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.13730G>A") does not appear to be in HGVS format


Variant: m.13730G>A

CA340936

9697 (ClinVar)

Gene: N/A
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 0f850d1f-cfef-499f-a684-37c64d676b11

HGVS expressions

NC_012920.1:m.13730G>A
J01415.2:m.13730G>A
ENST00000361567.2:c.1394G>A

Uncertain Significance

Met criteria codes 2
PP3 PM2_Supporting
Not Met criteria codes 5
PS3 PS4 PS2 PP1 PM6

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

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.13730G>A (p.G465E) variant in MT-ND5 has been reported in one individual from one family to date (PMID: 8213825), in a male with Leber Hereditary Optic Neuropathy (LHON). The variant was present at 80% heteroplasmy in blood. The variant was presumed to have occurred de novo as it was absent in blood from his mother, maternal grandmother, and two maternal uncles (PMID: 8213825), however no additional tissues were tested and technology performed at the time of publication would not detect low heteroplasmy levels of the variant. The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.83, which predicts a damaging effect on gene function (PP3). This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). 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 November 13, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PM2_supporting, PP3.
Met criteria codes
PP3
The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.83, which predicts a damaging effect on gene function (PP3).
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.
PS4
The m.13730 G>A variant in MT-ND5 has been reported in one individual from one family (PMID: 8213825), in a male with LHON. The variant was present at 80% heteroplasmy in blood.
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
There are no reports of large families with this variant segregating with disease.
PM6
The variant was reported de novo in the first case report as it was absent in mother, maternal grandmother, and 2 maternal uncle's blood (PMID: 8213825), however no additional tissues were tested and technology performed at the time of publication would not detect low heteroplasmy levels of the variant.
Approved on: 2023-11-13
Published on: 2024-03-28
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