ATP13A4

Chr 3

ATPase 13A4

NCBI Gene: 84239 ENSG00000127249 UniProt: Q4VNC1 OMIM: 609556

Predicted to enable ATPase-coupled monoatomic cation transmembrane transporter activity and polyamine transmembrane transporter activity. Predicted to be involved in intracellular calcium ion homeostasis and polyamine transmembrane transport. Predicted to be located in early endosome membrane and recycling endosome membrane. Predicted to be active in endoplasmic reticulum membrane and late endosome membrane. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.95

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.95LOEUF

pLI 0.000

Z-score 1.90

OE 0.75 (0.59–0.95)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.05Z-score

OE missense 0.99 (0.93–1.06)

636 obs / 639.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.75 (0.59–0.95)

0≤0.351.4

Missense OE?0.99 (0.93–1.06)

0≤0.61.4

Synonymous OE?1.04

0≤1.21.6

LoF obs/exp: 49 / 65.6Missense obs/exp: 636 / 639.5Syn Z: -0.43

Background carrier burden — how many people carry a rare variant somewhere in ATP13A4?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 42

1,503 rare PASS variants

Rare truncating (LoF)

1 in 560

233 rare PASS variants

Rare synonymous (reference)

1 in 95

534 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for ATP13A4. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 53	1 in 580
South Asian	~43k	1 in 37	1 in 480
Remaining (unassigned)	~30k	1 in 37	1 in 400
European (Finnish)	~27k	1 in 150	1 in 520
Admixed American	~22k	1 in 33	1 in 870
African / African American	~21k	1 in 42	1 in 500
East Asian	~20k	1 in 50	1 in 800
Ashkenazi Jewish	~13k	1 in 140	≈ 1 in 6,500
Middle Eastern	~2,884	1 in 45	≈ 1 in 1,400

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 27 of 30 coding exons well covered in gnomAD exomes; exons 6, 28, 30 marginal. Genomes: all 30.? see exons ↓