Variant: m.3251A>G

CA120565

9595 (ClinVar)

Gene: N/A

Condition: mitochondrial disease

Inheritance Mode: Mitochondrial inheritance

UUID: 64b01c2e-118f-4992-9301-8219f48a4dde

Approved on: 2024-04-22

Published on: 2024-11-20

HGVS expressions

NC_012920.1:m.3251A>G
J01415.2:m.3251A>G

Likely Pathogenic

• Met criteria codes: PS3_Supporting PS4_Moderate PP1 PM2_Supporting

• Not Met criteria codes: PS2 PP3 PM6

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.3251A>G variant in MT-TL1 has been reported in four unrelated individuals with primary mitochondrial disease to date. Age of onset ranged from the first decade of life to adulthood and clinical features in affected individuals were variably consistent with chronic progressive external ophthalmoplegia (CPEO), myoclonic epilepsy with ragged red fibers (MERRF), mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS), and early death. Heteroplasmy ranged from 13-95% in affected individuals (PS4_moderate; PMIDs: 8265770, 38465286, 8786060, 30837005). This variant segregated with clinical manifestations in one family with CPEO, progressive muscle weakness, and early death. The variant was present in the proband at 81% in muscle and 13% in blood and was present in maternal cousins at heteroplasmy levels of 25-16% (PP1; PMID: 8265770). There are no reported de novo occurrences of this variant to our knowledge. This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). Computational predictors are conflicting (MitoTIP: 43.5%; HmtVAR: 0.75). Single fiber testing showed higher levels of the variant in COX-negative fibers (61%, range 15-88%) than in COX-positive fibers (28%, range 3%-86%; p<0.001; PS3_supporting, PMID: 8786060). There is additional evidence showing deleterious effects of this variant on the tRNA (PMID: 33380464). In summary, this variant meets criteria to be classified as uncertain significance for primary mitochondrial disease however, after extensive discussion, this Expert Panel elected to modify the classification to likely pathogenic given the compelling functional validation and consistent phenotype observed in reported cases. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Variant Curation Expert Panel on April 22, 2024. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_moderate, PP1, PM2_supporting, PS3_supporting.

Met criteria codes

• PS3_Supporting: Computational predictors are conflicting (MitoTIP: 43.5%; HmtVAR: 0.75). Single fiber testing showed higher levels of the variant in COX-negative fibers (61%, range 15-88%) than in COX-positive fibers (28%, range 3%-86%; p<0.001; PS3_supporting, PMID: 8786060). There is additional evidence showing deleterious effects of this variant on the tRNA (PMID: 33380464).
• PS4_Moderate: The m.3251A>G variant in MT-TL1 has been reported in four unrelated individuals with primary mitochondrial disease to date. Age of onset ranged from the first decade of life to adulthood and clinical features in affected individuals were variably consistent with chronic progressive external ophthalmoplegia (CPEO), myoclonic epilepsy with ragged red fibers (MERRF), mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS), and early death. Heteroplasmy ranged from 13-95% in affected individuals (PS4_moderate; PMIDs: 8265770, 38465286, 8786060, 30837005).
• PP1: This variant segregated with clinical manifestations in one family with CPEO, progressive muscle weakness, and early death. The variant was present in the proband at 81% in muscle and 13% in blood and was present in maternal cousins at heteroplasmy levels of 25-16% (PP1; PMID: 8265770).
• PM2_Supporting: This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).

Not Met criteria codes

• PS2: There are no reported de novo occurrences of this variant to our knowledge.
• PP3: The computational predictor MitoTIP suggests this variant is pathogenic (43.5 percentile) and HmtVAR predicts it to be pathogenic score of 0.75.
• PM6: There are no reported de novo occurrences of this variant to our knowledge.