ClinVar Miner

Submissions for variant NM_001001344.3(ATP2B3):c.2105G>A (p.Arg702His)

gnomAD frequency: 0.00003  dbSNP: rs782587313
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV000996033 SCV001150471 uncertain significance not provided 2017-09-01 criteria provided, single submitter clinical testing
New York Genome Center RCV003448355 SCV004176143 uncertain significance X-linked progressive cerebellar ataxia 2023-09-01 criteria provided, single submitter clinical testing The c.2105G>A variant in ATP2B3 has not previously been reported in the literature; it has been deposited in ClinVar [ClinVar ID: 807831] as Variant of Uncertain Significance with affected status provided. The c.2105G>A is observed in 22 alleles (~0.0044% minor allele frequency with 3 hemizygotes and 2 homozygotes) in population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8), suggesting it is not a common benign variant in the populations represented in those databases. The c.2105G>A variant is located in exon 14 of this 22-exon gene and predicted to replace an evolutionarily conserved arginine amino acid with histidine at position 702 within the p-type ATPase domain of the encoded protein [UniProt ID: Q16720]. In silico predictions are in favor of damaging effect for the p.(Arg702His) variant [(CADD v1.6 = 28.9, REVEL = 0.944)]; however, there are no functional studies to support or refute these predictions. Based on available evidence this maternally inherited hemizygous c.2105G>A p.(Arg702His) variant identified in ATP2B3 is classified as a Variant of Uncertain Significance.

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