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Gene

ATP2A1

ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1

Summary

Cytogenetic location
16p11.2
Coordinates
Chromosome 16: 28,878,488–28,904,466 (GRCh38)
Exons
23 exons across 26 kb
Protein
994 amino acids
Also known as
SERCA1
Previous symbols
ATP2A
MANE Select transcript
ENST00000395503.9NM_004320.6
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

No Genome Test report reads ATP2A1 yet. The test sequences your whole genome, so your data includes it all the same.

How ATP2A1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 16, with a bracket where ATP2A1 sits. ATP2A1 and 22 genes near it on chromosome 16, from 28,391,477 to 29,391,476.Chromosome 1616p11.2p13.3p13.2p13.13p13.12p13.11p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q13q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.328.4 Mb28.6 Mb28.8 Mb29 Mb29.2 MbEIF3CL: 28,376,676–28,403,851, reverse strandEIF3CLNPIPB7: 28,456,322–28,472,336, reverse strand: 28,456,371–28,492,098, reverse strandCLN3: 28,474,111–28,495,575, reverse strandCLN3APOBR: 28,494,635–28,498,964, forward strandAPOBRIL27: 28,499,360–28,512,051, reverse strandIL27NUPR1: 28,532,708–28,539,068, reverse strandNUPR1SGF29: 28,538,176–28,591,792, forward strandSGF29SULT1A2: 28,589,688–28,599,913, reverse strandSULT1A2SULT1A1: 28,604,997–28,612,503, reverse strandSULT1A1NPIPB8: 28,637,654–28,658,744, forward strandNPIPB8EIF3C: 28,688,558–28,745,938, forward strandEIF3CNPIPB9: 28,751,787–28,772,864, forward strandNPIPB9ATXN2L: 28,822,983–28,837,237, forward strandATXN2LTUFM: 28,841,618–28,846,419, reverse strandTUFMSH2B1: 28,846,584–28,875,103, forward strandSH2B1ATP2A1: 28,878,488–28,904,466, forward strandATP2A1RABEP2: 28,898,740–28,936,526, reverse strandRABEP2CD19: 28,931,965–28,939,342, forward strandCD19NFATC2IP: 28,950,807–28,967,092, forward strandNFATC2IPSPNS1: 28,974,126–28,984,548, forward strandSPNS1LAT: 28,984,808–28,990,784, forward strandLATNPIPB11: 29,381,310–29,406,711, reverse strandNPIPB11Diagram of ATP2A1: 23 exons on the forward strand of chromosome 16Exon 1: 2 known disease-causing sitesExon 3: 1 known disease-causing siteExon 5: 1 known disease-causing siteExon 6: 1 known disease-causing siteExon 7: 5 known disease-causing sitesExon 8: 5 known disease-causing sitesExon 9: 1 known disease-causing siteExon 11: 1 known disease-causing siteExon 13: 2 known disease-causing sitesExon 14: 8 known disease-causing sitesExon 15: 6 known disease-causing sitesExon 16: 2 known disease-causing sitesExon 17: 3 known disease-causing sitesExon 18: 1 known disease-causing siteExon 19: 3 known disease-causing sitesExon 20: 1 known disease-causing siteExon 21: 1 known disease-causing siteExon 1: 28,878,488–28,878,789, 302 basesExon 2: 28,879,099–28,879,116, 18 basesExon 3: 28,879,501–28,879,583, 83 basesExon 4: 28,880,915–28,881,019, 105 basesExon 5: 28,882,451–28,882,589, 139 basesExon 6: 28,884,575–28,884,655, 81 basesExon 7: 28,887,189–28,887,274, 86 basesExon 8: 28,887,425–28,887,722, 298 basesExon 9: 28,888,787–28,888,953, 167 basesExon 10: 28,894,155–28,894,243, 89 basesExon 11: 28,894,505–28,894,607, 103 basesExon 12: 28,894,822–28,894,953, 132 basesExon 13: 28,898,000–28,898,125, 126 basesExon 14: 28,898,233–28,898,451, 219 basesExon 15: 28,900,581–28,900,916, 336 basesExon 16: 28,901,863–28,902,083, 221 basesExon 17: 28,902,184–28,902,386, 203 basesExon 18: 28,902,580–28,902,665, 86 basesExon 19: 28,902,778–28,902,911, 134 basesExon 20: 28,903,030–28,903,147, 118 basesExon 21: 28,903,323–28,903,440, 118 basesExon 22: 28,903,700–28,903,741, 42 basesExon 23: 28,904,180–28,904,466, 287 bases15101520235′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 3.5 kb of the gene's 26 kb; 2,985 of those bases code for the protein.

How a genome test reads ATP2A1

56

positions in ATP2A1 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 ATP2A1, introns included, not only the 3.5 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.
  • 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.). ATP2A1 gene: ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/atp2a1

Vancouver

Dante Labs. ATP2A1 gene: ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/atp2a1

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