephalomyopathies and the Leigh disease / French Canadian Leigh disease we have currently and move them all under DOID:3762?

Also, the DO has mitochondrial deficiency I-III grouping diseases. What about renaming DOID:3762 to 'mitochondrial deficiency IV disease' for consistency?

I've adjusted the expectation for adding and reorganization of the subtypes to a later release.

[allenbaron]

The ROBOT template for updating these diseases can be found at https://docs.google.com/spreadsheets/d/1ZhuNnS_Yaba5qEs4-M50op-jJ_PGd8FktRaYsqsinYQ/edit#gid=1279657869.

[lschriml]

Reviewed: moved: fatal infantile cardioencephalomyopathy due to cytochrome c oxidase deficiency to be a child of :
cytochrome-c oxidase deficiency disease

I have revised the cytochrome-c oxidase deficiency disease to have the four subtypes see: https://rarediseases.org/rare-diseases/cytochrome-c-oxidase-deficiency/

For this term and its subtypes, I researched the classification/nomenclature, and then fit the OMIM terms into that hierarchy. OMIM describes this in: https://omim.org/entry/220110

https://medlineplus.gov/genetics/condition/cytochrome-c-oxidase-deficiency/

https://www.nature.com/articles/pr2000240

https://www.umdf.org/complex-iv-deficiency-cox-deficiency/

New DO terms can follow the OMIM naming, mitochondrial deficiency IV disease

[allenbaron]

Apologies Victoria. The requested updates have been delayed by summer plans/conferences and probably won't be included until the Sept release, except for the classification adjustments noted by Lynn that were included in the June release.

[vjenkinsFB]

No worries, I get that there's a lot to decide on with some of these. Thank you!

[allenbaron]

The disease 'COX deficiency, benign infantile mitochondrial myopathy' was accidentally added in the June 2023 release (v2023-06-29) with a duplicate IRI (http://purl.obolibrary.org/obo/DOID_0080035) matching a historically obsoleted disease, and this error persisted in the July releases (v2023-07-20 & v2023-07-24). We have deleted that IRI and re-created the disease with a new, unique IRI (http://purl.obolibrary.org/obo/DOID_0081377) in the latest release v2023-08-08. If you have used this disease with DOID:0080035, please update to DOID:0081377.

We apologize for any inconvenience this may cause.

@vjenkinsFB remaining work is still scheduled for inclusion in the Sept release.

[lschriml]

Looking at what has been added to the DO and what needs to be added: --> there are already 5 members of this phenotypic series that are in the DO:

To Do: Add the following OMIM IDs as child terms to: DOID:0050713 COX deficiency, infantile mitochondrial myopathy

Mitochondrial complex IV deficiency, nuclear type 1 220110 Mitochondrial complex IV deficiency, nuclear type 2 604377 DOID:0080357 Mitochondrial complex IV deficiency, nuclear type 3 619046 Mitochondrial complex IV deficiency, nuclear type 4 619048 Mitochondrial complex IV deficiency, nuclear type 5, (French-Canadian) 220111 DOID:0111180 Mitochondrial complex IV deficiency, nuclear type 6 615119 DOID:0080358 Mitochondrial complex IV deficiency, nuclear type 7 619051 Mitochondrial complex IV deficiency, nuclear type 8 619052 Mitochondrial complex IV, deficiency, nuclear type 9 616500 DOID:0080359 Mitochondrial complex IV deficiency, nuclear type 10 619053 Mitochondrial complex IV deficiency, nuclear type 11 619054 Mitochondrial complex IV deficiency, nuclear type 12 619055 Mitochondrial complex IV deficiency, nuclear type 13 616501 DOID:0080360 Mitochondrial complex IV deficiency, nuclear type 14 619058 Mitochondrial complex IV deficiency, nuclear type 15 619059 Mitochondrial complex IV deficiency, nuclear type 16 619060 Mitochondrial complex IV deficiency, nuclear type 17 619061 Mitochondrial complex IV deficiency, nuclear type 18 619062 Mitochondrial complex IV deficiency, nuclear type 19 619063 Mitochondrial complex IV deficiency, nuclear type 20 619064 Mitochondrial complex IV deficiency, nuclear type 21 619065 Mitochondrial complex IV deficiency, nuclear type 22 619355 Mitochondrial complex IV deficiency, nuclear type 23 620275

[lschriml]

@allenbaron -- these can be added via your robot template.

[lschriml]

COX deficiency, benign infantile mitochondrial myopathy

• COX deficiency is limited (localized) to tissues of the skeletal muscles

• COX deficiency, infantile mitochondrial myopathy. [DOID:0050713]

• COX deficiency affects tissues of the skeletal muscles as well as several other tissues

COX deficiency, known as Leigh’s disease

• a generalized (systemic) form of COX deficiency
• characterized by progressive degeneration of the brain and dysfunction of other organs of the body including the heart, kidneys, muscles, and liver.

COX deficiency French-Canadian type,

• the COX deficiency affects tissues of the skeletal muscles, connective tissue, and, in particular, the brain and the liver

=====================================================

parent: [DOID:0050713] COX deficiency, infantile mitochondrial myopathy Mitochondrial complex IV deficiency, nuclear type 2 604377 DOID:0080357 Mitochondrial complex IV deficiency, nuclear type 6 615119 DOID:0080358 Mitochondrial complex IV, deficiency, nuclear type 9 616500 DOID:0080359 Mitochondrial complex IV deficiency, nuclear type 13 616501 DOID:0080360

parent: COX deficiency, benign infantile mitochondrial myopathy [DOID:0081377] OMIM IDs: Mitochondrial complex IV deficiency, nuclear type 1 220110 Mitochondrial complex IV deficiency, nuclear type 3 619046 Mitochondrial complex IV deficiency, nuclear type 4 619048 Mitochondrial complex IV deficiency, nuclear type 7 619051 Mitochondrial complex IV deficiency, nuclear type 8 619052 Mitochondrial complex IV deficiency, nuclear type 10 619053 Mitochondrial complex IV deficiency, nuclear type 11 619054 Mitochondrial complex IV deficiency, nuclear type 12 619055 Mitochondrial complex IV deficiency, nuclear type 14 619058 Mitochondrial complex IV deficiency, nuclear type 15 619059 Mitochondrial complex IV deficiency, nuclear type 16 619060 Mitochondrial complex IV deficiency, nuclear type 17 619061 Mitochondrial complex IV deficiency, nuclear type 18 619062 Mitochondrial complex IV deficiency, nuclear type 19 619063 Mitochondrial complex IV deficiency, nuclear type 20 619064 Mitochondrial complex IV deficiency, nuclear type 21 619065 Mitochondrial complex IV deficiency, nuclear type 22 619355

parent: cytochrome-c oxidase deficiency disease [DOID:3762] Mitochondrial complex IV deficiency, nuclear type 23 620275

parent: cytochrome-c oxidase deficiency disease [DOID:3762] Mitochondrial complex IV deficiency, nuclear type 5, (French-Canadian) 220111 DOID:0111180

[vjenkinsFB]

Thanks so much, this was an even larger request than I realized when I made it!