The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • The variant label for this record ("m.5703G>A") does not appear to be in HGVS format
  • 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: m.5703G>A

CA120583

9620 (ClinVar)

Gene: MT-TN
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: ab5eb1f8-521d-459b-83f1-8f9933b52cb7
Approved on: 2023-02-13
Published on: 2023-03-30

HGVS expressions

NC_012920.1:m.5703G>A
J01415.2:m.5703G>A

Pathogenic

Met criteria codes 5
PM6_Strong PS3_Supporting PM2_Supporting PS4_Moderate PP3
Not Met criteria codes 1
PP1

Evidence Links 3

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.5703G>A variant in MT-TN has been reported in four unrelated individuals with primary mitochondrial disease (PS4_moderate). These four individuals were from three different backgrounds including African American (one individual), Chinese (one individual), and Caucasian (two individuals, one from France and one from Spain). Features seen in affected individuals include myoclonic epilepsy with ragged red fibers (MERRF) and chronic progressive external ophthalmoplegia (CPEO), as well as exercise intolerance, severe underweight, and hearing loss (PMIDs: 8254046, 14518831, 30897601, 32419253). The variant in these four cases was seen at varying degrees of heteroplasmy in muscle (14-80%), blood (5-48%), urine (4-11%), and buccal (7-59%). The variant was reported to have arisen de novo in three of the four affected individuals (PM6_strong, PMIDs: 8254046, 30897601, 32419253) and no details about family member testing were provided for the other individual. Furthermore, the variant’s presence in individuals of different ethnic backgrounds was also considered as indirect evidence of a de novo occurrence at some time in the past. There are no other large families reported in the medical literature to consider for evidence of segregation. There is one occurrence of this variant in GenBank dataset and it is absent in gnomAD v3.1.2 and in the Helix dataset, therefore the overall frequency is still very low (PM2_supporting). The computational predictor MitoTIP predicts this variant to be pathogenic, scoring in the 89.9 percentile and HmtVAR also predicts it to be pathogenic with a score of 0.85 (PP3). Multiple independent studies support the functional impact of this variant (PS3_supporting). Single-fiber testing in two of the four affected individuals was performed and showed that the variant was present at higher heteroplasmy in COX-negative fibers than COX-positive fibers (93% heteroplasmy in COX-negative fibers compared to 2% in COX-positive fibers in one individual, P<.0001, PMID: 32419253; and 97-100% in COX-negative fibers compared to 3-63% in COX-positive fibers in the other individual, PMID: 8254046). Furthermore, cybrids with high levels of the variant demonstrated a severe mitochondrial protein synthesis defect and impaired oxidative phosphorylation (PMIDs: 8254046, 9372914). tRNA conformational studies showed impaired aminoacylation with severe reduction of the tRNA Asn pool (PMID: 9372914). In summary, this variant meets criteria to be classified as likely pathogenic however, after extensive discussion, this Expert Panel elected to modify the classification to pathogenic given consistent functional evidence of severe deleterious effect across multiple independent studies and given repeated apparent de novo occurrences across individuals of different ethnic backgrounds. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Variant Curation Expert Panel on February 13, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_moderate, PS3_supporting, PP3, PM2_supporting, PM6_strong.
Met criteria codes
PM6_Strong
The variant was reported to have arisen de novo in three of the four affected individuals (PM6_strong, PMIDs: 8254046, 30897601, 32419253) and no details about family member testing were provided for the other individual.
PS3_Supporting
Multiple independent studies support the functional impact of this variant (PS3_supporting). Single-fiber testing in two of the four affected individuals was performed and showed that the variant was present at higher heteroplasmy in COX-negative fibers than COX-positive fibers (93% heteroplasmy in COX-negative fibers compared to 2% in COX-positive fibers in one individual, P<.0001, PMID: 32419253; and 97-100% in COX-negative fibers compared to 3-63% in COX-positive fibers in the other individual, PMID: 8254046). Furthermore, cybrids with high levels of the variant demonstrated a severe mitochondrial protein synthesis defect and impaired oxidative phosphorylation (PMIDs: 8254046, 9372914). tRNA conformational studies showed impaired aminoacylation with severe reduction of the tRNA Asn pool (PMID: 9372914).

PM2_Supporting
There is one occurrence of this variant in GenBank dataset and it is absent in gnomAD v3.1.2 and in the Helix dataset, therefore the overall frequency is still very low (PM2_supporting).
PS4_Moderate
The m.5703G>A variant in MT-TN has been reported in four unrelated individuals with primary mitochondrial disease (PS4_moderate). These four individuals were from three different backgrounds including African American (one individual), Chinese (one individual), and Caucasian (two individuals, one from France and one from Spain). Features seen in affected individuals include myoclonic epilepsy with ragged red fibers (MERRF) and chronic progressive external ophthalmoplegia (CPEO), as well as exercise intolerance, severe underweight, and hearing loss (PMIDs: 8254046, 14518831, 30897601, 32419253). The variant in these four cases was seen at varying degrees of heteroplasmy in muscle (14-80%), blood (5-48%), urine (4-11%), and buccal (7-59%).
PP3
The computational predictor MitoTIP predicts this variant to be pathogenic, scoring in the 89.9 percentile and HmtVAR also predicts it to be pathogenic with a score of 0.85 (PP3).
Not Met criteria codes
PP1
There are no other large families reported in the medical literature to consider for evidence of segregation.
Curation History
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