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Gene

HPS1

HPS1 biogenesis of lysosomal organelles complex 3 subunit 1

Summary

Cytogenetic location
10q24.2
Coordinates
Chromosome 10: 98,416,198–98,446,935 (GRCh38)
Exons
20 exons across 30.7 kb
Protein
700 amino acids
Inheritance
Autosomal recessive
Also known as
BLOC3S1
Previous symbols
HPS
MANE Select transcript
ENST00000361490.9NM_000195.5
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 report relevant to this gene

  • Hermansky-Pudlak Syndrome

    • Autosomal recessive

      Hermansky-Pudlak syndrome (HSP) is a multi-system disorder characterized by oculocutaneous albinism, bleeding diathesis and, in some cases, neutropenia, pulmonary fibrosis, or granulomatous colitis. HPS comprises eight known disorders (HPS-1 to HPS-8), the majority of which present with the same clinical phenotype to varying degrees of severity.

      • ClinGen rates the link definitive
      • 5 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 HPS1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 10, with a bracket where HPS1 sits. HPS1 and 6 genes near it on chromosome 10, from 97,931,567 to 98,931,566.Chromosome 1010q24.2p15.3p15.2p15.1p14p13p12.33p12.32p12.31p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.31q23.32q23.33q24.1q24.2q24.31q24.32q24.33q25.1q25.2q25.3q26.11q26.12q26.13q26.2q26.398 Mb98.2 Mb98.4 Mb98.6 Mb98.8 MbCRTAC1: 97,854,711–98,030,828, reverse strandCRTAC1R3HCC1L: 98,134,608–98,245,624, forward strandR3HCC1LLOXL4: 98,247,686–98,268,650, reverse strandLOXL4PYROXD2: 98,379,888–98,415,215, reverse strandPYROXD2: 98,414,002–98,446,920, reverse strandHPS1: 98,416,198–98,446,935, reverse strandHPS1HPSE2: 98,457,077–99,235,878, reverse strandHPSE2Diagram of HPS1: 20 exons on the reverse strand of chromosome 10Exon 20: 6 known disease-causing sitesExon 19: 3 known disease-causing sitesExon 18: 7 known disease-causing sitesExon 17: 5 known disease-causing sitesExon 15: 9 known disease-causing sitesExon 14: 5 known disease-causing sitesExon 13: 8 known disease-causing sitesExon 12: 9 known disease-causing sitesExon 11: 4 known disease-causing sitesExon 10: 6 known disease-causing sitesExon 9: 6 known disease-causing sitesExon 8: 6 known disease-causing sitesExon 7: 16 known disease-causing sitesExon 6: 7 known disease-causing sitesExon 5: 8 known disease-causing sitesExon 4: 9 known disease-causing sitesExon 3: 10 known disease-causing sitesExon 20: 98,416,198–98,417,726, 1,529 basesExon 19: 98,418,175–98,418,257, 83 basesExon 18: 98,420,045–98,420,158, 114 basesExon 17: 98,422,369–98,422,513, 145 basesExon 16: 98,423,603–98,423,668, 66 basesExon 15: 98,423,753–98,423,887, 135 basesExon 14: 98,424,313–98,424,374, 62 basesExon 13: 98,425,541–98,425,720, 180 basesExon 12: 98,425,818–98,425,985, 168 basesExon 11: 98,427,215–98,427,264, 50 basesExon 10: 98,429,573–98,429,642, 70 basesExon 9: 98,429,791–98,429,889, 99 basesExon 8: 98,430,571–98,430,670, 100 basesExon 7: 98,431,131–98,431,291, 161 basesExon 6: 98,433,983–98,434,091, 109 basesExon 5: 98,435,272–98,435,414, 143 basesExon 4: 98,435,635–98,435,772, 138 basesExon 3: 98,443,124–98,443,240, 117 basesExon 2: 98,445,300–98,445,404, 105 basesExon 1: 98,446,807–98,446,935, 129 bases201816141210864215′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 3.7 kb of the gene's 30.7 kb; 2,103 of those bases code for the protein.

How a genome test reads HPS1

149

positions in HPS1 where ClinVar classes a change as pathogenic or likely pathogenic

29 of them (19%) fall in regions short reads find hard.

  • Segmental duplications (29 sites)Copies of at least 1 kb sharing at least 90% identity with another part of the genome (paralogues, pseudogenes); reads may align to the wrong copy.

A whole genome covers all 30.7 kb of HPS1, introns included, not only the 3.7 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.). HPS1 gene: HPS1 biogenesis of lysosomal organelles complex 3 subunit 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/hps1

Vancouver

Dante Labs. HPS1 gene: HPS1 biogenesis of lysosomal organelles complex 3 subunit 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/hps1

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