Variant: m.5132_5133delAA

CA120641

9719 (ClinVar)

Gene: MT-ND2

Condition: mitochondrial disease

Inheritance Mode: Mitochondrial inheritance

UUID: 6506135d-9e1d-4ce6-aa48-f2f51c87cdb9

Approved on: 2023-10-09

Published on: 2024-03-28

HGVS expressions

NC_012920.1:m.5133_5134del
J01415.2:m.5133_5134del
ENST00000361453.3:c.664_665del

Uncertain Significance

• Met criteria codes: PM4 PM2_Supporting PS2_Supporting

• Not Met criteria codes: PM6 PS3 PS4 PP3

Expert Panel

Mitochondrial Diseases VCEP

Criteria Specification Information

Evidence submitted by expert panel

Mitochondrial Diseases VCEP

The m.5133_5134delAA variant in MT-ND2 has been reported in one individual from one family (PMID: 12192017), in a male with exercise intolerance, ragged red fibers, and reduced complex I activity. The variant was present at 93% heteroplasmy (PMID:19273755). This variant was reported to have occurred on the paternal mitochondrial DNA as two haplogroups were reportedly present in the proband, one matching his mother’s haplogroup and the other matching his father’s, although the variant was not present in his mother or father (PS2_supporting, PMID: 12192017). This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). There are no in silico predictors for this type of variant in mitochondrial DNA. There are no cybrids, single fiber studies, or other functional assays reported on this variant. This 2 base pair deletion starting at amino acid L221 in the MT-ND2 gene results in a stop codon at position 251 (L251Ter). This results in a truncated MT-ND2 gene product (PM4). Of note, this expert panel considered whether this variant should be reviewed for several reasons: (1) analysis of the mitochondrial genome was limited at the time of this report in 2002, raising concern on whether this variant was truly present in the proband or technical artifact; (2) it is possible the variant was present in the nuclear DNA but erroneously assigned to mitochondrial DNA; (3) nuclear DNA etiologies were not assessed in this proband; and (4) there are no other validated occurrences of paternal inheritance of mitochondrial DNA. However, this expert panel elected to review this variant with the current evidence and it 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): PS2_supporting, PM2_supporting, PM4.

Met criteria codes

• PM4: The 2 base pair deletion starting at amino acid L221 in the MT-ND2 gene results in a stop codon AGG at position 251 (L251Ter). This results in truncated MT-ND2 gene product (PM4).
• PM2_Supporting: This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
• PS2_Supporting: This variant occurred de novo in one individual (absent in blood from mother, father, paternal uncle and sister; sister's muscle as well PS2_supporting, PMID: 12192017).

Not Met criteria codes

• PM6: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PS3: There are no cybrids, single fiber studies, or other functional assays reported on this variant.
• PS4: The m.5132_5133delAA variant in MT-ND2 has been reported in one individual from one family (PMID: 12192017), in a male with exercise intolerance. The variant was present at 93% heteroplasmy (PMID:19273755) in haplogroup U5.
• PP3: There are no in silico predictors for this type of variant in mitochondrial DNA.