Variant: m.3949T>C

CA254863

9735 (ClinVar)

Gene: N/A

Condition: mitochondrial disease

Inheritance Mode: Mitochondrial inheritance

UUID: 6ad567be-ea04-426b-9758-a1ec8e6ec883

Approved on: 2023-08-22

Published on: 2024-11-25

HGVS expressions

NC_012920.1:m.3949T>C
J01415.2:m.3949T>C
ENST00000361390.2:c.643T>C

Uncertain Significance

• Met criteria codes: PP3 PM6_Supporting PS3_Supporting PM2_Supporting

• Not Met criteria codes: PS4 PP4

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.3949T>C (p.Y215H) variant in MT-ND1 has been reported in one individual to date with primary mitochondrial disease. This individual had features consistent with mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS) and harbored the variant at 93% heteroplasmy in muscle, 45% in blood, and 88% in fibroblasts (PMID:15466014). This variant occurred de novo in one individual (absent in blood from mother and two brothers; PM6_supporting, PMID: 15466014). Electron transport chain (ETC) enzyme activity in fibroblasts and muscles was consistent with severe isolated defect of complex I, and levels of assembled complex I was approximately 12% of control; however, nuclear etiologies were not excluded (PMID: 15466014). Studies in E. coli (PMID: 16849371) and cybrids (PMID: 15466014) support the functional impact of this variant and independent studies showed independent deleterious effects of the variant (PS3_supporting). The m.3949GT>C variant is present in Mitomap’s GenBank dataset at less than 1/50,000 or 0.002% (1/61,168 sequences, 0.00163%, haplogroup K1a). This variant is absent in gnomAD v3.1.2 and in Helix dataset therefore this variant is absent in healthy individuals (PM2_supporting). The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.54 (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 August 22, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PM6_supporting, PS3_supporting, PP3, PM2_supporting.

Met criteria codes

• PP3: The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.54 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3).
• PM6_Supporting: This variant occurred de novo in one individual (absent in blood from mother and two brothers; PM6_supporting, PMID: 15466014).
• PS3_Supporting: Studies in E. coli (PMID: 16849371) and hybrids (PMID: 15466014) support the functional impact of this variant and independent studies showed independent deleterious effects of the variant (PS3_supporting).
• PM2_Supporting: The m.3949GT>C variant is present in Mitomap’s GenBank dataset at less than 1/50,000 or 0.002% (1/61,168 sequences, 0.00163%, haplogroup K1a). This variant is absent in gnomAD v3.1.2 and in Helix dataset therefore this variant is absent in healthy individuals.

Not Met criteria codes

• PS4: The m.3949T>C (p.Y215H) variant in MT-ND1 has been reported in one individual to date with primary mitochondrial disease. This individual had features consistent with MELAS and harbored the variant at 93% heteroplasmy in muscle, 45% in blood, and 88% in fibroblasts (PMID:15466014). This does not meet criteria for PS4_supporting which requires at least two unrelated affected individuals.
• PP4: Electron transport chain (ETC) enzyme activity in fibroblasts and muscles was consistent with severe isolated defect of complex I, and levels of assembled complex I was approximately 12% of control; however, nuclear etiologies were not excluded.