ClinVar Miner

Submissions for variant NC_012920.1(MT-ND2):m.5293G>A

dbSNP: rs28690990
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 2
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel, ClinGen RCV002221591 SCV002498777 likely benign Mitochondrial disease 2022-03-24 reviewed by expert panel curation The m.5293G>A (p.S275N) variant in MT-ND2 was reviewed by the Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel as part of the variant pilot for mitochondrial DNA variant specifications (McCormick et al., 2020; PMID: 32906214). This variant is present in 1/49,487 sequences (1/509 in H1c) in Genbank per MITOMAP queried 10/29/2019. This variant is seen at homoplasmy in a proband, healthy brother, and healthy mother (PMID: 23813926). The proband had a pathogenic mtDNA variant, m.14487T>C, present at high heteroplasmy levels (BP2). The proband was particularly severe having Leigh syndrome at 6 months old however the m.5293G>A variant is homoplasmic in all family members including healthy individuals. Of note, this family is haplogroup H1 as is report in GenBank sequences. Additionally, the computational predictor APOGEE gives a consensus rating of neutral with a low pathogenicity predictor score, 0.46 (Min=0, Max=1), evidence that does not predict a damaging effect on gene function (BP4). In summary, this variant meets criteria to be classified as likely benign. This classification was approved by the NICHD U24 Mitochondrial Disease Variant Curation Expert Panel as of August 20, 2020. Mitochondrial DNA-specific ACMG/AMP criteria applied: BP2, BP4.
Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine RCV000853884 SCV000996917 likely benign Leigh syndrome 2019-10-17 criteria provided, single submitter clinical testing The NC_012920.1:m.5293G>A (YP_003024027.1:p.Ser275Asn) variant in MTND2 gene is interpretated to be a Likely Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: BS4, BP4, BP6

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. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.