ATP13A2

Chr 1

ATPase cation transporting 13A2

Also known as: CLN12, HSA9947, KRPPD, PARK9, SPG78

NCBI Gene: 23400ENSG00000159363UniProt: Q9NQ11

This gene encodes a member of the P5 subfamily of ATPases which transports inorganic cations as well as other substrates. Mutations in this gene are associated with Kufor-Rakeb syndrome (KRS), also referred to as Parkinson disease 9. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Nov 2008]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtKufor-Rakeb syndrome
UniProtSpastic paraplegia 78, autosomal recessive

Clinical highlights

Gene-disease validity (ClinGen)
Kufor-Rakeb syndrome · ARDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.
1
Active trials
57
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.58
LOEUF
LOF
Mechanism· G2P
📖
GeneReview available — ATP13A2
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?
0.58LOEUF
pLI 0.000
Z-score 4.12
OE 0.42 (0.30–0.58)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
1.40Z-score
OE missense 0.85 (0.80–0.91)
624 obs / 730.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.42 (0.30–0.58)
0≤0.351.4
Missense OE?0.85 (0.80–0.91)
0≤0.61.4
Synonymous OE?1.04
0≤1.21.6
LoF obs/exp: 24 / 57.8Missense obs/exp: 624 / 730.5Syn Z: -0.54

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

ATP13A2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients