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
  • Gene listed was thus derived from ClinVar and/or CAR


Variant: NC_012920.1:m.3890G>A

CA345911

155881 (ClinVar)

Gene: MT-ND1
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: e510313a-82fc-4562-8b0d-29a412c38c26

HGVS expressions

NC_012920.1:m.3890G>A
J01415.2:m.3890G>A
ENST00000361390.2:n.584G>A

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PS3_Supporting PP1_Moderate PS4_Moderate PP3
Not Met criteria codes 3
PP4 PM6 PS2

Evidence Links 1

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.3890G>A (p.R195Q) variant in MT-ND1 has been reported in at least nine individuals from nine families in the literature, who had features falling within the Leber Hereditary Optic Neuropathy (LHON) or Leigh syndrome spectrums (PS4_moderate; PMIDs: 34390870, 33337510, 27798429, 18504678, 30095618, 23246842, 23847141). There are no reports of de novo occurrence of this variant to our knowledge. Although this variant most often is seen in the homoplasmic state, in one multi-generational family, there were five unaffected relatives with low heteroplasmy levels in urine and blood, compared to much higher levels in the proband (PP1_moderate; PMID 2324842). This variant is absent in population databases after removing sequences from individuals with mitochondrial disease (one occurrence in GenBank sequences is from individual with mitochondrial disease – PMID: 23246842; variant absent in gnomAD v3.1.2 and Helix dataset; PM2_supporting). The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.73 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3). Cybrid studies showed that the homoplasmic mutant clones had statistically significant decreases in Complex I and ATP synthesis activities (PS3_supporting, PMID: 23246842). In summary, this variant meets criteria to be classified as likely pathogenic for primary mitochondrial disease inherited in a mitochondrial manner. This classification was approved by the NICHD/NINDS U24 Mitochondrial Disease Variant Curation Expert Panel on March 28, 2022. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PP1_moderate, PS4_moderate, PP3, PM2_supporting, PS3_supporting.
Met criteria codes
PM2_Supporting
This variant is absent in population databases after removing sequences from individuals with mitochondrial disease (one occurrence in GenBank sequences is from individual with mitochondrial disease – PMID: 23246842; variant absent in gnomAD v3.1.2 and Helix dataset; PM2_supporting). [homoplasmic AF = 0% [0.0000185% in Mitomap (1/54594), but that one is Caporali’s patient cybrid line), 0% in gnomAD (0/56434), and 0% in Helix (0/195983)]
PS3_Supporting
Cybrid studies showed that the homoplasmic mutant clones had statistically significant decreases in Complex I and ATP synthesis activities (PS3_supporting, PMID: 2324842).

PP1_Moderate
Although this variant most often is seen in the homoplasmic state, in one multi-generational family, there were five unaffected relatives with low heteroplasmy levels in urine and blood, compared to much higher levels in the proband (PP1_moderate; PMID 2324842). In Caporali 2013 PMID 2324842, 5 unaffected maternal relatives of the proband were tested and had 0-50% heteroplasmy in urine epithelial cells vs proband's ~75%. Mom's blood test had ~5% het vs proband's ~50%.
PS4_Moderate
The m.3890G>A (p.R195Q) variant in MT-ND1 has been reported in at least nine individuals from nine families in the literature, who had features falling within the Leber Hereditary Optic Neuropathy (LHON) or Leigh syndrome spectrums (PS4_moderate; PMIDs: 34390870, 33337510, 27798429, 18504678, 30095618, 23246842, 23847141). 9 reported cases in the literature, PMIDs 18504678, 23246842, 23847141, 27798429, 30095618, 29253894, 34390870. Five of these were LHON or LHON-like; 2 were Leigh or Leigh-like; 2 were in a mitochondrial disease cohort with no clinical details given.
PP3
The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.73 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3).
Not Met criteria codes
PP4
Nuclear sequencing was not performed to rule out other causes of ETC defect, although Moslemi 2008 [PMID: 18504678] showed complex I deficiency in muscle and Bannwarth 2013[ PMID: 23847141] showed decreased complex I, III, & IV activities in fibroblasts.
PM6
There are no reports of de novo occurrence of this variant to our knowledge.
PS2
There are no reports of de novo occurrence of this variant to our knowledge.
Approved on: 2022-06-30
Published on: 2022-06-30
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