ATP13A2

Summary

ATP13A2 (ATPase cation transporting 13A2, HGNC:30213) is a protein-coding gene on chromosome 1p36.13, encoding Polyamine-transporting ATPase 13A2 (Q9NQ11). ATPase which acts as a lysosomal polyamine exporter with high affinity for spermine.

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.

Source: NCBI Gene 23400 — RefSeq curated summary.

At a glance

• Gene–disease (curated): Kufor-Rakeb syndrome (Definitive, ClinGen) — +2 more curated relationships
• GWAS associations: 38
• Clinical variants (ClinVar): 1,258 total — 54 pathogenic, 33 likely-pathogenic
• Phenotypes (HPO): 104
• Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
• MANE Select transcript: NM_022089

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30213
Approved symbol	ATP13A2
Name	ATPase cation transporting 13A2
Location	1p36.13
Locus type	gene with protein product
Status	Approved
Aliases	HSA9947, CLN12
Ensembl gene	ENSG00000159363
Ensembl biotype	protein_coding
OMIM	610513
Entrez	23400

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 10 protein_coding, 4 retained_intron

ENST00000326735, ENST00000341676, ENST00000452699, ENST00000463860, ENST00000466561, ENST00000502418, ENST00000502860, ENST00000503552, ENST00000506174, ENST00000508222, ENST00000509392, ENST00000509619, ENST00000510069, ENST00000511957

RefSeq mRNA: 3 — MANE Select: NM_022089 NM_001141973, NM_001141974, NM_022089

CCDS: CCDS175, CCDS44072, CCDS44073

Canonical transcript exons

ENST00000326735 — 29 exons

Exon	Start	End
ENSE00001045127	16995976	16996164
ENSE00001045132	16986463	16986632
ENSE00001045148	16992486	16992581
ENSE00001045159	16993629	16993835
ENSE00001045169	16992243	16992402
ENSE00001045175	16992009	16992129
ENSE00001269149	17004692	17004821
ENSE00001269261	16986805	16986956
ENSE00001595216	17005014	17005072
ENSE00001668184	17005374	17005556
ENSE00001712002	17002296	17002373
ENSE00001714765	17005684	17005778
ENSE00001741647	17000400	17000534
ENSE00001749836	17004332	17004411
ENSE00001760891	17002034	17002103
ENSE00002308211	17011729	17011928
ENSE00003495349	16996386	16996496
ENSE00003511365	16991734	16991858
ENSE00003515248	16996254	16996300
ENSE00003519727	16989887	16990003
ENSE00003563233	16985958	16986358
ENSE00003588633	16989691	16989770
ENSE00003594185	16988138	16988234
ENSE00003616538	16990127	16990287
ENSE00003640034	16988322	16988474
ENSE00003642245	16997020	16997175
ENSE00003651965	16987046	16987269
ENSE00003681412	17000246	17000312
ENSE00003785986	17000011	17000142

Expression profiles

Bgee: expression breadth ubiquitous, 249 present calls, max score 97.51.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.0567 / max 200.1066, expressed in 1801 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
10564	20.8436	1798
10565	0.7879	516
10563	0.4252	236

Top tissues by expression

283 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right frontal lobe	UBERON:0002810	97.51	gold quality
right hemisphere of cerebellum	UBERON:0014890	96.78	gold quality
prefrontal cortex	UBERON:0000451	96.73	gold quality
anterior cingulate cortex	UBERON:0009835	96.61	gold quality
cingulate cortex	UBERON:0003027	96.56	gold quality
cerebellar hemisphere	UBERON:0002245	96.38	gold quality
cerebellar cortex	UBERON:0002129	96.36	gold quality
pons	UBERON:0000988	96.17	gold quality
cortical plate	UBERON:0005343	95.97	gold quality
Brodmann (1909) area 9	UBERON:0013540	95.80	gold quality
adenohypophysis	UBERON:0002196	95.71	gold quality
frontal cortex	UBERON:0001870	95.67	gold quality
neocortex	UBERON:0001950	95.35	gold quality
amygdala	UBERON:0001876	95.29	gold quality
hypothalamus	UBERON:0001898	95.28	gold quality
nucleus accumbens	UBERON:0001882	95.19	gold quality
cerebellum	UBERON:0002037	95.17	gold quality
pituitary gland	UBERON:0000007	95.00	gold quality
superior vestibular nucleus	UBERON:0007227	94.88	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	94.87	gold quality
dorsal root ganglion	UBERON:0000044	94.77	gold quality
lateral nuclear group of thalamus	UBERON:0002736	94.25	gold quality
cerebral cortex	UBERON:0000956	94.10	gold quality
forebrain	UBERON:0001890	93.87	gold quality
brain	UBERON:0000955	93.76	gold quality
telencephalon	UBERON:0001893	93.76	gold quality
caudate nucleus	UBERON:0001873	93.57	gold quality
putamen	UBERON:0001874	93.45	gold quality
body of pancreas	UBERON:0001150	93.12	gold quality
temporal lobe	UBERON:0001871	93.12	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.38

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): EGLN1, HIF1A

miRNA regulators (miRDB)

15 targeting ATP13A2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-199A-5P	99.51	69.71	1107
HSA-MIR-199B-5P	99.51	69.74	1098
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-6799-5P	99.14	65.72	2093
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-4270	99.02	66.26	1987
HSA-MIR-7155-5P	98.65	66.14	1290
HSA-MIR-3135B	98.61	65.33	1470
HSA-MIR-6754-5P	98.60	65.54	1627
HSA-MIR-1233-5P	98.19	66.71	1201
HSA-MIR-6778-5P	98.19	66.59	1239
HSA-MIR-4518	98.12	66.82	1030
HSA-MIR-1266-5P	97.71	66.92	1052

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

• Our data also suggest that ATP13A2 single heterozygous mutations might be etiologically relevant for patients with YOPD and further studies of this gene in Parkinson disease are warranted. (PMID:17485642)
• Findings expand the phenotypic spectrum associated with PARK9-linked parkinsonism into multiple-system disorders. (PMID:18413573)
• Mutations in ATP13A2 gene may be rare in Chinese families with autosomal recessive early-onset Parkinsonism. (PMID:18785233)
• A rare variant(AL746Thr) of the ATP13A2 was associated with an increased risk of Parkinson disease among ethnic Chinese in Asia. Further studies are needed to clarify the functional role of this genetic risk factor. (PMID:19015489)
• Neither ATP13A2 genetic variability nor quantitative gene expression in brain appears to contribute to familial parkinsonism or nonfamilial PD. (PMID:19085912)
• This study found that no associations were seen for ATP13A2 in Australia patient with Parkinson’s disease (PMID:19224617)
• Our data suggest that two mutated ATP13A2 alleles are not a common cause of Parkinson’s disease (PMID:19705361)
• ATP13A2 gene mutations are rare in Chinese patients with familial autosomal recessive early-onset parkinsonism. (PMID:19806583)
• ATP13A2 G2236A variant is rare in early-onset Parkinson’s disease and familial Parkinson’s disease patients from mainland China, which differs from the study in ethnic Chinese patients from Taiwan and Singapore (PMID:20036179)
• Research studied the prevalence of mutations in ATP13A2 genes in 30 unrelated Chinese families with AREP and found no pathogenic mutations. (PMID:20137506)
• Ala746Thr variant was not a major susceptible factor for PD in Han Chinese people. (PMID:20227461)
• KRD should be considered in patients with dystonia-parkinsonism with iron on brain imaging and we suggest classifying as NBIA type 3 (PMID:20310007)
• We identified genetic deficits in ATP13A2 that were associated with Levodopa responsive parkinsonism with pyramidal signs. (PMID:20669327)
• No clearly pathogenic mutations are identified in ATP13A2 and GIGYF2 in Brazilian patients with early-onset Parkinson’s disease. (PMID:20816920)
• We found no evidence for a correlation between a single heterozygous mutation in the ATP13a2 gene and the development of distinct oculomotor disturbances. (PMID:20842691)
• report clinical, instrumental, and genetic findings in an Italian family with novel PARK9 and PARK15 mutations (PMID:20853184)
• These results suggested that ATP13A2 p.A746T variant is unlikely to play a role as a common risk factor or a pathogenic mutation for PD at least in Japanese. Our data on Japanese differ from those reported recently on Han-Chinese. (PMID:20976737)
• Single ATP13A2 heterozygous mutations may be associated with clinical signs of parkinsonism and contribute to structural and functional brain changes. (PMID:21060012)
• A novel frameshift mutation in ATP13A2 causes juvenile dystonia-parkinsonism and dementia. (PMID:21094623)
• To see if ATP13A2 mutations could be responsible for some cases of human adult-onset NCL (Kufs disease), we resequenced ATP13A2 from 28 Kufs disease patients. None of these patients had ATP13A2 sequence variants likely to be causal for their disease (PMID:21362476)
• premature degradation of mutant ATP13A2 mRNA contribute to the aetiology of Kufor-Rakeb syndrome (KRS). (PMID:21542062)
• Mutant Atp13a2 proteins are degraded by endoplasmic reticulum-associated degradation and sensitize cells to cell death. (PMID:21665991)
• a novel frame-shift mutation in exon 22 of ATP13A2 (c.2473C>AA, p.Leu825AsnfsX32). (PMID:21696388)
• rare variants of ATP13A2 may contribute to Parkinson’s disease susceptibility in Taiwan (PMID:21714071)
• Regulation of intracellular manganese homeostasis by Kufor-Rakeb syndrome-associated ATP13A2 protein. (PMID:21724849)
• This study demonistrated that contralateral silent period duration was increased in the symptomatic ATP13A2 mutation carriers suggested that compound heterozygous mutation in the ATP13A2 gene is associated with increased intracortical inhibition. (PMID:22104014)
• The altered apoptotic pattern of subjects with mutated ATP13A2 suggests a correlation between apoptosis alteration and the mutated ATP13A2 protein (PMID:22117566)
• study reveals a number of intriguing neuronal phenotypes due to the loss- or gain-of-function of ATP13A2 that support a role for this protein in regulating intracellular cation homeostasis and neuronal integrity (PMID:22186024)
• ATP13A2 variation may be a risk marker for neurotoxic effects of manganese in humans. (PMID:22285144)
• hypoxia signaling plays a very important role in the regulation of human ATP13A2 gene expression (PMID:22288903)
• These findings collectively suggest that ATP13A2 contributes to the maintenance of a healthy mitochondrial pool, supporting the hypothesis that impaired mitochondrial clearance represents an important pathogenic mechanism underlying KRS. (PMID:22296644)
• Data show that a family with typical neuronal ceroid lipofuscinoses (NCLs) pathology carried a single homozygous mutation in ATP13A2 that fully segregates with disease. (PMID:22388936)
• This study demonistrated that restoration of ATP13A2 function may lead to improved lysosomal function and decreased accumulation of alpha-syn. (PMID:22442086)
• results confirm a role for Ypk9 in manganese homeostasis and illuminates cellular pathways and biological processes in which Ypk9 likely functions (PMID:22457822)
• The SNPs investigated in the BST1, PARK15 and PARK9 genes associated with PD susceptibility are not associated with PD in the northern Han Chinese population. (PMID:22490479)
• ATP13A2 and alpha-syn are functionally linked in neurodegeneration. (PMID:22645275)
• results unravel an instrumental role of ATP13A2 deficiency on lysosomal function and cell viability and demonstrate the feasibility and therapeutic potential of modulating ATP13A2 levels in the context of PD (PMID:22647602)
• Our results indicate that ATP13A2 mutations are a rare cause of both NBIA and dystonia-parkinsonism. (PMID:22743658)
• This study provides support for common loss-of-function effects of homozygous and heterozygous missense mutations in ATP13A2 associated with early-onset forms of parkinsonism. (PMID:22768177)
• ATP13A2 protects against manganese & nickel toxicity, & proteasomal, mitochondrial, & oxidative stress. ATP13A2 may import a cofactor required for the function of a lysosome enzyme(s). (PMID:22847264)

Cross-species orthologs

12 orthologs

Organism	Symbol	Gene ID
danio_rerio	atp13a2	ENSDARG00000061890
mus_musculus	Atp13a2	ENSMUSG00000036622
rattus_norvegicus	Atp13a2	ENSRNOG00000008052
drosophila_melanogaster	anne	FBGN0052000
drosophila_melanogaster	SPoCk	FBGN0052451
drosophila_melanogaster	CG45062	FBGN0266432
drosophila_melanogaster	CG45063	FBGN0266433
caenorhabditis_elegans		WBGENE00000834
caenorhabditis_elegans	pmr-1	WBGENE00004063
caenorhabditis_elegans		WBGENE00012341
caenorhabditis_elegans		WBGENE00015338
caenorhabditis_elegans		WBGENE00015660

Paralogs (21): ATP2C1 (ENSG00000017260), ATP1A2 (ENSG00000018625), ATP2B4 (ENSG00000058668), ATP2C2 (ENSG00000064270), ATP2B3 (ENSG00000067842), ATP2B1 (ENSG00000070961), ATP2A3 (ENSG00000074370), ATP12A (ENSG00000075673), ATP1A3 (ENSG00000105409), ATP4A (ENSG00000105675), ATP13A1 (ENSG00000105726), ATP7B (ENSG00000123191), ATP13A4 (ENSG00000127249), ATP1A4 (ENSG00000132681), ATP13A3 (ENSG00000133657), ATP2B2 (ENSG00000157087), ATP1A1 (ENSG00000163399), ATP7A (ENSG00000165240), ATP2A2 (ENSG00000174437), ATP13A5 (ENSG00000187527), ATP2A1 (ENSG00000196296)

Protein

Protein identifiers

Polyamine-transporting ATPase 13A2 — Q9NQ11 (reviewed: Q9NQ11)

All UniProt accessions (8): Q9NQ11, H0Y8I1, H0Y8V5, H0Y8Z6, H0Y953, H0Y9K0, H0Y9K4, H0YAI7

UniProt curated annotations — full annotation on UniProt →

Function. ATPase which acts as a lysosomal polyamine exporter with high affinity for spermine. Also stimulates cellular uptake of polyamines and protects against polyamine toxicity. Plays a role in intracellular cation homeostasis and the maintenance of neuronal integrity. Contributes to cellular zinc homeostasis. Confers cellular protection against Mn(2+) and Zn(2+) toxicity and mitochondrial stress. Required for proper lysosomal and mitochondrial maintenance. Regulates the autophagy-lysosome pathway through the control of SYT11 expression at both transcriptional and post-translational levels. Facilitates recruitment of deacetylase HDAC6 to lysosomes to deacetylate CTTN, leading to actin polymerization, promotion of autophagosome-lysosome fusion and completion of autophagy. Promotes secretion of exosomes as well as secretion of SCNA via exosomes. Plays a role in lipid homeostasis.

Subunit / interactions. Interacts with MYCBP2; the interaction inhibits the ubiquitination of TSC2 by MYCBP2. Interacts with HDAC6; the interaction results in recruitment of HDAC6 to lysosomes to promote CTTN deacetylation.

Subcellular location. Lysosome membrane. Late endosome membrane. Endosome. Multivesicular body membrane. Cytoplasmic vesicle. Autophagosome membrane.

Tissue specificity. Expressed in brain; protein levels are markedly increased in brain from subjects with Parkinson disease and subjects with dementia with Lewy bodies. Detected in pyramidal neurons located throughout the cingulate cortex (at protein level). In the substantia nigra, it is found in neuromelanin-positive dopaminergic neurons (at protein level).

Post-translational modifications. Autophosphorylated. Accumulates in an inactive autophosphorylated state and autophosphorylation is stimulated by phosphatidic acid and phosphatidylinositol 3,5-bisphosphate but not by Mn(2+) or Zn(2+). The presence of spermine results in a dose-dependent reduction in autophosphorylation.

Disease relevance. Kufor-Rakeb syndrome (KRS) [MIM:606693] A rare form of autosomal recessive juvenile or early-onset, levodopa-responsive parkinsonism. In addition to typical parkinsonian signs, clinical manifestations of Kufor-Rakeb syndrome include behavioral problems, facial tremor, pyramidal tract dysfunction, supranuclear gaze palsy, and dementia. The disease is caused by variants affecting the gene represented in this entry. KRS has also been referred to as neuronal ceroid lipofuscinosis 12 (CLN12), due to neuronal and glial lipofuscin deposits detected in the cortex, basal nuclei and cerebellum of some patients. Spastic paraplegia 78, autosomal recessive (SPG78) [MIM:617225] A form of spastic paraplegia, a neurodegenerative disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs. Rate of progression and the severity of symptoms are quite variable. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. Accumulates in an inactive autophosphorylated state. The presence of spermine results in a dose-dependent reduction in autophosphorylation.

Domain organisation. The N-terminal region is required for targeting to late endosomes/lysosomes. It does not traverse the membrane but contains a membrane-embedded intramembrane domain and interacts with the lipids phosphatidic acid (PA) and phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2). PA and PI(3,5)P2 are required for the protective effect against mitochondrial stress.

Similarity. Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type V subfamily.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9NQ11-1	A	yes
Q9NQ11-2	B
Q9NQ11-3	3

RefSeq proteins (3): NP_001135445, NP_001135446, NP_071372* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001757	P_typ_ATPase	Family
IPR006544	P-type_TPase_V	Family
IPR008250	ATPase_P-typ_transduc_dom_A_sf	Homologous_superfamily
IPR018303	ATPase_P-typ_P_site	PTM
IPR023214	HAD_sf	Homologous_superfamily
IPR023298	ATPase_P-typ_TM_dom_sf	Homologous_superfamily
IPR023299	ATPase_P-typ_cyto_dom_N	Homologous_superfamily
IPR036412	HAD-like_sf	Homologous_superfamily
IPR044492	P_typ_ATPase_HD_dom	Domain
IPR047819	P5A-ATPase_N	Domain
IPR047821	P5B-type_ATPase	Family
IPR059000	ATPase_P-type_domA	Domain

Pfam: PF00122, PF12409, PF13246

Catalyzed reactions (Rhea), 2 shown:

• spermidine(out) + ATP + H2O = spermidine(in) + ADP + phosphate + H(+) (RHEA:29999)
• spermine(out) + ATP + H2O = spermine(in) + ADP + phosphate + H(+) (RHEA:63368)

UniProt features (178 total): strand 50, helix 45, sequence variant 20, turn 17, topological domain 12, transmembrane region 10, mutagenesis site 10, splice variant 3, sequence conflict 3, binding site 2, glycosylation site 2, chain 1, intramembrane region 1, active site 1, modified residue 1

Structure

Experimental structures (PDB)

25 structures.

PDB	Method	Resolution (Å)
7N72	ELECTRON MICROSCOPY	2.5
7M5X	ELECTRON MICROSCOPY	2.7
7N70	ELECTRON MICROSCOPY	2.8
7N74	ELECTRON MICROSCOPY	2.8
7M5V	ELECTRON MICROSCOPY	2.9
7N73	ELECTRON MICROSCOPY	2.9
7N75	ELECTRON MICROSCOPY	2.9
7N76	ELECTRON MICROSCOPY	2.9
7FJP	ELECTRON MICROSCOPY	3
7M5Y	ELECTRON MICROSCOPY	3
7N78	ELECTRON MICROSCOPY	3
7N77	ELECTRON MICROSCOPY	3.2
8IEK	ELECTRON MICROSCOPY	3.2
8IEN	ELECTRON MICROSCOPY	3.25
7FJM	ELECTRON MICROSCOPY	3.3
8IEM	ELECTRON MICROSCOPY	3.35
7VPJ	ELECTRON MICROSCOPY	3.54
7FJQ	ELECTRON MICROSCOPY	3.6
7VPI	ELECTRON MICROSCOPY	3.6
8IES	ELECTRON MICROSCOPY	3.73
7VPL	ELECTRON MICROSCOPY	3.78
8IEO	ELECTRON MICROSCOPY	3.78
7VPK	ELECTRON MICROSCOPY	3.92
8IER	ELECTRON MICROSCOPY	4.87
8IEL	ELECTRON MICROSCOPY	5.65

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NQ11-F1	80.03	0.30

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 513 (4-aspartylphosphate intermediate)

Ligand- & substrate-binding residues (2): 878; 882

Post-translational modifications (1): 151

Glycosylation sites (2): 1033, 1110

Mutagenesis-validated functional residues (10):

Position	Phenotype
59	no effect on lipid binding.
66–68	reduces lipid binding.
74–78	reduces lipid binding.
160–164	reduces lipid binding.
348	autophosphorylated but displays limited spermine-induced atpase activity and lacks spermine-induced dephosphorylation.
472	reduced spermine-induced atpase activity and lack of spermine-induced dephosphorylation.
513	loss of atpase function, autophosphorylation and protection against mitochondrial stress.
967	reduced spermine-induced atpase activity.
1033	abolishes glycosylation.
1067	reduced spermine-induced atpase activity.

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-936837	Ion transport by P-type ATPases
R-HSA-382551	Transport of small molecules
R-HSA-983712	Ion channel transport

MSigDB gene sets: 468 (showing top): GOBP_REGULATION_OF_AUTOPHAGY, GOBP_RESPONSE_TO_ZINC_ION, GOBP_LYSOSOMAL_TRANSPORT, GOBP_VACUOLE_ORGANIZATION, GOBP_VESICLE_LOCALIZATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOCC_VACUOLAR_MEMBRANE, ZHAN_MULTIPLE_MYELOMA_MF_UP, GOBP_VESICLE_ORGANIZATION, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOBP_MEMBRANE_FUSION, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_INTRACELLULAR_IRON_ION_HOMEOSTASIS, GOBP_POSITIVE_REGULATION_OF_PROTEIN_LOCALIZATION

GO Biological Process (32): intracellular calcium ion homeostasis (GO:0006874), intracellular iron ion homeostasis (GO:0006879), intracellular zinc ion homeostasis (GO:0006882), autophagy (GO:0006914), lysosomal transport (GO:0007041), positive regulation of gene expression (GO:0010628), regulation of mitochondrion organization (GO:0010821), regulation of macroautophagy (GO:0016241), regulation of autophagosome size (GO:0016243), intracellular monoatomic cation homeostasis (GO:0030003), regulation of intracellular protein transport (GO:0033157), monoatomic ion transmembrane transport (GO:0034220), cellular response to oxidative stress (GO:0034599), regulation of neuron apoptotic process (GO:0043523), positive regulation of protein secretion (GO:0050714), lipid homeostasis (GO:0055088), protein localization to lysosome (GO:0061462), autophagosome-lysosome fusion (GO:0061909), cellular response to manganese ion (GO:0071287), cellular response to zinc ion (GO:0071294), extracellular exosome biogenesis (GO:0097734), regulation of protein localization to nucleus (GO:1900180), polyamine transmembrane transport (GO:1902047), regulation of autophagy of mitochondrion (GO:1903146), positive regulation of exosomal secretion (GO:1903543), spermine transmembrane transport (GO:1903710), regulation of chaperone-mediated autophagy (GO:1904714), autophagosome organization (GO:1905037), regulation of lysosomal protein catabolic process (GO:1905165), negative regulation of lysosomal protein catabolic process (GO:1905166), transmembrane transport (GO:0055085), monoatomic cation transmembrane transport (GO:0098655)

GO Molecular Function (17): ATP binding (GO:0005524), zinc ion binding (GO:0008270), polyamine transmembrane transporter activity (GO:0015203), ABC-type polyamine transporter activity (GO:0015417), P-type ion transporter activity (GO:0015662), ATP hydrolysis activity (GO:0016887), ATPase-coupled monoatomic cation transmembrane transporter activity (GO:0019829), manganese ion binding (GO:0030145), phosphatidic acid binding (GO:0070300), phosphatidylinositol-3,5-bisphosphate binding (GO:0080025), cupric ion binding (GO:1903135), nucleotide binding (GO:0000166), transporter activity (GO:0005215), protein binding (GO:0005515), lipid binding (GO:0008289), metal ion binding (GO:0046872), P-type transmembrane transporter activity (GO:0140358)

GO Cellular Component (17): autophagosome membrane (GO:0000421), lysosome (GO:0005764), lysosomal membrane (GO:0005765), late endosome (GO:0005770), multivesicular body (GO:0005771), autophagosome (GO:0005776), membrane (GO:0016020), transport vesicle (GO:0030133), late endosome membrane (GO:0031902), vesicle (GO:0031982), multivesicular body membrane (GO:0032585), neuron projection (GO:0043005), neuronal cell body (GO:0043025), lysosomal lumen (GO:0043202), endosome (GO:0005768), vesicle membrane (GO:0012506), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Ion channel transport	1
Transport of small molecules	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular monoatomic cation homeostasis	3
inorganic ion homeostasis	2
transmembrane transport	2
macroautophagy	2
cellular response to metal ion	2
transition metal ion binding	2
ATPase-coupled transmembrane transporter activity	2
binding	2
lysosome	2
late endosome	2
endomembrane system	2
cytoplasmic vesicle	2
calcium ion homeostasis	1
catabolic process	1
process utilizing autophagic mechanism	1
vacuolar transport	1
gene expression	1
regulation of gene expression	1
positive regulation of macromolecule biosynthetic process	1
mitochondrion organization	1
regulation of organelle organization	1
regulation of autophagy	1
regulation of cellular component size	1
autophagosome organization	1
intracellular monoatomic ion homeostasis	1
monoatomic cation homeostasis	1
intracellular protein transport	1
regulation of intracellular transport	1
regulation of protein transport	1
monoatomic ion transport	1
response to oxidative stress	1
cellular response to chemical stress	1
regulation of apoptotic process	1
neuron apoptotic process	1
protein secretion	1
regulation of protein secretion	1
positive regulation of protein transport	1
positive regulation of secretion by cell	1
chemical homeostasis	1
protein localization to vacuole	1

Protein interactions and networks

STRING

2012 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ATP13A2	PARK7	Q99497	957
ATP13A2	SNCA	P37840	940
ATP13A2	PINK1	Q9BXM7	923
ATP13A2	FBXO7	Q9Y3I1	884
ATP13A2	GBA1	P04062	869
ATP13A2	VPS35	Q96QK1	853
ATP13A2	LRRK2	Q5S007	844
ATP13A2	PLA2G6	O60733	841
ATP13A2	PRKN	O60260	837
ATP13A2	SLC6A3	Q01959	816
ATP13A2	C19orf12	Q9NSK7	782
ATP13A2	DNAJC6	O75061	764
ATP13A2	VPS13C	Q709C8	759
ATP13A2	DNAJC13	O75165	731
ATP13A2	SYNJ1	O43426	730

IntAct

118 interactions, top by confidence:

A	B	Type	Score
NDUFA13	NDUFS8	psi-mi:“MI:0914”(association)	0.640
TMEM9	ESYT2	psi-mi:“MI:0914”(association)	0.530
SLC39A4	TMEM120B	psi-mi:“MI:0914”(association)	0.530
HLA-DPA1	TYW5	psi-mi:“MI:0914”(association)	0.530
HAVCR2	TCAF2	psi-mi:“MI:0914”(association)	0.530
MCOLN3	UPK3BL1	psi-mi:“MI:0914”(association)	0.530
PBXIP1	GOLIM4	psi-mi:“MI:0914”(association)	0.530
SCN3B	ABCC5	psi-mi:“MI:0914”(association)	0.530
PEX19	FAM20B	psi-mi:“MI:0914”(association)	0.530
ANKRD22	ESYT2	psi-mi:“MI:0914”(association)	0.530
EVA1C	STK25	psi-mi:“MI:0914”(association)	0.530
LDLRAD1	ADAM10	psi-mi:“MI:0914”(association)	0.530
SLC30A2	ESYT2	psi-mi:“MI:0914”(association)	0.530
ATP13A2	HDAC6	psi-mi:“MI:0915”(physical association)	0.510
ATP13A2	YIF1A	psi-mi:“MI:0915”(physical association)	0.510
ATP13A2	AAK1	psi-mi:“MI:0915”(physical association)	0.510
ATP13A2	GAK	psi-mi:“MI:0915”(physical association)	0.510
ATP13A2	SYT11	psi-mi:“MI:0915”(physical association)	0.510
HSPA8	ATP13A2	psi-mi:“MI:0915”(physical association)	0.510
HDAC6	ATP13A2	psi-mi:“MI:0915”(physical association)	0.510
ATP13A2	BNIP3L	psi-mi:“MI:0915”(physical association)	0.510
AAK1	ATP13A2	psi-mi:“MI:0915”(physical association)	0.510
ATP13A2	HSPA8	psi-mi:“MI:0915”(physical association)	0.510
BNIP3L	ATP13A2	psi-mi:“MI:0915”(physical association)	0.510
YIF1A	ATP13A2	psi-mi:“MI:0915”(physical association)	0.510
SPCS2	ATP13A2	psi-mi:“MI:0915”(physical association)	0.370
LMAN2	ATP13A2	psi-mi:“MI:0915”(physical association)	0.370
ATP13A2	PDIA6	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (137): ATP13A2 (Affinity Capture-MS), ATP13A2 (Affinity Capture-MS), ATP13A2 (Affinity Capture-MS), ATP13A2 (Affinity Capture-MS), ATP13A2 (Affinity Capture-MS), ATP13A2 (Affinity Capture-MS), ATP13A2 (Affinity Capture-MS), ATP13A2 (Affinity Capture-MS), ATP13A2 (Affinity Capture-MS), ATP13A2 (Affinity Capture-MS), ATP13A2 (Affinity Capture-MS), ATP13A2 (Affinity Capture-MS), ATP13A2 (Affinity Capture-MS), ATP13A2 (Affinity Capture-MS), ATP13A2 (Affinity Capture-MS)

ESM2 similar proteins: A0A494BA31, G3C7W6, O08812, O43246, O97704, P02730, P04919, P15575, P23562, P26430, P31639, P45380, P53792, P58735, P70423, P92946, Q06495, Q06496, Q28615, Q28728, Q58DD2, Q5EBI0, Q60825, Q63008, Q7LBE3, Q80SU6, Q80ZD3, Q86U10, Q86WA9, Q8BLQ7, Q8BU91, Q8CIW6, Q8K4R8, Q8K4V2, Q8N130, Q8NG04, Q8R2Z3, Q923I7, Q92911, Q96Q91

Diamond homologs: A0R3Y2, B9QMJ0, O53114, P0A505, P35597, P9WPT0, P9WPT1, Q08853, Q12697, Q21286, Q27533, Q9EPE9, Q9HD20, Q9NQ11, O14022, O74431, P0ABB8, P0ABB9, P22036, P54211, Q3TYU2, Q4VNC0, Q4VNC1, Q5XF89, Q5XF90, Q5ZKB7, Q95JN5, Q9CTG6, Q9H7F0, A0A143ZZK9, P90747, Q4WYP6, Q95050, O14072, P13587, P39986, Q01896, Q04956, Q12691, P22180

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

1258 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	54
Likely pathogenic	33
Uncertain significance	484
Likely benign	483
Benign	35

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
1075283	NM_022089.4(ATP13A2):c.3136G>T (p.Glu1046Ter)	Pathogenic
1075284	NM_022089.4(ATP13A2):c.2146del (p.Asp715_Leu716insTer)	Pathogenic
1220	NM_022089.4(ATP13A2):c.1633_1654dup (p.Leu552fs)	Pathogenic
1333442	NM_022089.4(ATP13A2):c.688C>T (p.Gln230Ter)	Pathogenic
1341268	GRCh37/hg19 1p36.13(chr1:17284531-17770100)x1	Pathogenic
1385899	NM_022089.4(ATP13A2):c.1113del (p.His372fs)	Pathogenic
1442231	NM_022089.4(ATP13A2):c.619C>T (p.Gln207Ter)	Pathogenic
1456750	NC_000001.10:g.(?17316166)(17332293_?)del	Pathogenic
1458906	NC_000001.10:g.(?17330807)(17332293_?)del	Pathogenic
1751269	NM_022089.4(ATP13A2):c.604del (p.His202fs)	Pathogenic
1810422	NM_022089.4(ATP13A2):c.1045_1046del (p.Ser349fs)	Pathogenic
1968613	NM_022089.4(ATP13A2):c.3153dup (p.Ser1052fs)	Pathogenic
1996186	NM_022089.4(ATP13A2):c.2113C>T (p.Gln705Ter)	Pathogenic
1999337	NM_022089.4(ATP13A2):c.1825G>T (p.Glu609Ter)	Pathogenic
2013159	NM_022089.4(ATP13A2):c.1296dup (p.Ser433fs)	Pathogenic
2021882	NM_022089.4(ATP13A2):c.965del (p.Gln322fs)	Pathogenic
2022009	NM_022089.4(ATP13A2):c.2587del (p.Val863fs)	Pathogenic
2039313	NM_022089.4(ATP13A2):c.572dup (p.Arg192fs)	Pathogenic
2046647	NM_022089.4(ATP13A2):c.774G>A (p.Trp258Ter)	Pathogenic
2064277	NM_022089.4(ATP13A2):c.533_536dup (p.Gln179fs)	Pathogenic
2151865	NM_022089.4(ATP13A2):c.217dup (p.Val73fs)	Pathogenic
2179757	NM_022089.4(ATP13A2):c.1378del (p.Arg460fs)	Pathogenic
2419737	NM_022089.4(ATP13A2):c.213G>A (p.Trp71Ter)	Pathogenic
2572413	NM_022089.4(ATP13A2):c.2540_2550del (p.Gln847fs)	Pathogenic
2629777	NM_022089.4(ATP13A2):c.1033_1034del (p.Leu345fs)	Pathogenic
2663862	NM_022089.4(ATP13A2):c.2097del (p.Ser700fs)	Pathogenic
2923611	NM_022089.4(ATP13A2):c.1932del (p.Ala646fs)	Pathogenic
2931003	NM_022089.4(ATP13A2):c.217del (p.Val73fs)	Pathogenic
30833	NM_022089.4(ATP13A2):c.1101_1102dup (p.Thr368fs)	Pathogenic
30834	NM_022089.4(ATP13A2):c.2552_2553del (p.Phe851fs)	Pathogenic

SpliceAI

4284 predictions. Top by Δscore:

Variant	Effect	Δscore
1:16986354:ACGCT:A	acceptor_gain	1.0000
1:16986355:CGCT:C	acceptor_gain	1.0000
1:16986355:CGCTC:C	acceptor_gain	1.0000
1:16986356:GCT:G	acceptor_gain	1.0000
1:16986357:CT:C	acceptor_gain	1.0000
1:16986357:CTC:C	acceptor_gain	1.0000
1:16986358:TCT:T	acceptor_gain	1.0000
1:16986358:TCTG:T	acceptor_loss	1.0000
1:16986359:C:CC	acceptor_gain	1.0000
1:16986359:CTGC:C	acceptor_loss	1.0000
1:16986459:CCACC:C	donor_loss	1.0000
1:16986460:CACC:C	donor_loss	1.0000
1:16986461:ACCTC:A	donor_loss	1.0000
1:16986464:T:TA	donor_gain	1.0000
1:16986633:C:CC	acceptor_gain	1.0000
1:16986762:C:A	donor_gain	1.0000
1:16986766:C:CA	donor_gain	1.0000
1:16986782:C:CA	donor_gain	1.0000
1:16986792:C:CA	donor_gain	1.0000
1:16986837:C:CA	donor_gain	1.0000
1:16986868:A:AC	donor_gain	1.0000
1:16986869:C:CC	donor_gain	1.0000
1:16986952:CGAAC:C	acceptor_gain	1.0000
1:16986955:AC:A	acceptor_gain	1.0000
1:16986956:CC:C	acceptor_gain	1.0000
1:16986957:C:CA	acceptor_loss	1.0000
1:16986957:C:CC	acceptor_gain	1.0000
1:16986958:T:C	acceptor_loss	1.0000
1:16987040:A:AC	donor_gain	1.0000
1:16987041:C:CC	donor_gain	1.0000

AlphaMissense

7560 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:16995980:T:A	D513V	0.999
1:16988174:G:C	S941R	0.998
1:16988174:G:T	S941R	0.998
1:16988176:T:G	S941R	0.998
1:16988439:T:G	D882A	0.998
1:16995980:T:G	D513A	0.998
1:16988438:G:C	D882E	0.997
1:16988438:G:T	D882E	0.997
1:16988439:T:A	D882V	0.997
1:16990284:T:A	D752V	0.997
1:16990284:T:G	D752A	0.997
1:17000499:G:C	S247R	0.997
1:17000499:G:T	S247R	0.997
1:17000501:T:G	S247R	0.997
1:16987240:G:C	F963L	0.996
1:16987240:G:T	F963L	0.996
1:16987242:A:G	F963L	0.996
1:16988418:G:T	A889D	0.996
1:16988440:C:G	D882H	0.996
1:16990285:C:G	D752H	0.996
1:16995976:C:A	K514N	0.996
1:16995976:C:G	K514N	0.996
1:17000489:A:G	W251R	0.996
1:17000489:A:T	W251R	0.996
1:16988419:C:G	A889P	0.995
1:16988439:T:C	D882G	0.995
1:16989742:C:G	R853P	0.995
1:16989745:G:T	A852D	0.995
1:16996278:G:C	S443R	0.995
1:16996278:G:T	S443R	0.995

dbSNP variants (sampled 300 via entrez): RS1000082436 (1:17001318 T>A,C), RS1000316318 (1:16985722 T>C), RS1000395970 (1:16990575 T>C), RS1000785920 (1:16990600 C>T), RS1000804867 (1:17007476 C>T), RS1000950962 (1:17013223 G>A), RS1000987805 (1:17013874 C>A,T), RS1001030076 (1:17002122 C>T), RS1001258673 (1:17006485 A>C,G), RS1001458749 (1:17013116 G>C), RS1001497764 (1:17012072 A>C,G), RS1001553690 (1:17012369 C>A), RS1001678554 (1:16986182 G>A), RS1001874386 (1:16991380 C>A,T), RS1001886860 (1:17012803 A>G)

Disease associations

OMIM: gene MIM:610513 | disease phenotypes: MIM:606693, MIM:617225, MIM:234200, MIM:213000

GenCC curated gene-disease

Disease	Classification	Inheritance
Kufor-Rakeb syndrome	Definitive	Autosomal recessive
autosomal recessive spastic paraplegia type 78	Strong	Autosomal recessive
parkinsonism due to ATP13A2 deficiency	Supportive	Autosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
Kufor-Rakeb syndrome	Definitive	AR

Mondo (5): Kufor-Rakeb syndrome (MONDO:0011706), autosomal recessive spastic paraplegia type 78 (MONDO:0014975), neurodegeneration with brain iron accumulation (MONDO:0018307), parkinsonism due to ATP13A2 deficiency (MONDO:0017809), isolated cerebellar hypoplasia/agenesis (MONDO:0008939)

Orphanet (6): Kufor-Rakeb syndrome (Orphanet:306674), CLN12 disease (Orphanet:314632), Autosomal recessive spastic paraplegia type 78 (Orphanet:513436), Neurodegeneration with brain iron accumulation (Orphanet:385), Isolated cerebellar agenesis (Orphanet:1398), Cerebellar hypoplasia-tapetoretinal degeneration syndrome (Orphanet:2246)

HPO phenotypes

104 total (30 of 104 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000011	Neurogenic bladder
HP:0000012	Urinary urgency
HP:0000020	Urinary incontinence
HP:0000183	Tongue muscle weakness
HP:0000298	Mask-like facies
HP:0000317	Facial myokymia
HP:0000338	Hypomimic face
HP:0000458	Anosmia
HP:0000473	Torticollis
HP:0000486	Strabismus
HP:0000511	Vertical supranuclear gaze palsy
HP:0000514	Slow saccadic eye movements
HP:0000605	Supranuclear gaze palsy
HP:0000639	Nystagmus
HP:0000643	Blepharospasm
HP:0000658	Eyelid apraxia
HP:0000666	Horizontal nystagmus
HP:0000716	Depression
HP:0000718	Aggressive behavior
HP:0000725	Psychotic episodes
HP:0000726	Dementia
HP:0000736	Short attention span
HP:0000738	Hallucinations
HP:0000741	Apathy
HP:0001167	Abnormal finger morphology
HP:0001250	Seizure
HP:0001251	Ataxia
HP:0001254	Lethargy
HP:0001256	Mild intellectual disability

GWAS associations

38 associations (top):

Study	Trait	p-value
GCST000611_7	Height	2.000000e-07
GCST002702_25	Height	1.000000e-24
GCST004067_141	Hip circumference adjusted for BMI	7.000000e-13
GCST004067_5	Hip circumference adjusted for BMI	4.000000e-09
GCST004067_98	Hip circumference adjusted for BMI	4.000000e-18
GCST004563_72	Waist circumference adjusted for BMI (joint analysis main effects and physical activity interaction)	7.000000e-10
GCST004564_53	Waist circumference adjusted for BMI in active individuals	4.000000e-10
GCST005580_114	Intraocular pressure	4.000000e-08
GCST007293_17	Body fat distribution (arm fat ratio)	3.000000e-08
GCST007294_73	Body fat distribution (trunk fat ratio)	4.000000e-16
GCST007294_99	Body fat distribution (trunk fat ratio)	7.000000e-19
GCST007295_46	Body fat distribution (leg fat ratio)	3.000000e-11
GCST007295_81	Body fat distribution (leg fat ratio)	3.000000e-10
GCST008156_4	Hip circumference adjusted for BMI	2.000000e-09
GCST008161_137	Waist circumference adjusted for body mass index	4.000000e-08
GCST008839_102	Height	1.000000e-37
GCST010083_220	Hemoglobin levels	2.000000e-09
GCST010696_16	Cortical thickness (min-P)	8.000000e-11
GCST010697_21	Cortical surface area (min-P)	1.000000e-08
GCST010698_46	Subcortical volume (min-P)	2.000000e-11
GCST010699_5	Brain morphology (min-P)	7.000000e-11
GCST010700_46	Cortical thickness (MOSTest)	2.000000e-10
GCST010701_63	Cortical surface area (MOSTest)	3.000000e-14
GCST010702_161	Subcortical volume (MOSTest)	2.000000e-20
GCST010703_70	Brain morphology (MOSTest)	2.000000e-08
GCST012226_408	Waist circumference adjusted for body mass index	3.000000e-18
GCST012226_409	Waist circumference adjusted for body mass index	2.000000e-09
GCST012227_1129	Hip circumference adjusted for BMI	2.000000e-25
GCST012227_1376	Hip circumference adjusted for BMI	7.000000e-11
GCST012227_1378	Hip circumference adjusted for BMI	2.000000e-16

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0008039	BMI-adjusted hip circumference
EFO:0007789	BMI-adjusted waist circumference
EFO:0008002	physical activity measurement
EFO:0004695	intraocular pressure measurement
EFO:0004341	body fat distribution
EFO:0004509	hemoglobin measurement
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness
EFO:0007788	BMI-adjusted waist-hip ratio

MeSH disease descriptors (3)

Descriptor	Name	Tree numbers
C562568	Cerebellar Hypoplasia (supp.)
C537177	Kufor-Rakeb syndrome (supp.)
C538421	Neurodegeneration with brain iron accumulation (NBIA) (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — P5 P-type ATPases: Mn²⁺-ATPases

CTD chemical–gene interactions

42 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects expression, increases expression	3
Benzo(a)pyrene	affects methylation, increases expression, increases methylation	3
Manganese	affects response to substance, decreases response to substance	3
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, increases expression	2
Hydrogen Peroxide	decreases response to substance	2
Nickel	decreases response to substance, increases response to substance	2
Smoke	decreases expression, increases abundance, increases expression	2
Tobacco Smoke Pollution	decreases expression, increases expression	2
Valproic Acid	increases expression, increases methylation	2
aristolochic acid I	increases expression	1
FR900359	increases phosphorylation	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
beta-lapachone	increases expression	1
sulforaphane	increases expression	1
benzo(e)pyrene	increases methylation	1
ferrous chloride	decreases expression	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
benzyloxycarbonylleucyl-leucyl-leucine aldehyde	decreases response to substance	1
2-palmitoylglycerol	increases expression	1
abrine	decreases expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Cadmium	increases response to substance	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Dieldrin	decreases expression	1
Doxorubicin	decreases expression	1
Lead	affects expression	1
Methapyrilene	increases methylation	1

Cellosaurus cell lines

16 cell lines: 7 embryonic stem cell, 5 induced pluripotent stem cell, 3 cancer cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B1AP	Abcam HEK293 ATP13A2 KO	Transformed cell line	Female
CVCL_D3Y7	WIBRe001-A-52	Embryonic stem cell	Female
CVCL_D3Y8	WIBRe001-A-50	Embryonic stem cell	Female
CVCL_D3Y9	WIBRe001-A-49	Embryonic stem cell	Female
CVCL_D3YA	WIBRe001-A-53	Embryonic stem cell	Female
CVCL_D3YB	WIBRe001-A-51	Embryonic stem cell	Female
CVCL_D9Y7	Ubigene HeLa ATP13A2 KO	Cancer cell line	Female
CVCL_E4TU	KOLF2.1J ATP13A2 18.4kbdel DEL/DEL	Induced pluripotent stem cell	Male
CVCL_F0PL	H9 AAVS1-TRE3G-NGN2 TMEM192-3xHA (heterozygous) ATP13A2-/-	Embryonic stem cell	Female
CVCL_F0Y3	WIBR3_ATP13A2_FS_Homo_6_2	Embryonic stem cell	Female

Clinical trials (associated diseases)

6 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT05522374	Not specified	RECRUITING	TIRCON International NBIA Registry
NCT04613089	Not specified	RECRUITING	Natural History and Longitudinal Clinical Assessments in NCL / Batten Disease, the International DEM-CHILD Database
NCT02587858	Not specified	UNKNOWN	NBIAready: Online Collection of Natural History Patient-reported Outcome Measures
NCT05615571	Not specified	COMPLETED	Testing of NBIA Genes: Analysis of Genetic Heterogeneity and Validation of Mitochondrial Markers for Assessing Causality of Sequence Variants.
NCT05696912	Not specified	UNKNOWN	Functional Tests to Resolve Unsolved Rare Diseases. Rares.
NCT06596746	Not specified	RECRUITING	Neurodegenerative Diseases Progression Markers (MARKERS-NDD)