Variant: NC_012920.1(MT-ND2):m.4681T>C

CA120644

9721 (ClinVar)

Gene: N/A

Condition: mitochondrial disease

Inheritance Mode: Mitochondrial inheritance

UUID: 92f2d6ba-328b-45c6-87db-439696ffdd80

Approved on: 2023-10-23

Published on: 2025-06-05

HGVS expressions

NC_012920.1:m.4681T>C
J01415.2:m.4681T>C
ENST00000361453.3:c.212T>C

Uncertain Significance

• Met criteria codes: PM2_Supporting PP3 PS3_Supporting

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.4681T>C (p.L71P) variant in MT-ND2 has been reported in one individual with primary mitochondrial disease to date, in a boy with Leigh syndrome and generalized muscle atrophy (PMIDs: 16996290, 16738010). He had elevated blood and cerebrospinal fluid lactate. Complex I deficiency was noted in skin fibroblasts. The variant was present at >95% heteroplasmy in blood, muscle, and fibroblasts. The variant was absent in his mother although technology performed at the time was limited in detecting low heteroplasmy levels. This variant is absent in the MITOMAP GenBank dataset, gnomAD v3.1.2, and the Helix dataset (PM2_supporting, note the single occurrence in MITOMAP is likely from the reported patient). The computational predictor APOGEE suggests this variant is pathogenic (0.52, range 0-1; PP3). Cybrid studies supported the functional impact of this variant as mutant cybrids had reduced complex I activity and impaired complex I assembly (PS3_supporting; PMID: 16996290). 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 October 23, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PM2_supporting, PP3, PS3_supporting.

Met criteria codes

• PM2_Supporting: This variant is absent in in the MITOMAP GenBank dataset, gnomAD v3.1.2, and the Helix dataset (PM2_supporting, note the single occurrence in MITOMAP is likely from the reported patient).
• PP3: The computational predictor APOGEE suggests this variant is pathogenic (0.52, range 0-1; PP3).
• PS3_Supporting: Cybrid studies supported the functional impact of this variant as mutant cybrids had reduced complex I activity and assembly (PS3_supporting; PMID: 16996290).