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 ("NC_012920.1(MT-ATP6"):m.8803A>T) does not appear to be in HGVS format


Variant: NC_012920.1(MT-ATP6):m.8803A>T

CA10581289

235370 (ClinVar)

Gene: N/A
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: c1200847-103a-491e-b17f-6e5a4ea94893
Approved on: 2023-07-10
Published on: 2023-08-03

HGVS expressions

NC_012920.1:m.8803A>T
J01415.2:m.8803A>T
ENST00000361899.2:n.277A>T

Uncertain Significance

Met criteria codes 1
BP4
Not Met criteria codes 8
PS3 PS2 PS4 PP1 PM6 PM2 BA1 BS1

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.8803A>T variant in MT-ATP6 was reviewed by the Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel on July 10, 2023. This variant has been reported twice in the medical literature in affected individuals but there was no attribution of pathogenic involvement in either case (one case had Leber Hereditary Optic Neuropathy, PMID 15465027; one case had Alzheimer disease, PMID 20700462). There are no other individuals or families with primary mitochondrial disease with this variant reported in the medical literature to our knowledge. This variant is present at low frequency in population databases. The frequency in gnomAD v3.1.2 was 22/56,434 (0.039%) with all 22 being homoplasmic and in top level haplogroup H. The frequency in the MITOMAP GenBank sequences was 8/59,389 (0.013%); all eight of these individuals (100%) are in H5a haplogroup, with one of them being the individual with Alzheimer disease discussed above. The frequency of homoplasmic occurrences in the Helix dataset was 159/195,983 (0.081%); 152 of these Helix variants were in haplogroup H; seven were in haplogroup U. An additional five variants were reported as heteroplasmic; these were all in haplogroup H. Of note, the individual with Leber Hereditary Optic Neuropathy discussed above types to haplogroup U1a. Therefore, the frequency of this variant meets neither criteria for pathogenicity (<0.002%) nor benign (>0.5%). The computational predictor APOGEE gives a consensus rating of benign with scores of 0.37 (“neutral”) in APOGEE1 and 0.101 (“likely benign” in APOGEE2; Min=0, Max=1), predicting no impact on gene function (BP4). There are no cybrids, single fiber studies, or other functional assays found in the literature for this variant to date. 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 10, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied: BP4.
Met criteria codes
BP4
This variant has raw scores in both APOGEE1 (0.37) and APOGEE2 (0.1010) of <0.5, which meets the criteria for a neutral or benign impact.
Not Met criteria codes
PS3
There are no cybrids, single fiber studies, or other functional assays found in the literature for this variant to date.
PS2
There are no individuals or families with primary mitochondrial disease with this variant reported in the medical literature to our knowledge.
PS4
This variant has been reported twice in the medical literature in affected individuals but there was no attribution of pathogenic involvement in either case (one case had Leber Hereditary Optic Neuropathy, PMID 15465027; one case had Alzheimer disease, PMID 20700462). There are no individuals or families with primary mitochondrial disease with this variant reported in the medical literature to our knowledge. There are two reports in ClinVar: one submittal for an individual reportedly with Leigh Syndrome, asserted as Benign, and another submittal with no clinical condition provided. We do not count undocumented ClinVar reports for curation.
PP1
There are no individuals or families with primary mitochondrial disease with this variant reported in the medical literature to our knowledge.
PM6
There are no individuals or families with primary mitochondrial disease with this variant reported in the medical literature to our knowledge.
PM2
This variant is present at low frequency in population databases. The frequency in gnomAD v3.1.2 was 22/56,434 (0.039%) with all 22 being homoplasmic and in top level haplogroup H. The frequency in the MITOMAP GenBank sequences was 8/59,389 (0.013%); all eight of these individuals (100%) are in H5a haplogroup, with one of them being the individual with Alzheimer disease discussed above. The frequency of homoplasmic occurrences in the Helix dataset was 159/195,983 (0.081%); 152 of these Helix variants were in haplogroup H; seven were in haplogroup U. An additional five variants were reported as heteroplasmic; these were all in haplogroup H. Of note, the individual wit Leber Hereditary Optic Neuropathy discussed above types to haplogroup U1a. Therefore, the frequency of this variant meets neither criteria for pathogenicity (<0.002%) nor benign (>0.5%).
BA1
This variant is present at low frequency in population databases. The frequency in gnomAD v3.1.2 was 22/56,434 (0.039%) with all 22 being homoplasmic and in top level haplogroup H. The frequency in the MITOMAP GenBank sequences was 8/59,389 (0.013%); all eight of these individuals (100%) are in H5a haplogroup, with one of them being the individual with Alzheimer disease discussed above. The frequency of homoplasmic occurrences in the Helix dataset was 159/195,983 (0.081%); 152 of these Helix variants were in haplogroup H; seven were in haplogroup U. An additional five variants were reported as heteroplasmic; these were all in haplogroup H. Of note, the individual wit Leber Hereditary Optic Neuropathy discussed above types to haplogroup U1a. Therefore, the frequency of this variant meets neither criteria for pathogenicity (<0.002%) nor benign (>0.5%).
BS1
Database frequencies are not >0.5%: Mitomap 8/59,389 FL Seq (0.013%) 8/8 = H5a1d; gnomAD 22/56,434 (0.039%), 22 homoplasmic + 0 het; all in hg H (European); Helix 159/195,983 seq (0.081%), 159 homoplasmic and 5 het; all in H except for 7 in U (European).
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