The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Despite there being a valid 'cspec' property in the messages there's a discrepancy in message contents and CSPEC data: * Message Gene: MT-TN CSPEC Genes: [] * Message MONDOs: MONDO:0044970 CSPEC MONDO: []
  • No CSPEC computed assertion could be determined for this classification!


Variant: NC_012920.1(MT-TN):m.5702A>G

CA913180290

812543 (ClinVar)

Gene: MT-TN
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 58f201de-639e-4d11-aa88-4af94f7df55f
Approved on: 2024-09-24
Published on: 2024-11-21

HGVS expressions

NC_012920.1:m.5702A>G
J01415.2:m.5702A>G

Uncertain Significance

Met criteria codes 2
PM6_Supporting PM2_Supporting
Not Met criteria codes 6
PS3 PS2 PS4 PP3 PP1 BP4

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.5702A>G variant in MT-TN has been reported in one individual with primary mitochondrial disease to date (PMID: 32161153; this appears to be the same individual reported in an abstract, https://www.nmd-journal.com/article/S0960-8966(16)30622-8/abstract, and included in the ClinVar submission for this variant). Clinical features in this woman include ophthalmoplegia, ptosis, myopathy, and ragged red and COX-negative fibers on muscle biopsy. The variant is present in the proband at 60% heteroplasmy muscle, 10% in urine, and absent in blood and skin fibroblasts. The variant is absent in blood and urine from her mother and four asymptomatic siblings (PM6_supporting; https://www.nmd-journal.com/article/S0960-8966(16)30622-8/abstract). There are no additional individuals or families reported with de novo occurrences of this variant or with this variant segregating with clinical manifestations to our knowledge. This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). Computational predictors are conflicting (MitoTIP: 73.9%; HmtVAR: 0.05). There are no cybrids, single fiber studies, or other functional assays reported on this variant. 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 September 24, 2024. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PM6_supporting, PM2_supporting.
Met criteria codes
PM6_Supporting
The variant is present in the proband at 60% heteroplasmy muscle, 10% in urine, and absent in blood and skin fibroblasts. The variant is absent in blood and urine from her mother and four asymptomatic siblings (PM6_supporting; https://www.nmd-journal.com/article/S0960-8966(16)30622-8/abstract).
PM2_Supporting
This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
Not Met criteria codes
PS3
There are no cybrids, single fiber studies, or other functional assays reported on this variant.
PS2
The variant is present in the proband at 60% heteroplasmy muscle, 10% in urine, and absent in blood and skin fibroblasts. The variant is absent in blood and urine from her mother and four asymptomatic siblings (PM6_supporting; https://www.nmd-journal.com/article/S0960-8966(16)30622-8/abstract).
PS4
The m.5702A>G variant in MT-TN has been reported in one individual with primary mitochondrial disease to date (PMID: 32161153; this appears to be the same individual reported in an abstract, https://www.nmd-journal.com/article/S0960-8966(16)30622-8/abstract, and included in the ClinVar submission for this variant). Clinical features in this woman include ophthalmoplegia, ptosis, myopathy, and ragged red and COX-negative fibers on muscle biopsy.
PP3
Computational predictors are conflicting (MitoTIP: 73.9%; HmtVAR: 0.05).
PP1
There are no additional individuals or families reported with de novo occurrences of this variant or with this variant segregating with clinical manifestations to our knowledge.
BP4
Computational predictors are conflicting (MitoTIP: 73.9%; HmtVAR: 0.05).
Curation History
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