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
  • The variant label for this record ("m.5244G>A") does not appear to be in HGVS format


Variant: m.5244G>A

CA340940

9717 (ClinVar)

Gene: N/A
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 9cc4558c-8e90-491e-9d29-4ba4c5c706d3

HGVS expressions

NC_012920.1:m.5244G>A
J01415.2:m.5244G>A
ENST00000361453.3:c.775G>A

Uncertain Significance

Met criteria codes 2
PM2_Supporting PP3
Not Met criteria codes 1
PS4

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.5244G>A (p.G259S) variant in MT-ND2 has been reported in one family (PMID: 1634041) with Leber Hereditary Optic Neuropathy (LHON), however individuals in this family also harbored other mitochondrial DNA variants also associated with LHON, making the association of this variant to the primary mitochondrial disease features in these individuals unclear. Furthermore, to our knowledge, nuclear genetic testing was not performed. There are no reports of large families with this variant segregating with disease. There are no reported de novo occurrences of this variant to our knowledge. The computational predictor MitoTIP suggests this variant is pathogenic (77 percentile, PP3). This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). 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 October 9, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PM2_supporting, PP3.
Met criteria codes
PM2_Supporting
This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
PP3
The computational predictor MitoTIP suggests this variant is pathogenic (77 percentile) (PP3).
Not Met criteria codes
PS4
The m.5244 G>A variant in MT-ND2 has been reported in one family (PMID: 1634041), with LHON and another primary LHON causing variant. The variant was present at heteroplasmic level and no additional data were reported.
Approved on: 2023-10-09
Published on: 2023-11-03
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.