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
  • The variant label for this record ("m.3635G>A") does not appear to be in HGVS format


Variant: m.3635G>A

CA344827

65518 (ClinVar)

Gene: MT-ND1
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: ab6a1216-a322-4e50-ae90-3e1f64c8cc57

HGVS expressions

NC_012920.1:m.3635G>A
J01415.2:m.3635G>A
ENST00000361390.2:n.329G>A

Likely Pathogenic

Met criteria codes 4
PM2_Supporting PS3_Supporting PS4 PP3
Not Met criteria codes 5
BS4 PS2 PP1 PP4 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.3635G>A (p.S110N) variant in MT-ND1 has been reported in >16 individuals with primary mitochondrial disease, and more specifically Leber's hereditary optic neuropathy (LHON). This variant has been observed in affected individuals primarily in the homoplasmic state to date (20/21 cases) (PS4; PMIDs: 25194554, 21074518, 23304069,19527690, 19497304, 11479733, 33417421). There are no large families reported in the medical literature to consider for evidence of segregation. There are no reported de novo occurrences of this variant to our knowledge. This variant is absent in Helix and the GenBank dataset. It is present in gnomAD 3.1 in 1/56428 individuals (0.002%). Although there is one occurrence, the frequency is still low (PM2_supporting). The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.75 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3). Cybrid studies supported the functional impact of this variant (PS3_supporting; PMIDs: 25194554, 11479733). 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 August 23, 2022. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PM2_supporting, PS3_supporting, PP3, PS4.
Met criteria codes
PM2_Supporting
This variant is absent in Helix and the GenBank dataset. It is present in gnomAD 3.1 in 1/56428 individuals (0.002%).
PS3_Supporting
Cybrid studies supported the functional impact of this variant (PS3_supporting; PMIDs: 25194554, 11479733).
PS4
The m.3635G>A variant in MT-ND1 has been reported in >16 individuals with primary mitochondrial disease, and more specifically Leber's hereditary optic neuropathy (LHON). This variant has been observed in affected individuals primarily in the homoplasmic state to date (20/21 cases) (PS4; PMIDs: 25194554, 21074518, 23304069,19527690, 19497304, 11479733, 33417421).
PP3
The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.75 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3).
Not Met criteria codes
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
There are no large families reported in the medical literature to consider for evidence of segregation.
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
There are no reported de novo occurrences of this variant to our knowledge.
Approved on: 2022-08-23
Published on: 2022-09-02
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