GeneBe

ATP13A4

protein-coding

ATPase 13A4, the group of ATPase orphan transporters

Gene summary

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]

MANE transcript

NM_032279.4

Inheritance

—

ClinVar variants

U:186B:30

Top phenotype

ATP13A4-related disorder

gnomAD constraint

pLI —, LoF o/e 0.75

Max pathogenic AF

—

Genomic locus

chr3:193,398,967-193,593,111

External References & Databases

Ensembl (ENSG00000127249)NCBI Gene (84239)OMIM (609556)HGNC:25422GenCCUniProt (Q4VNC1)AlphaFoldClinVar (ATP13A4)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~194.1 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATP13A4 variants in ClinVar

3 Conditions Cataloged
not specifiedTotal: 180
ATP13A4-related disorderTotal: 19
not providedTotal: 16

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032279.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
10
clinvar
5
clinvar
 16
missense
179
clinvar
12
clinvar
3
clinvar
 194
nonsense
1
clinvar
 1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
5
clinvar
 5
Total00186228216
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_032279.4RefSeqNP_115655.230MANE Select
ENST00000342695.9EnsemblENSP00000339182.430MANE Select
ENST00000295548.3EnsemblENSP00000295548.314Standard
ENST00000392443.7EnsemblENSP00000376238.330Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Ion channel transport
  • Transport of small molecules
  • Ion transport by P-type ATPases

Biological Process

  • cellular calcium ion homeostasis
  • ion transmembrane transport
  • ATP hydrolysis coupled cation transmembrane transport

Molecular Function

  • ATP binding
  • cation-transporting ATPase activity
  • metal ion binding

Cellular Component

  • plasma membrane
  • integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000342695
Coding exons
30
Length
191035
Individuals with no LoFs
125604
Homozygous LoFs
0
Heterozygous LoFs
144
Defined
125748
p
0.000573
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.04866366390.9950.00003347841
Missense (PolyPhen)211236.790.891083042
Synonymous-0.4352462371.040.00001372310
Loss of Function1.904965.60.7460.00000314793

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000740.00074rare
Latino/Admixed American0.000430.00043rare
Ashkenazi Jewish0.0000990.000099rare
East Asian0.000330.00033rare
Finnish0.000690.00069rare
European (Non-Finnish)0.000630.00062rare
South Asian0.000690.00069rare
Other0.000650.00065rare

dbNSFP Gene Annotations

Source: dbNSFP

Disease
DISEASE: Note=A chromosomal aberration involving ATP13A4 is found in 2 patients with specific language impairment (SLI) disorders. Paracentric inversion inv(3)(q25;q29). The inversion produces a disruption of the protein. {ECO:0000269|PubMed:15925480}.;

Recessive Scores

pRec
0.0986

Intolerance Scores

LoFtool
0.242
RVIS EVS
-1.38
RVIS percentile EVS
4.36

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.160

Gene Damage Prediction

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh
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