Variant: NC_012920.1(MT-CO3):m.9804G>A

CA340930

9652 (ClinVar)

Gene: N/A

Condition: mitochondrial disease

Inheritance Mode: Mitochondrial inheritance

UUID: 02f5a79b-7780-40c9-99e7-0c310d09f6eb

Approved on: 2023-09-26

Published on: 2025-06-04

HGVS expressions

NC_012920.1:m.9804G>A
J01415.2:m.9804G>A
ENST00000362079.2:c.598G>A

Uncertain Significance

• Met criteria codes: PS4_Moderate PP3

• Not Met criteria codes: PM2 PM6 PS2 PP1

Expert Panel

Mitochondrial Diseases VCEP

Criteria Specification Information

Criteria Specification: ClinGen Mitochondrial Disease Nuclear and Mitochondrial Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1_mtDNA

Evidence submitted by expert panel

Mitochondrial Diseases VCEP

The m.9804G>A (p.A200T) variant in MT-CO3 has been reported in seven unrelated individuals with primary mitochondrial disease (PS4_moderate; PMIDs: 8240356, 17895983, 11339587, 11579587, 30831606). Six cases had Leber Hereditary Optic Neuropathy (LHON; PMIDs: 8240356, 11339587, 11579587, 30831606) and the variant was reported to be homoplasmic in four, heteroplasmic in one (level not provided), and the level was not provided in another. Limited clinical details were available from the seventh case but this child was described as having encephalopathy and the variant present at homoplasmy (PMID: 17895983). There were no reported de novo occurrences and there were no reports of the variant segregating with clinical manifestations in a family. This variant is present in population databases and is seen in individuals from several different haplogroups (MITOMAP: 0.296%, 183/61,883; gnomAD v3.1.2: 0.363%, 205/56,420 homoplasmic occurrences in addition to 15 heteroplasmic occurrences; Helix: 0.472%, 926/195,893 homoplasmic occurrences in addition to 30 heteroplasmic occurrences).The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.866 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3). In summary, this variant meets criteria to be classified as uncertain significance for primary mitochondrial disease inherited in a mitochondrial manner. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Variant Curation Expert Panel on September 26, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_moderate, PP3.

Met criteria codes

• PS4_Moderate: The m.9804G>A (p.A200T) variant in MT-CO3 has been reported in seven unrelated individuals with primary mitochondrial disease (PS4_moderate; PMIDs: 8240356, 17895983, 11339587, 11579587, 30831606). Six cases had Leber Hereditary Optic Neuropathy (LHON; PMIDs: 8240356, 11339587, 11579587, 30831606) and the variant was reported to be homoplasmic in four, heteroplasmic in one (level not provided), and the level was not provided in another. Limited clinical details were available from the seventh case but this child was described as having encephalopathy and the variant present at homoplasmy (PMID: 17895983).
• PP3: The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.866 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3).

Not Met criteria codes

• PM2: This variant is present in population databases and is seen in individuals from several different haplogroups (MITOMAP: 0.296%, 183/61,883; gnomAD v3.1.2: 0.363%, 205/56,420 homoplasmic occurrences in addition to 15 heteroplasmic occurrences; Helix: 0.472%, 926/195,893 homoplasmic occurrences in addition to 30 heteroplasmic occurrences).
• PM6: There were no reported de novo occurrences.
• PS2: There were no reported de novo occurrences.
• PP1: There were no reports of the variant segregating with clinical manifestations in a family.