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
  • The variant label for this record ("m.13045A>C") does not appear to be in HGVS format
  • No CSPEC computer assertion could be determined for this classification!


Variant: m.13045A>C

CA120629

9700 (ClinVar)

Gene: N/A
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 672c235f-2edc-41e7-8b0c-9c926f8764ab
Approved on: 2023-11-13
Published on: 2024-08-15

HGVS expressions

NC_012920.1:m.13045A>C
J01415.2:m.13045A>C
ENST00000361567.2:c.709A>C

Uncertain Significance

Met criteria codes 3
PM2_Supporting PP3 PM6_Supporting
Not Met criteria codes 2
PS3 PS4

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.13045A>C (p.M237L) variant in MT-ND5 has been reported in one individual with primary mitochondrial disease to date (PMID: 12509858), in a boy with migraine-like symptoms (dizziness, vomiting, photophobia), clonic seizures that developed into epilepsia partialis continua, bilateral optic atrophy, ophthalmoplegia, ataxia, and cognitive impairment. He also had elevated cerebrospinal fluid lactate (normal lactate in blood) and muscle biopsy showed mildly reduced complex I activity. His brain imaging findings were consistent with Leigh syndrome and mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS). The variant was present at 82% heteroplasmy in muscle and 13% in blood. The variant was absent in blood from his healthy mother (PM6_supporting). There are several occurrences in population databases (absent in gnomAD v3.1.2 and the Helix dataset; present in one individual in the MITOMAP GenBank sequences, 1/61168, 0.00163%). Although there are several occurrences, the frequency is still low (PM2_supporting). The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.73 (Min=0, Max=1; score of 0.905 in APOGEE2), which predicts a damaging effect on gene function (PP3). There are no cybrids, supporting single fiber studies, or de novo occurrences reported for this variant. In summary, this variant meets criteria to be classified as uncertain significance for primary mitochondrial disease inherited in a mitochondrial manner. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Variant Curation Expert Panel on November 13, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PM2_supporting, PM6_supporting, PP3.
Met criteria codes
PM2_Supporting
There are several occurrences in population databases (absent in gnomAD v3.1.2 and the Helix dataset; present in one individual in the MITOMAP GenBank sequences, 1/61168, 0.00163%). Although there are several occurrences, the frequency is still low (PM2_supporting).
PP3
The computational predictor APOGEE gives a consensus rating of pathogenic with a score of 0.73 (Min=0, Max=1; score of 0.905 in APOGEE2), which predicts a damaging effect on gene function (PP3).
PM6_Supporting
The variant was absent in blood from his healthy mother (PM6_supporting).
Not Met criteria codes
PS3
There are no cybrids, supporting single fiber studies, or de novo occurrences reported for this variant.
PS4
The m.13045A>C (p.M237L) variant in MT-ND5 has been reported in one individual with primary mitochondrial disease to date (PMID: 12509858), in a boy with migraine-like symptoms (dizziness, vomiting, photophobia), clonic seizures that developed into epilepsia partialis continua, bilateral optic atrophy, ophthalmoplegia, ataxia, and cognitive impairment. He also had elevated cerebrospinal fluid lactate (normal lactate in blood) and muscle biopsy showed mildly reduced complex I activity. His brain imaging findings were consistent with Leigh syndrome and mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS). The variant was present at 82% heteroplasmy in muscle and 13% in blood.
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.