Is ATP2A3 p.Asp800= (c.2400C>T) pathogenic?

ATP2A3 p.Asp800= (c.2400C>T) is classified Benign in ATP2A3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-28). Common (popmax 23.3%, mid) — too common for a highly-penetrant pathogenic allele; Associated with ATP2A3-related disorder.

What condition is associated with ATP2A3 p.Asp800= (c.2400C>T)?

ATP2A3 p.Asp800= (c.2400C>T) is associated with ATP2A3-related disorder (ClinVar).

ATP2A3 p.Asp800=

Q: How common is ATP2A3 p.Asp800= (c.2400C>T) in the general population?

ATP2A3 p.Asp800= (c.2400C>T) is common (popmax 23.3%, mid) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2400C>T · rs1062683 · VCV3060281

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 23.3%, mid) — too common for a highly-penetrant pathogenic allele

Conditions

ATP2A3-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.2	GERP -3.8
Overall
CADD	12.04	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 23.3% Middle Eastern · 1,413/6,058 alleles

Filtering AF 22.3% ClinGen BA1/BS1 input FAF95, joint · FAF99 21.9%

Overall 18% 290,072/1,613,926 alleles · common

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	26.8%	4
Middle Easterngrpmax	23.3%	4
African / African-American	20.8%	5
Admixed American	19.4%	5
Remaining individualsnot grpmax-eligible	18.6%	5
European (non-Finnish)	18.2%	5
South Asian	18.2%	6
Amishnot grpmax-eligible	14.1%	7
Finnishnot grpmax-eligible	12.7%	8
East Asian	5.04%	20

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ATP2A3
Protein: p.Asp800=
Coding: c.2400C>T
MANE Select: NM_005173
dbSNP: rs1062683
Type: single nucleotide variant
Location: chr17:3936391 (GRCh38)
Gene constraint: LOEUF 0.759 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.75
Residue 800: the 'interaction with phospholamban 2' region; a binding site

Full ATP2A3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ATP2A3-related disorder

Similar variants

ATP2A3 c.1095+9C>T Likely benign same condition
ATP2A3 c.1419+10G>A Benign same condition
ATP2A3 c.1420-4G>A Likely benign same condition
ATP2A3 c.2863-5G>A Benign same condition
ATP2A3 c.*14A>G Benign same condition
ATP2A3 c.*19A>G Benign same condition
ATP2A3 p.Ala223= Likely benign same condition
ATP2A3 p.Ala331= Likely benign same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/atp2a3-p-asp800 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown