Is ATP2A3 p.Thr484= (c.1452C>T) pathogenic?

ATP2A3 p.Thr484= (c.1452C>T) is classified Benign in ATP2A3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-06-26). Rare (popmax 0.805%, eas); Associated with ATP2A3-related disorder.

What condition is associated with ATP2A3 p.Thr484= (c.1452C>T)?

ATP2A3 p.Thr484= (c.1452C>T) is associated with ATP2A3-related disorder (ClinVar).

How common is ATP2A3 p.Thr484= (c.1452C>T) in the general population?

ATP2A3 p.Thr484= (c.1452C>T) is rare (popmax 0.805%, eas) (gnomAD).

ATP2A3 p.Thr484=

c.1452C>T · rs17846886 · VCV3042789

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.805%, eas)

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 0.36	GERP -1.8, phastCons 0.96
Overall
CADD	5.428	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.805% East Asian · 361/44,846 alleles

Filtering AF 0.737% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.71%

Overall 0.0287% 463/1,613,612 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.805%	124
Remaining individualsnot grpmax-eligible	0.0384%	2,604
South Asian	0.0198%	5,060
Middle Eastern	0.0165%	6,062
Finnishnot grpmax-eligible	0.00629%	15,899
European (non-Finnish)	0.00458%	21,852
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,602

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.Thr484=
Coding: c.1452C>T
MANE Select: NM_005173
dbSNP: rs17846886
Type: single nucleotide variant
Location: chr17:3942699 (GRCh38)
Gene constraint: LOEUF 0.759 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.75

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-thr484 (accessed [today's date]).

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