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.10663T>C") 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-TL1 CSPEC Genes: [] * Message MONDOs: MONDO:0044970 CSPEC MONDO: []
  • No CSPEC computed assertion could be determined for this classification!


Variant: m.10663T>C

CA340938

9707 (ClinVar)

Gene: MT-TL1
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 5e1ddfb7-92ac-4f1e-a211-12a19e645406
Approved on: 2022-06-13
Published on: 2022-10-13

HGVS expressions

NC_012920.1:m.10663T>C
J01415.2:m.10663T>C
ENST00000361335.1:c.194T>C

Likely Pathogenic

Met criteria codes 4
PP3 PS3_Supporting PS4_Moderate 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.10663T>C (p.V65A) variant in MT-ND4L has been reported in at least 28 individuals from eight families, all of whom had Leber Hereditary Optic Neuropathy (LHON) and were haplogroup J and L (PS4_moderate; PMIDs: 29210930, 11935318, 24568867, 22879922, 17003408). There are three reported cases with no family history and, while these variants were assumed to occur de novo, family members were not tested for the variant. Several extended families have been reported in the medical literature (PMID: 24568867) however the variant was homoplasmic and thus prevented consideration for PP1. The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.9 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3). There are several occurrences in population databases, however some of these are from reported affected individuals (two occurrences in the GenBank dataset however one is from a patient with known mitochondrial disease, one occurrence in the Helix dataset, absent in gnomAD). Although there are several occurrences, the frequency is still low (PM2_supporting). Cybrid studies supported the functional impact of this variant (PS3_supporting; PMID: 11935318). This variant meets criteria to be classified as uncertain significance however this Expert Panel elected to modify the classification to likely pathogenic given the overwhelming evidence of pathogenicity. Furthermore, the mitochondrial DNA variant specifications are known to not be optimized for pathogenic variants that tend to be homoplasmic in nature and/or have reduced penetrance, such as the common variants associated with LHON. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Variant Curation Expert Panel on June 13, 2022. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS3_supporting, PS4_moderate, PM2_supporting, PP3.
Met criteria codes
PP3
The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.9 (Min=0, Max=1), which predicts a damaging effect on gene function (PP3).
PS3_Supporting
Cybrid studies supported the functional impact of this variant (PS3_supporting; PMID: 11935318). Complex I deficiency was noted as seen in other LHON-associated variants.
PS4_Moderate
The m.10663T>C (p.V65A) variant in MT-ND4L has been reported in at least 28 individuals from eight families, all of whom had Leber Hereditary Optic Neuropathy (LHON) and were haplogroup J and L (PS4_moderate; PMIDs: 29210930, 11935318, 24568867, 22879922, 17003408).
PM2_Supporting
There are several occurrences in population databases, however some of these are from reported affected individuals (two occurrences in the GenBank dataset however one is from a patient with known mitochondrial disease, one occurrence in the Helix dataset, absent in gnomAD). Although there are several occurrences, the frequency is still low (PM2_supporting).
Not Met criteria codes
PP1
Several extended families have been reported in the medical literature (PMID: 24568867) however the variant was homoplasmic and thus prevented consideration for PP1.
PM6
There are three reported cases with no family history and while these variants were assumed to occur de novo, family members were not tested for the variant.
Curation History
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