Variant: NC_012920.1:m.3280A>G

CA658682658

Gene: N/A

Condition: mitochondrial disease

Inheritance Mode: Mitochondrial inheritance

UUID: c18d7368-20fb-4979-a0f2-4245bec5db02

HGVS expressions

NC_012920.1:m.3280A>G
J01415.2:m.3280A>G

Uncertain Significance

• Met criteria codes: PS4_Supporting PM2_Supporting PP3 PS3_Supporting

• Not Met criteria codes: PS2 PP1 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.3280A>G variant in MT-TL1 has been reported in three unrelated individuals with primary mitochondrial disease. Although there was limited clinical information on some these cases and haplogroups were not provided, the reported cases had similar features and consistent enzymology. The three reported individuals had variable ages of onset, with 1/3 presenting in childhood and 2/3 presenting in their mid-30s. Features included myopathy and ataxia. Heteroplasmy levels were not specified in one individual but the variant was present at 75% in muscle and 23% in blood in one individual and homoplasmic in the other (PS4_supporting; PMIDs: 11335700, 12402350, 12798797). There is one report of this variant segregating with disease features as a healthy mother of a proband had the variant present at 15% in blood (PMID: 12798797), however this does not meet criteria to apply PP1_supporting (at least two segregations). Another reported case had a daughter with similar muscle concerns, however there was no mention of testing for the variant in this family member (PMID: 11335700). 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). Single fiber testing showed higher levels of the variant in ragged red fibers (78.6 ± 11%; n = 9) than in non-ragged red fibers (10.9 ± 15.9%, n = 9; P < 0:001; PS3_supporting, PMID: 12798797). The computational predictor MitoTIP suggests this variant is pathogenic (82.9 percentile) and HmtVAR predicts it to be pathogenic score of 0.8 (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 Mitochondrial Disease Variant Curation Expert Panel on August 23, 2022. Mitochondrial DNA-specific ACMG/AMP criteria applied: PM2_supporting, PP3, PS4_supporting, PS3_supporting.

Met criteria codes

• PS4_Supporting: The m.3280A>G variant in MT-TL1 has been reported in three unrelated individuals with primary mitochondrial disease. Although there was limited clinical information on some these cases and haplogroups were not provided, the reported cases had similar features and consistent muscle enzymology. The three reported individuals had variable ages of onset, with 1/3 presenting in childhood and 2/3 presenting in their mid-30s. Features included myopathy and ataxia. Heteroplasmy levels were not specified in one individual but the variant was present at 75% in muscle and 23% in blood in one individual and homoplasmic in the other (PS4_supporting; PMIDs: 11335700, 12402350, 12798797).
• PM2_Supporting: This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
• PP3: The computational predictor MitoTIP suggests this variant impacts the function of this tRNA with a score of 82.9%, as does HmtVar with a score of 0.8 (PP3).
• PS3_Supporting: Single fiber studies showed a greater abundance of mutant genomes in RRF (78.6 +/-11%; n = 9), than in normal fibers (10.9 +/- 15.9%, n = 9; P<0:001, Mann–Whitney’s U-test; PMID: 12798787, PS3_supporting).

Not Met criteria codes

• PS2: There are no reports of de novo occurrence of this variant to our knowledge.
• PP1: There is one report of this variant segregating with disease features as a healthy mother of a proband had the variant present at 15% in blood (PMID: 12798797), however this does not meet criteria to apply PP1_supporting (at least two segregations). Another reported case had a daughter with similar muscle concerns, however there was no mention of testing for the variant in this family member (PMID: 11335700).
• PM6: There are no reports of de novo occurrence of this variant to our knowledge.

Approved on: 2022-08-23

Published on: 2022-09-02