The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • No ClinVar Id was directly found from the curated document
  • There was no gene found in the curated document received from the VCI/VCEP
  • Gene was also not found in ClinVar or the Allele Registry


Variant: NC_012920.1:m.4450G>A

CA913178210

Gene: N/A
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 1806e24c-7e4f-4774-ac6d-77bacb921cdb
Approved on: 2023-02-27
Published on: 2023-03-16

HGVS expressions

NC_012920.1:m.4450G>A
J01415.2:m.4450G>A

Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 5
PP3 PS3_Supporting PM2_Supporting PS4_Supporting PS2_Moderate
Not Met criteria codes 2
PP1 PM6

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Mitochondrial Disease Nuclear and Mitochondrial Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1_mtDNA

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.4450G>A variant in MT-TM has been reported in two unrelated individuals with primary mitochondrial disease (PS4_supporting). The first individual reported was a girl with childhood onset myopathy (fatigue, proximal muscle weakness, exercise intolerance) and developmental delay. Muscle biopsy revealed COX-negative fibers and a combined respiratory chain enzyme deficiency. The variant was present at 67% in muscle, 10% in fibroblasts, and was undetectable in blood and buccal samples (PMID: 25468263). The variant was undetectable in her healthy mother’s blood, muscle, and urinary sediment (PS2_moderate). The second individual reported was a girl with mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) and the variant was present at varying levels (20-59%) in several tissues tested. Fibroblasts in this individual showed reduced oxygen consumption and reduced activities of respiratory chain complexes I and IV (PMID: 30739820). There are no other large families reported in the medical literature to consider for evidence of segregation. The computational predictor MitoTIP suggests this variant is pathogenic (83.7 percentile) and HmtVAR predicts it to be pathogenic score of 1 (PP3). This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). Single fiber testing showed high heteroplasmy levels in ragged blue fibers (94% ± 5.4%) and variant was not detected in normal appearing fibers (PMID: 25468263, PS3_supporting). In summary, this variant meets criteria to be classified as likely pathogenic 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 February 27, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_supporting, PS2_moderate, PM2_supporting, PP3, PS3_supporting.
Met criteria codes
PP3
The computational predictor MitoTIP suggests this variant is pathogenic (83.7 percentile) and HmtVAR predicts it to be pathogenic score of 1 (PP3).
PS3_Supporting
Single fiber testing showed high heteroplasmy levels in ragged blue fibers (94% ± 5.4%) and variant was not detected in normal appearing fibers (PMID: 25468263, PS3_supporting).
PM2_Supporting
This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
PS4_Supporting
The m.4450G>A variant in MT-TM has been reported in two unrelated individuals with primary mitochondrial disease (PS4_supporting). The first individual reported was a girl with childhood onset myopathy (fatigue, proximal muscle weakness, exercise intolerance) and developmental delay. Muscle biopsy revealed COX-negative fibers and a combined respiratory chain enzyme deficiency. The variant was present at 67% in muscle, 10% in fibroblasts, and was undetectable in blood and buccal samples (PMID: 25468263). The second individual reported was a girl with mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) and the variant was present at varying levels (20-59%) in several tissues tested. Fibroblasts in this individual showed reduced oxygen consumption and reduced activities of respiratory chain complexes I and IV (PMID: 30739820).
PS2_Moderate
The first individual reported with this variant was a girl with childhood onset myopathy (fatigue, proximal muscle weakness, exercise intolerance) and developmental delay. Muscle biopsy revealed COX-negative fibers and a combined respiratory chain enzyme deficiency. The variant was present at 67% in muscle, 10% in fibroblasts, and was undetectable in blood and buccal samples (PMID: 25468263). The variant was undetectable in her healthy mother’s blood, muscle, and urinary sediment (PS2_moderate).
Not Met criteria codes
PP1
There are no other large families reported in the medical literature to consider for evidence of segregation.
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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