The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • There was no gene found in the curated document received from the VCI/VCEP
  • Gene listed was thus derived from ClinVar and/or CAR
  • The variant label for this record ("m.5521G>A") does not appear to be in HGVS format


Variant: m.5521G>A

CA254831

9556 (ClinVar)

Gene: MT-TW
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 1d89ede2-5ff3-4a4c-85d9-1e1c62d68766
Approved on: 2022-10-03
Published on: 2022-10-12

HGVS expressions

NC_012920.1:m.5521G>A
J01415.2:m.5521G>A

Likely Pathogenic

Met criteria codes 4
PM2_Supporting PS3_Moderate PS4_Moderate PP3
Not Met criteria codes 3
PM6 PS2 PP1

Evidence Links 1

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

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.5521G>A variant in MT-TW has been reported in four unrelated individuals to date. Ages of onset included childhood (2/4 affected individuals), 20s (1/4 affected individuals), and 50s (1/4 affected individuals). Affected individuals had features including myopathy, seizures, cerebellar ataxia, mood disorders, and eating disorders. Muscle biopsies showed ragged red fibers (RRF) and COX-negative fibers, whereas respiratory chain enzyme deficiencies were variable. Heteroplasmy levels of the variant were not specified in one affected individual, were 98% muscle and undetectable in blood in another affected individual, were homoplasmic in muscle and 87% brain in another affected individual, and were homoplasmic in blood in the last individual (PS4_moderate; PMIDs: 20360171, 23841600, 23847141, 9673981). There are no de novo occurrences of this variant to our knowledge. 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). The computational predictor MitoTIP suggests this variant is pathogenic (89.7 percentile) and HmtVAR predicts it to be pathogenic score of 1 (PP3). Single fiber testing showed higher levels of the variant in COX-negative RRF (89.9% +/- 11.76) than in COX-positive fibers (69.35% +/- 26.22), p<0.005 (PS3_supporting, PMID: 9673981). 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 October 3, 2022. Mitochondrial DNA-specific ACMG/AMP criteria applied: PS4_moderate, PM2_supporting, PP3, PS3_supporting.
Met criteria codes
PM2_Supporting
This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
PS3_Moderate
Single fiber testing showed higher levels of the variant in COX negative RRF (89.9% +/- 11.76) than in COX positive fibers (69.35% +/- 26.22), p<0.005 (PS3_supporting, PMID: 9673981).

PS4_Moderate
This variant is present in four individuals with features of primary mitochondrial disease.
PP3
The computational predictor MitoTIP suggests this variant is pathogenic (89.7 percentile) and HmtVAR predicts it to be pathogenic score of 1 (PP3).
Not Met criteria codes
PM6
There are no de novo occurrences of this variant to our knowledge.
PS2
There are no de novo occurrences of this variant to our knowledge.
PP1
There are no large families reported in the medical literature to consider for evidence of segregation.
Curation History
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