The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Despite there being a valid 'cspec' property in the messages there's a discrepancy in message contents and CSPEC data: * Message Gene: MT-CO1 CSPEC Genes: [] * Message MONDOs: MONDO:0044970 CSPEC MONDO: []
  • No CSPEC computed assertion could be determined for this classification!


Variant: NC_012920.1(MT-TS1):m.7445A>C

CA340923

9568 (ClinVar)

Gene: MT-CO1
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 67fb5ef8-406b-452f-96c6-c53854070e8c
Approved on: 2024-07-08
Published on: 2024-12-09

HGVS expressions

NC_012920.1:m.7445A>C
J01415.2:m.7445A>C
ENST00000361624.2:c.1542A>C

Uncertain Significance

Met criteria codes 3
PM5_Supporting PS3_Supporting PS4_Moderate
Not Met criteria codes 6
BP4 PS2 PP3 PP1 PM6 PM2

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.7445A>C (p.*514S) variant in MT-CO1 has been reported in five unrelated individuals with primary mitochondrial disease to date (PS4_moderate; PMIDs: 10577941, 17659260, 18639500, 19705751). These individuals were of Asian background and had childhood onset hearing loss. Some had hearing loss after illness and in others no precipitating event could be identified. The variant was present at homoplasmy in these individuals. Detailed family history information was not provided in several cases. One family had three affected siblings however all were homoplasmic, precluding consideration for PP1 (PMID: 19705751). This variant is present in population databases (Mitomap's 51,863 sequences: AF=0.028%; Helix's 196,554 sequences: AF=0.001%; gnomAD v3.1.2: absent). There are no in-silico prediction tools for a stop-loss variant in mitochondrial DNA, although this variant would not be expected to cause run-through due to the excision of the tRNA immediately adjacent. Functional studies showed inefficient processing by tRNAseZ in the presence of this variant (PS3_supporting; PMID: 16361254). Another variant at this position has been classified as pathogenic – m.7445A>G (PM5_supporting). 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 July 8, 2024. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_moderate, PS3_supporting, PM5_supporting.
Met criteria codes
PM5_Supporting
Another variant at this position has been classified as pathogenic – m.7445A>G (PM5_supporting).
PS3_Supporting
Functional studies showed inefficient processing by tRNAseZ in the presence of this variant (PS3_supporting; PMID: 16361254).
PS4_Moderate
The m.7445A>C (p.*514S) variant in MT-CO1 has been reported in five unrelated individuals with primary mitochondrial disease to date (PS4_moderate; PMIDs: 10577941, 17659260, 18639500, 19705751). These individuals were of Asian background and had childhood onset hearing loss. Some had hearing loss after illness and in others no precipitating event could be identified. The variant was present at homoplasmy in these individuals. Detailed family history information was not provided in several cases. One family had three affected siblings however all were homoplasmic, precluding consideration for PP1 (PMID: 19705751).
Not Met criteria codes
BP4
There are no in-silico prediction tools for a stop-loss variant in mitochondrial DNA, although this variant would not be expected to cause run-through due to the excision of the tRNA immediately adjacent.
PS2
The m.7445A>C (p.*514S) variant in MT-CO1 has been reported in five unrelated individuals with primary mitochondrial disease to date (PS4_moderate; PMIDs: 10577941, 17659260, 18639500, 19705751). These individuals were of Asian background and had childhood onset hearing loss. Some had hearing loss after illness and in others no precipitating event could be identified. The variant was present at homoplasmy in these individuals. Detailed family history information was not provided in several cases. One family had three affected siblings however all were homoplasmic, precluding consideration for PP1 (PMID: 19705751).
PP3
There are no in-silico prediction tools for a stop-loss variant in mitochondrial DNA, although this variant would not be expected to cause run-through due to the excision of the tRNA immediately adjacent.
PP1
Detailed family history information was not provided in several cases. One family had three affected siblings however all were homoplasmic, precluding consideration for PP1 (PMID: 19705751).
PM6
The m.7445A>C (p.*514S) variant in MT-CO1 has been reported in five unrelated individuals with primary mitochondrial disease to date (PS4_moderate; PMIDs: 10577941, 17659260, 18639500, 19705751). These individuals were of Asian background and had childhood onset hearing loss. Some had hearing loss after illness and in others no precipitating event could be identified. The variant was present at homoplasmy in these individuals. Detailed family history information was not provided in several cases. One family had three affected siblings however all were homoplasmic, precluding consideration for PP1 (PMID: 19705751).
PM2
The variant was present at homoplasmy in these individuals. This variant is present in population databases (Mitomap's 51,863 sequences: AF=0.028%; Helix's 196,554 sequences: AF=0.001%; gnomAD v3.1.2: absent).
Curation History
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