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  • Despite there being a valid 'cspec' property in the messages there's a discrepancy in message contents and CSPEC data: * Message Gene: MT-ATP6 CSPEC Genes: [] * Message MONDOs: MONDO:0044970 CSPEC MONDO: []


Variant: NC_012920.1(MT-ATP6):m.9091A>G

CA16603197

376876 (ClinVar)

Gene: MT-ATP6
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 410eb9fb-4ff3-4452-b4e9-4ed304b0e126
Approved on: 2023-06-26
Published on: 2023-08-03

HGVS expressions

NC_012920.1:m.9091A>G
J01415.2:m.9091A>G
ENST00000361899.2:c.565A>G

Benign

Met criteria codes 2
BA1 BP4
Not Met criteria codes 6
PM6 PM2 PS2 PS3 PS4 PP1

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.9091A>G (p.T189A) variant in MT-ATP6 was reviewed by the Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel on June 26, 2023. This variant has not been reported in the medical literature as causative in affected individuals or families with primary mitochondrial disease to our knowledge. There has been a report of this variant being present in an individual from a control cohort (PMID: 15120634). This variant has also been reported in the homoplasmic state in a family with Leber Hereditary Optic Neuropathy (from haplogroup H10) caused by the m.3733G>A variant (PMID: 22879922). There are several occurrences in population databases. The frequency in the MITOMAP GenBank sequences is 21/59,389 (0.035%). The frequency in the Helix dataset is 108/195,983 (0.055%), including 107 homoplasmic occurrences and 1 heteroplasmic occurrence, and occurring in individuals from haplogroups H, U, HV, K, and R. The frequency in gnomAD v3.1.2 is 20/56432 (0.035%), and these occurrences are homoplasmic in individuals of European and African ancestry. Furthermore, this variant has been reported in 14 out of 14 individuals in the H10 haplogroup in addition to the case described above in haplogroup H10, meeting criteria to be considered a top-level haplogroup defining variant (BA1). The computational predictor APOGEE gives a consensus rating of benign with a score of 0.28 (Min=0, Max=1), which predicts a benign effect on gene function (BP4). There are no cybrids, single fiber studies, or other functional assays reported on this variant. In summary, this variant meets criteria to be classified as benign 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 June 26, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied BP4, BA1.
Met criteria codes
BA1
This variant has been reported in 14 out of 14 individuals in H10 haplogroup which is 100% plus the family in the literature, this meets criteria as a top-level haplogroup defining variants in individuals (PMID: 22879922, BA1).
BP4
The computational predictor APOGEE gives a consensus rating of benign with a score of 0.28 (Min=0, Max=1), which predicts a benign effect on gene function (BP4).
Not Met criteria codes
PM6
There are no reported de novo occurrences of this variant to our knowledge.
PM2
This variant is present in population databases (Mitomap's 21/59,389 sequences: AF=0.035%; Helix's 108/195,983 sequences: AF=0.055% 107 homoplasmic and 1 heteroplasmic in haplogroups H, U, HV, K, R; and gnomAD v3.1.2: AF=0.035% as this is homoplasmic in 20 individuals of European and African ancestry). Given the frequency of this variant, it does not meet PM2 criterion.
PS2
There are no reported de novo occurrences of this variant to our knowledge.
PS3
There are no cybrids, single fiber studies, or other functional assays reported on this variant.
PS4
This variant has not been reported in the medical literature as causative in affected individuals or families with primary mitochondrial disease to our knowledge. There has been a report of this variant being present in an individual from a control cohort (PMID: 15120634). This variant has also been reported in the homoplasmic state in a family with Leber Hereditary Optic Neuropathy (from haplogroup H10) caused by the m.3733G>A variant (PMID: 22879922).
PP1
There are no large families reported in the medical literature to consider for evidence of segregation.
Curation History
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