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.15579A>G") does not appear to be in HGVS format


Variant: m.15579A>G

CA120621

9683 (ClinVar)

Gene: MT-CYB
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 24728e64-d0be-480a-ab10-52451f02bac6

HGVS expressions

NC_012920.1:m.15579A>G
J01415.2:m.15579A>G
ENST00000361789.2:n.833A>G

Uncertain Significance

Met criteria codes 3
PS3_Supporting PP3 PM2_Supporting
Not Met criteria codes 4
PS2 PS4 PP1 PM6

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.15579A>G (p.Y278C) variant in MT-CYB has been reported in one individual with primary mitochondrial disease. This woman had exercise intolerance, epilepsy, intellectual disability, hearing loss, retinal dystrophy, and cataracts (PMID: 11601507). The variant was heteroplasmic in muscle (88%) and leucocytes (15%). The variant was reported as de novo as it was absent in mother’s blood, however no additional tissues were tested and technology performed at the time of publication would not detect low heteroplasmy levels of the variant. This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.78 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3). A dramatic reduction of Complex III activity and Complex III-driven ATP synthesis, enhanced superoxide production, and a perturbation of glutathione homeostasis were seen in a cybrid homoplasmic for this variant (PMID: 23418307; PS3_supporting). In summary, this variant meets criteria to be classified as uncertain significance for primary mitochondrial disease inherited in a mitochondrial manner. We note that two experts on this panel felt likely pathogenic or pathogenic was a more appropriate classification given the functional evidence of impact however the majority agreed with uncertain significance. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Variant Curation Expert Panel on July 11, 2022. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214); PM2_supporting, PP3, PS3_supporting.
Met criteria codes
PS3_Supporting
A cybrid study (PMID 23418307) showed dramatic reduction of Complex III activity and Complex III-driven ATP synthesis in a 100% mutant cell line, along with enhanced superoxide production and perturbation of glutathione homeostasis (PS3_supporting).

PP3
The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.78 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3).
PM2_Supporting
This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). Homoplasmic allele frequency is is 0% in Mitomap (0/54594), 0% gnomAD (0/56434), and 0% Helix (0/195983) .
Not Met criteria codes
PS2
The variant was reported as de novo as it was absent in mother’s blood, however no additional tissues were tested and technology performed at the time of publication would not detect low heteroplasmy levels of the variant.
PS4
The m.15579A>G (p.Y278C) variant in MT-CYB has been reported in one individual with primary mitochondrial disease. This woman had exercise intolerance, epilepsy, intellectual disability, hearing loss, retinal dystrophy, and cataracts (PMID: 11601507). The variant was heteroplasmic in muscle (88%) and leucocytes (15%). As of the curation date, only one case has been reported in the literature - the same case is referenced in all four papers to date (PMIDs: 11601507, 23376095, 23418307, 32652755). The case presented with a multisystem organ system involvement. Bilateral hearing loss was reported at age 6, years progressing to full deafness by age 11 years. By age 10 years, the patient was noted to have exercise intolerance, cognitive dysfunction, and growth retardation. The patient developed epilepsy at age 19 years. The variant was found to be heteroplasmic in muscle (88%) and leucocytes (15%). Numerous ragged red fibers were observed in the muscle. The variant was not found in the mother’s leukocytes, suggestive of, but not definitive for, a de novo variant.
PP1
Extended family members were not tested in the single case reported to date.
PM6
The variant was reported as de novo as it was absent in mother’s blood, however no additional tissues were tested and technology performed at the time of publication would not detect low heteroplasmy levels of the variant.
Approved on: 2022-07-11
Published on: 2023-03-13
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