Variant: m.4284G>A

CA120571

9604 (ClinVar)

Gene: MT-TI

Condition: mitochondrial disease

Inheritance Mode: Mitochondrial inheritance

UUID: 17722654-afd1-4480-9d5d-bc90908c7145

Approved on: 2023-11-28

Published on: 2024-03-19

HGVS expressions

NC_012920.1:m.4284G>A
J01415.2:m.4284G>A

Uncertain Significance

• Met criteria codes: PP1 PS3_Supporting

• Not Met criteria codes: BP4 PS4 PP3 PM2

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.4284G>A variant in MT-TI has been reported in one family to date (PMID: 11782991). The proband had isolated spastic paraparesis and normal muscle biopsy including normal respiratory chain enzyme activities. The variant was present at 55% muscle, 50% in hair, 40% in urine, 30% in skin, 20% in buccal, and 20% in blood. His mother had truncal ataxia, dysarthria, severe hearing loss, mental regression, ptosis, ophthalmoparesis, and diabetes. Her brain MRI showed cortical and subcortical diffuse atrophy and muscle biopsy showed reduced activities of complex I and complex IV. The variant was present at 80% in muscle, 20% in urine, and 30% in blood. The proband had one brother with a multisystem progressive disorder who ultimately died of cardiomyopathy. His brain imaging showed marked cortical and subcortical atrophy. His muscle biopsy showed reductions in complex I, complex IV, and complex V. The variant was present at 90% in muscle. As this is the only family reported to date, PS4 could not be applied. The proband had another brother who was healthy and had undetectable levels of the variant in blood and urine. Therefore, this variant segregated with disease in multiple affected family members and a healthy family member had undetectable levels of the variant (PP1; PMID: 11782991). In silico predictions are inconsistent as MitoTIP suggests this variant is benign (35th percentile) and HmtVAR predicts it to be deleterious (0.55). This variant is present in population databases (Mitomap's 61,168 sequences: AF=0.003%; Helix's 195,983 sequences: AF=0.001%; and gnomAD v3.1.2: AF=0.007% as this is homoplasmic in four individuals and heteroplasmic in two individual). Given the frequency of this variant, it does not meet PM2 criterion. Cybrid studies showed that the homoplasmic mutant clones had decreases in COX activity and oxygen consumption rates compared to controls (PS3_supporting, PMID: 11782991). 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 November 28, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PP1, PS3_supporting.

Met criteria codes

• PP1: The proband had isolated spastic paraparesis and normal muscle biopsy including normal respiratory chain enzyme activities. The variant was present at 55% muscle, 50% in hair, 40% in urine, 30% in skin, 20% in buccal, and 20% in blood. His mother had truncal ataxia, dysarthria, severe hearing loss, mental regression, ptosis, ophthalmoparesis, and diabetes. Her brain MRI showed cortical and subcortical diffuse atrophy and muscle biopsy showed reduced activities of complex I and complex IV. The variant was present at 80% in muscle, 20% in urine, and 30% in blood. The proband had one brother with a multisystem progressive disorder who ultimately died of cardiomyopathy. His brain imaging showed marked cortical and subcortical atrophy. His muscle biopsy showed reductions in complex I, complex IV, and complex V. The variant was present at 90% in muscle. The proband had another brother who was healthy and had undetectable levels of the variant in blood and urine. Therefore, this variant segregated with disease in multiple affected family members and a healthy family member had undetectable levels of the variant (PP1; PMID: 11782991).
• PS3_Supporting: Cybrid studies showed that the homoplasmic mutant clones had decreases in COX activity and oxygen consumption rates compared to controls (PS3_supporting, PMID: 11782991).

Not Met criteria codes

• BP4: In silico predictions are inconsistent as MitoTIP suggests this variant is benign (35th percentile) and HmtVAR predicts it to be deleterious (0.55).
• PS4: The m.4284G>A variant in MT-TI has been reported in one family to date (PMID: 11782991). The proband had isolated spastic paraparesis and normal muscle biopsy including normal respiratory chain enzyme activities. The variant was present at 55% muscle, 50% in hair, 40% in urine, 30% in skin, 20% in buccal, and 20% in blood. His mother had truncal ataxia, dysarthria, severe hearing loss, mental regression, ptosis, ophthalmoparesis, and diabetes. Her brain MRI showed cortical and subcortical diffuse atrophy and muscle biopsy showed reduced activities of complex I and complex IV. The variant was present at 80% in muscle, 20% in urine, and 30% in blood. The proband had one brother with a multisystem progressive disorder who ultimately died of cardiomyopathy. His brain imaging showed marked cortical and subcortical atrophy. His muscle biopsy showed reductions in complex I, complex IV, and complex V. The variant was present at 90% in muscle. As this is the only family reported to date, PS4 could not be applied.
• PP3: In silico predictions are inconsistent as MitoTIP suggests this variant is benign (35th percentile) and HmtVAR predicts it to be deleterious (0.55).
• PM2: This variant is present in population databases (Mitomap's 61,168 sequences: AF=0.003%; Helix's 195,983 sequences: AF=0.001%; and gnomAD v3.1.2: AF=0.007% as this is homoplasmic in four individuals and heteroplasmic in two individual). Given the frequency of this variant, it does not meet PM2 criterion.