The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • The variant label for this record ("m.4810G>A") does not appear to be in HGVS format
  • Despite there being a valid 'cspec' property in the messages there's a discrepancy in message contents and CSPEC data: * Message Gene: MT-ND2 CSPEC Genes: [] * Message MONDOs: MONDO:0044970 CSPEC MONDO: []
  • No CSPEC computed assertion could be determined for this classification!


Variant: m.4810G>A

CA120642

9720 (ClinVar)

Gene: MT-ND2
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 7afe2fe4-ebc4-4f13-846c-740c7f4c4c1d
Approved on: 2023-10-09
Published on: 2024-08-15

HGVS expressions

NC_012920.1:m.4810G>A
J01415.2:m.4810G>A
ENST00000361453.3:c.341G>A

Likely Pathogenic

Met criteria codes 3
PM2_Supporting PS3_Supporting PVS1_Strong
Not Met criteria codes 4
PM6 PS4 PP3 PP1

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.4810G>A (p.W114*) variant in MT-ND2 has been reported in three individuals with primary mitochondrial disease to date. One individual was reported to have severe exercise intolerance, muscle weakness, myalgia, ophthalmoplegia, ptosis, elevated blood lactate, elevated CK, electromyography consistent with myopathy, and ragged red fibers on muscle biopsy (PMID: 15781840). Complex I activity was reduced in muscle. The variant was present at 94% heteroplasmy in muscle and was undetectable in blood. The two additional individuals reported had ophthalmoplegia and ptosis, however no additional details were provided (Roisin 2022, Newcastle University, https://theses.ncl.ac.uk/jspui/bitstream/10443/5737/1/Stout%20R%20B%202022.pdf). There are no reported de novo occurrences of this variant to our knowledge. There are no reports of large families with this variant segregating with disease. This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting). The transition at base position m.4810 causes a W114Ter change. This causes a significant truncation (67%) of the ND2 protein (PVS1_strong). Single fiber testing showed numerous ragged-red fibers with the variant present at a mean of 84.27% (n=15) compared to the variant being present at a mean heteroplasmy of 7.15% in the normal fibers (n=14, PS3_supporting, PMID: 15781840). There are no in silico predictors for this type of variant in mitochondrial DNA. In summary, this variant meets criteria to be classified as likely pathogenic for primary mitochondrial disease inherited in a mitochondrial manner. We note that one expert on this panel felt uncertain significance was the more appropriate classification given only one case with clinical details has been reported and extensive functional validation is lacking. 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): PM2_supporting, PS3_supporting, PVS1_strong.
Met criteria codes
PM2_Supporting
This variant is absent in the GenBank dataset, Helix dataset, and gnomAD v3.1.2 (PM2_supporting).
PS3_Supporting
Single fiber testing showed numerous ragged-red fibers with the variant present at a mean of 84.27% (n=15) compared to the variant being present at a mean heteroplasmy of 7.15% in the normal fibers (n=14, PS3_supporting, PMID: 15781840).
PVS1_Strong
The transition at base position m.4810 causes a W114Ter change. This causes a significant truncation (67%) of the ND2 protein (PVS1_strong).
Not Met criteria codes
PM6
There are no reported de novo occurrences of this variant to our knowledge.
PS4
The m.4810G>A (p.W114*) variant in MT-ND2 has been reported in three individuals with primary mitochondrial disease to date. One individual was reported to have severe exercise intolerance, muscle weakness, myalgia, ophthalmoplegia, ptosis, elevated blood lactate, elevated CK, electromyography consistent with myopathy, and ragged red fibers on muscle biopsy (PMID: 15781840). Complex I activity was reduced in muscle. The variant was present at 94% heteroplasmy in muscle and was undetectable in blood. The two additional individuals reported had ophthalmoplegia and ptosis, however no additional details were provided (Roisin 2022, Newcastle University, https://theses.ncl.ac.uk/jspui/bitstream/10443/5737/1/Stout%20R%20B%202022.pdf).
PP3
There are no in silico predictors for this type of variant in mitochondrial DNA.
PP1
There are no reports of large families with this variant segregating with disease.
Curation History
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