The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • No CSPEC related information was provided by the message!
  • No CSPEC computed assertion could be determined for this classification!

  • See Evidence submitted by expert panel for details.

Variant: NC_012920.1:m.8993T>G

CA250380

9641 (ClinVar)

Gene: MT-ATP6
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 6cf1495e-53ff-4949-b2aa-ec1f11f3f24a
Approved on: 2021-05-07
Published on: 2021-06-10

HGVS expressions

NC_012920.1:m.8993T>G
J01415.2:m.8993T>G
ENST00000361899.2:c.467T>G

Pathogenic

Met criteria codes 7
PS3_Supporting PM2_Supporting PS4 PP1_Moderate PP3 PM5 PM6_Strong
Not Met criteria codes 4
BS1 BP4 BA1 PP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.8993T>G (p.L156R) variant in MT-ATP6 has been reported in >16 individuals with primary mitochondrial disease (PS4; PMIDs: 2137962, 8250532, 8240109, 7605802, 8505474, 9221962, 10208283, 16525806, 10660580). There are several reports of de novo occurrences of this variant (PM6_strong, PMIDs: 29602698, 27450679, 12134275). This variant is located at the same amino acid position as another well-known pathogenic variant, m.8993T>C (p.L156P) (PM5). This variant segregated with disease in multiple affected members in multiple families and several healthy family members had lower to undetectable levels of the variant (PP1_moderate; PMIDs: 2137962, 1436530, 1550128, 8095070, 9221962). This variant is absent in population databases after removing known patients with mitochondrial disease (PM2_supporting). In silico tools (APOGEE) predict this variant to be pathogenic (PP3). Cybrid studies supported the functional impact of this variant (PS3_supporting; PMID: 14998933, 8078883, 19875463). In summary, this variant meets criteria to be classified as pathogenic for primary mitochondrial disease inherited in a mitochondrial manner. This classification was approved by the NICHD U24 Mitochondrial Disease Variant Curation Expert Panel on March 22, 2021. Mitochondrial DNA-specific ACMG/AMP criteria applied: PS3_supporting, PS4, PM2_supporting, PM5, PM6_strong, PP1_moderate, PP3).
Met criteria codes
PS3_Supporting
Functional validation in cybrid studies (Trounce et al., 1994 - PMID: 8078883; Manfredi et al., 2002 - PMID: 11925565; Mattiazzi et al., 2004 - PMID: 14998933; D'Aurelio et al., 2010 - PMID: 19875463).
PM2_Supporting
Total AF in Mitomap is 0.012% (6/51673) BUT ALL SIX ARE PATIENTS (2) or cybrids (4) with the mutation. Zero are controls. Absent in gnomADv3.1 gnomAD.v3.1 (0 /56368 mt sequences): Karczewski et al. 2020 PMID:32461654 Absent or <0.002% in Helix (0 homoplasmic + 1 heteroplasmic (0% hom., 0.0005% het.) /195983 mt sequences)
PS4
Variant is present in ≥16 unrelated probands.
PP1_Moderate
Families found with varying levels of the mutant heteroplasmy correlating roughly with the severity of disease (Holt et al., 1990 - PMID: 2137962; Shoffner et al., 1992 - PMID: 1436530; Tatuch et al., 1992 - PMID: 1550128; Ciafaloni et al., 1993 - PMID: 8095070; Uziel et al., 1997 - PMID: 9221962).
PP3
APOGEE consensus is P at 0.95 [>0.5]
PM5
m.8993T>C is also pathogenic at this codon. Fujii et al. P PMID: 9568930.
PM6_Strong
5 counts assumed de novo - 0.5 points per case = 2.5 = strong (1 case in Uittenbogaard et al., 2018 - PMID: 29602698; 3 cases in Sallevelt et al., 2017 - PMID: 27450679; 1 case in Playan et al., 2002 - PMID: 12134275).
Not Met criteria codes
BS1
AF in Mitomap is<0.5%.
BP4
The APOGEE in-silico consensus score for pathogenicity is extremely high (0.95). To be a neutral variant, the score must be ≤ 0.5.
BA1
AF in Mitomap is <5%. Not a haplogroup marker.
PP4
Decreased ATP production and significantly reduced complex V activity in multiple patients. Parfait B et al. 1999 PMID:9950309; Morava et al. 2006 PMID: 16532470. However, to apply this criterion all other etiologies of CV deficiency would have to have been excluded which was not the case.
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.