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
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Variant: NC_012920.1:m.13051G>A

CA414816093

430689 (ClinVar)

Gene: N/A
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: cc7b6bfe-41bb-4007-99c0-5302ecb02ff0
Approved on: 2023-05-23
Published on: 2024-07-23

HGVS expressions

NC_012920.1:m.13051G>A
J01415.2:m.13051G>A
ENST00000361567.2:c.715G>A

Uncertain Significance

Met criteria codes 4
PS3_Supporting PS4_Moderate PP3 PM2_Supporting
Not Met criteria codes 2
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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.13051G>A (p.G239S) variant in MT-ND5 has been reported in thirteen individuals with primary mitochondrial disease from four kindreds (PS4_moderate; PMIDs: 12736867, 27164671). Age of onset varied from age 18 months to the 40s, and clinical features were consistent with Leber Hereditary Optic Neuropathy (LHON) and Leigh syndrome spectrum disorders, in addition to hearing loss, optic atrophy, retinal dystrophy, ophthalmoplegia, and seizures. Several individuals had elevated lactate levels. The variant was present at or near homoplasmy in all reported individuals, thus precluding consideration for segregation evidence. There are no reports of confirmed de novo occurrences to our knowledge. This variant is absent in the GenBank dataset and gnomAD v3.1.2, however there were three heteroplasmic occurrences in the Helix dataset (PM2_supporting). The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.71 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3). Comprehensive analysis in patient cells showed increased reactive oxygen species and increased mitophagy (PS3_supporting). In summary, this variant meets criteria to be classified as uncertain significance for primary mitochondrial disease inherited in a mitochondrial manner, although this Expert Panel notes this is a very compelling variant of uncertain significance. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Variant Curation Expert Panel on May 23, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_moderate, PM2_supporting, PP3, PS3_supporting.
Met criteria codes
PS3_Supporting
Comprehensive analysis in patient cells showed increased reactive oxygen species and increased mitophagy (PS3_supporting).
PS4_Moderate
The m.13051G>A (p.G239S) variant in MT-ND5 has been reported in thirteen individuals with primary mitochondrial disease from four kindreds (PS4_moderate; PMIDs: 12736867, 27164671). Age of onset varied from age 18 months to the 40s, and clinical features were consistent with Leber Hereditary Optic Neuropathy (LHON) and Leigh syndrome spectrum disorders, in addition to hearing loss, optic atrophy, retinal dystrophy, ophthalmoplegia, and seizures. Several individuals had elevated lactate levels. The variant was present at or near homoplasmy in all reported individuals.
PP3
The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.71 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3).
PM2_Supporting
This variant is absent in the GenBank dataset and gnomAD v3.1.2, however there were three heteroplasmic occurrences in the Helix dataset (PM2_supporting).
Not Met criteria codes
PP1
The variant was present at or near homoplasmy in all reported individuals, thus precluding consideration for segregation evidence.
PM6
There are no reports of confirmed de novo occurrences to our knowledge.
Curation History
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