Variant: NC_012920.1(MT-CYB):m.14710G>A

CA913171880

690207 (ClinVar)

Gene: MT-TE

Condition: mitochondrial disease

Inheritance Mode: Mitochondrial inheritance

UUID: 2cddaa4d-768d-423d-85d5-33fc6bf3d0ae

HGVS expressions

NC_012920.1:m.14710G>A
J01415.2:m.14710G>A

Uncertain Significance

• Met criteria codes: PM2_Supporting PS3_Supporting PS4_Supporting PP3

• Not Met criteria codes: 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.14710G>A variant in MT-TE has been reported in two affected individuals from two families (PMIDs: 15670724, 23847141; PS4_supporting). These two individuals had similar courses, as both were women with onset in childhood or adolescence of progressive external ophthalmoplegia (PEO), myopathy, pigmentary retinopathy, and migraines. Muscle biopsies performed in these two individuals showed ragged red fibers and COX-negative fibers. Respiratory chain enzyme activities were normal except for reduced complex I activity in one individual. Heteroplasmy levels were only reported in one individual (PMID: 15670724), but were 67-77% in muscle, trace amounts to 14% in hair roots, and were undetectable in buccal, blood, and fibroblasts. Of note, exercise testing in one subject (PMID: 15670724) is described in other manuscripts (PMIDs: 11506394 and 12538407), and her case is also included in a cohort study (PMID: 19718780). One of the affected individuals has a son with autism but he was not tested for this variant. The variant was not detected in blood from the subject’s mother and three sisters but it was also undetectable in the subject's blood, so de novo status could not be confirmed (PMID: 15670724). There are no large families reported in the medical literature to consider for evidence of segregation. 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 COX negative fibers (93 ± 1.0%) than in COX positive fibers (59 ± 28%), p<0.005. Furthermore, COX-positive fibers showed a much greater range of mutated mtDNA than COX-negative fibers (9–89% vs 92–95%; PMID: 15670724; PS3_supporting). The computational predictor MitoTIP suggests this variant is pathogenic (51.7 percentile) and HmtVAR predicts it to be pathogenic score of 0.55 (PP3). In summary, this variant meets criteria to be classified as uncertain significance for primary mitochondrial disease inherited in a mitochondrial manner. We note that some experts on this panel voted for a classification of likely pathogenic given the evidence of pathogenicity (strong single fiber studies, absent in population databases and present in two individuals with similar features of primary mitochondrial disease). This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Variant Curation Expert Panel on December 15, 2022. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_supporting, PM2_supporting, PS3_supporting, PP3.

Met criteria codes

• PM2_Supporting: This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
• PS3_Supporting: Single fiber testing showed higher levels of the variant in COX negative fibers (93 ± 1.0%) than in COX positive fibers (59 ± 28%), p<0.005. Furthermore, COX-positive fibers showed a much greater range of mutated mtDNA than COX-negative fibers (9–89% vs 92–95%; PS3_supporting, PMID: 15670724).
• PS4_Supporting: The m.14710G>A variant in MT-TE has been reported in two affected individuals from two families (PMIDs: 15670724, 23847141; PS4_supporting). These two individuals had similar courses, as both were women with onset in childhood or adolescence of progressive external ophthalmoplegia (PEO), myopathy, pigmentary retinopathy, and migraines. Muscle biopsies performed in these two individuals showed ragged red fibers and COX-negative fibers. Respiratory chain enzyme activities were normal except for reduced complex I activity in one individual. Heteroplasmy levels were only reported in one individual (PMID: 15670724), but were 67-77% in muscle, trace amounts to 14% in hair roots, and were undetectable in buccal, blood, and fibroblasts. Of note, exercise testing in one subject (PMID: 15670724) is described in other manuscripts (PMIDs: 11506394 and 12538407), and her case is also included in a cohort study (PMID: 19718780).
• PP3: The computational predictor MitoTIP suggests this variant is pathogenic (51.7 percentile) and HmtVAR predicts it to be pathogenic score of 0.55 (PP3).

Not Met criteria codes

• PP1: There are no large families reported in the medical literature to consider for evidence of segregation.
• PM6: One of the affected individuals has a son with autism but he was not tested for this variant. The variant was not detected in blood from the subject’s mother and three sisters but it was also undetectable in the subject's blood, so de novo status could not be confirmed (PMID: 15670724).

Approved on: 2022-12-15

Published on: 2023-01-05