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Gene

ATP13A2

ATPase cation transporting 13A2

Summary

Cytogenetic location
1p36.13
Coordinates
Chromosome 1: 16,985,958–17,011,928 (GRCh38)
Exons
29 exons across 26 kb
Protein
1,180 amino acids
Inheritance
Autosomal recessive
Also known as
HSA9947, CLN12
Previous symbols
PARK9
MANE Select transcript
ENST00000326735.13NM_022089.4
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Neurodegeneration with Brain Iron Accumulation (NBIA)

    • Neurodegeneration with Brain Iron Accumulation

      A group of disorders including PKAN (PANK2), PLAN (PLA2G6), MPAN (C19orf12), BPAN (WDR45), neuroferritinopathy (FTL) and aceruloplasminemia (CP), with mostly recessive inheritance.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      Symptom treatment for dystonia and parkinsonism, iron chelation for aceruloplasminemia, and carrier testing for relatives in recessive forms.

  • Neuronal Ceroid Lipofuscinosis

    • Kufor-Rakeb SyndromeAutosomal recessive

      Kufor-Rakeb syndrome (KRS) is a rare genetic neurodegenerative disorder characterized by juvenile Parkinsonism, pyramidal degeneration (dystonia), supranuclear palsy, and cognitive impairment.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong

  • Parkinson Disease

    • A progressive degenerative disorder of the central nervous system characterized by loss of dopamine producing neurons in the substantia nigra and the presence of Lewy bodies in the substantia nigra and locus coeruleus. Signs and symptoms include tremor which is most pronounced during rest, muscle rigidity, slowing of the voluntary movements, a tendency to fall back, and a mask-like facial expression.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      LRRK2 kinase inhibitor trials, substrate reduction therapy for GBA variants, α-synuclein-targeted approaches, dopaminergic medications, levodopa

Broader groupings

  • Hereditary Spastic Paraplegia

    • Hereditary Spastic Paraplegia (All Types)

      One of 66 genes linked to it

      Umbrella term covering all hereditary spastic paraplegias, including SPG4 (SPAST), the most common dominant form, and SPG5A, SPG6, SPG10, SPG18, SPG30 and SPG31.

      • 2 GenCC submitters rate it definitive or strong

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How ATP13A2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 1, with a bracket where ATP13A2 sits. ATP13A2 and 11 genes near it on chromosome 1, from 16,498,943 to 17,498,942.Chromosome 11p36.13p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q4416.6 Mb16.8 Mb17 Mb17.2 Mb17.4 MbNBPF1: 16,562,319–16,613,562, reverse strandNBPF1CROCC: 16,740,273–16,972,964, forward strandCROCCMFAP2: 16,972,933–16,981,616, reverse strandMFAP2ATP13A2: 16,985,958–17,011,928, reverse strandATP13A2: 17,005,068–17,011,757, reverse strandSDHB: 17,018,664–17,054,210, reverse strandSDHBPADI2: 17,066,761–17,119,459, reverse strandPADI2PADI1: 17,205,120–17,246,007, forward strandPADI1PADI3: 17,249,093–17,284,233, forward strandPADI3PADI4: 17,308,195–17,364,004, forward strandPADI4PADI6: 17,372,196–17,401,699, forward strandPADI6RCC2: 17,406,755–17,439,992, reverse strandRCC2Diagram of ATP13A2: 29 exons on the reverse strand of chromosome 1Exon 29: 1 known disease-causing siteExon 28: 1 known disease-causing siteExon 27: 6 known disease-causing sitesExon 26: 1 known disease-causing siteExon 25: 1 known disease-causing siteExon 23: 4 known disease-causing sitesExon 22: 2 known disease-causing sitesExon 21: 1 known disease-causing siteExon 20: 3 known disease-causing sitesExon 19: 3 known disease-causing sitesExon 18: 3 known disease-causing sitesExon 17: 2 known disease-causing sitesExon 16: 2 known disease-causing sitesExon 15: 8 known disease-causing sitesExon 14: 2 known disease-causing sitesExon 13: 2 known disease-causing sitesExon 12: 3 known disease-causing sitesExon 11: 2 known disease-causing sitesExon 9: 1 known disease-causing siteExon 8: 1 known disease-causing siteExon 7: 4 known disease-causing sitesExon 6: 1 known disease-causing siteExon 5: 3 known disease-causing sitesExon 3: 2 known disease-causing sitesExon 2: 1 known disease-causing siteExon 29: 16,985,958–16,986,358, 401 basesExon 28: 16,986,463–16,986,632, 170 basesExon 27: 16,986,805–16,986,956, 152 basesExon 26: 16,987,046–16,987,269, 224 basesExon 25: 16,988,138–16,988,234, 97 basesExon 24: 16,988,322–16,988,474, 153 basesExon 23: 16,989,691–16,989,770, 80 basesExon 22: 16,989,887–16,990,003, 117 basesExon 21: 16,990,127–16,990,287, 161 basesExon 20: 16,991,734–16,991,858, 125 basesExon 19: 16,992,009–16,992,129, 121 basesExon 18: 16,992,243–16,992,402, 160 basesExon 17: 16,992,486–16,992,581, 96 basesExon 16: 16,993,629–16,993,835, 207 basesExon 15: 16,995,976–16,996,164, 189 basesExon 14: 16,996,254–16,996,300, 47 basesExon 13: 16,996,386–16,996,496, 111 basesExon 12: 16,997,020–16,997,175, 156 basesExon 11: 17,000,011–17,000,142, 132 basesExon 10: 17,000,246–17,000,312, 67 basesExon 9: 17,000,400–17,000,534, 135 basesExon 8: 17,002,034–17,002,103, 70 basesExon 7: 17,002,296–17,002,373, 78 basesExon 6: 17,004,332–17,004,411, 80 basesExon 5: 17,004,692–17,004,821, 130 basesExon 4: 17,005,014–17,005,072, 59 basesExon 3: 17,005,374–17,005,556, 183 basesExon 2: 17,005,684–17,005,778, 95 basesExon 1: 17,011,729–17,011,928, 200 bases2925201510515′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 4 kb of the gene's 26 kb; 3,543 of those bases code for the protein.

How a genome test reads ATP13A2

79

positions in ATP13A2 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 26 kb of ATP13A2, introns included, not only the 4 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). ATP13A2 gene: ATPase cation transporting 13A2. Retrieved 17 October 2026, from https://dantelabs.com/genes/atp13a2

Vancouver

Dante Labs. ATP13A2 gene: ATPase cation transporting 13A2 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/atp13a2

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