NM_001001344.3(ATP2B3):c.2105G>A (p.Arg702His) AND X-linked progressive cerebellar ataxia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 1, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003448355.1

Allele description [Variation Report for NM_001001344.3(ATP2B3):c.2105G>A (p.Arg702His)]

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

Gene:

ATP2B3:ATPase plasma membrane Ca2+ transporting 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

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

HGVS:

NC_000023.11:g.153556095G>A
NG_015896.1:g.24974G>A
NM_001001344.2:c.2105G>A
NM_001001344.3:c.2105G>AMANE SELECT
NM_001388360.1:c.2105G>A
NM_001388361.1:c.2105G>A
NM_001388362.1:c.2105G>A
NM_021949.4:c.2105G>A
NP_001001344.1:p.Arg702His
NP_001375289.1:p.Arg702His
NP_001375290.1:p.Arg702His
NP_001375291.1:p.Arg702His
NP_068768.2:p.Arg702His
NC_000023.10:g.152821553G>A

Protein change:

R702H

Links:

dbSNP: rs782587313

Molecular consequence:

NM_001001344.3:c.2105G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001388360.1:c.2105G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001388361.1:c.2105G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001388362.1:c.2105G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_021949.4:c.2105G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: X-linked progressive cerebellar ataxia
Synonyms:: OLIVOPONTOCEREBELLAR ATROPHY, X-LINKED; OPCA, X-LINKED; Spinocerebellar ataxia, X-linked 1
Identifiers:: MONDO: MONDO:0010547; MedGen: C0796205; Orphanet: 1175; OMIM: 302500

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004176143	New York Genome Center	criteria provided, single submitter (NYGC Assertion Criteria 2020)	Uncertain significance (Sep 1, 2023)	inherited	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004176143

New York Genome Center

criteria provided, single submitter

(NYGC Assertion Criteria 2020)

Uncertain significance
(Sep 1, 2023)

inherited

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	inherited	unknown	1	not provided	not provided	1	not provided	clinical testing

Details of each submission

From New York Genome Center, SCV004176143.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	not provided

Description

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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	inherited	unknown	1	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Apr 25, 2026

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