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

CA340923

9568 (ClinVar)

Gene: N/A

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: PS4_Moderate PM5_Supporting PS3_Supporting

• Not Met criteria codes: PM6 PM2 PS2 BP4 PP3 PP1

Expert Panel

Mitochondrial Diseases VCEP

Criteria Specification Information

Criteria Specification: ClinGen Mitochondrial Disease Nuclear and Mitochondrial Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1_mtDNA

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

• 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).
• 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).

Not Met criteria codes

• 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).
• 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).
• 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.
• 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).