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Gene

VPS16

VPS16 core subunit of CORVET and HOPS complexes

Summary

Cytogenetic location
20p13
Coordinates
Chromosome 20: 2,840,745–2,866,732 (GRCh38)
Exons
24 exons across 26 kb
Protein
839 amino acids
MANE Select transcript
ENST00000380445.8NM_022575.4
Locus type
Protein-coding
  • Very high
  • Confident
  • Low
  • Very low

Curated report relevant to this gene

  • Dystonia, Myotonia, Paroxysmal Dyskinesia

    • Dystonia 30Autosomal dominant
      • 2 GenCC submitters rate it definitive or strong
    • Inherited Dystonia

      Umbrella term covering inherited dystonias, including DYT-TOR1A early-onset generalized dystonia, DYT-THAP1, myoclonus-dystonia (SGCE) and KMT2B-related dystonia.

      • 2 GenCC submitters rate it definitive or strong

How VPS16 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 20, with a bracket where VPS16 sits. VPS16 and 25 genes near it on chromosome 20, from 2,353,739 to 3,353,738.Chromosome 2020p13p13p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q12q13.11q13.12q13.13q13.2q13.31q13.32q13.332.4 Mb2.6 Mb2.8 Mb3 Mb3.2 MbTGM6: 2,380,901–2,432,753, forward strandTGM6SNRPB: 2,461,634–2,470,884, reverse strandSNRPB: 2,467,212–2,508,907, reverse strandZNF343: 2,471,467–2,525,028, reverse strandZNF343TMC2: 2,536,573–2,643,580, forward strandTMC2NOP56: 2,652,460–2,658,396, forward strandNOP56IDH3B: 2,658,393–2,664,219, reverse strandIDH3BEBF4: 2,692,724–2,760,228, forward strandEBF4CPXM1: 2,794,069–2,800,835, reverse strand: 2,814,968–2,818,066, forward strandC20orf141: 2,814,987–2,815,833, forward strandC20orf141TMEM239: 2,816,302–2,820,284, forward strandTMEM239PCED1A: 2,835,070–2,841,190, reverse strandPCED1AVPS16: 2,840,745–2,866,732, forward strandVPS16PTPRA: 2,870,754–3,039,247, forward strandPTPRAGNRH2: 3,042,814–3,045,747, forward strandGNRH2MRPS26: 3,046,016–3,048,254, forward strandMRPS26OXT: 3,071,476–3,072,517, forward strandOXTAVP: 3,082,556–3,084,724, reverse strandAVPUBOX5: 3,107,573–3,160,196, reverse strandUBOX5FASTKD5: 3,146,519–3,160,196, reverse strandFASTKD5LZTS3: 3,162,617–3,174,504, reverse strandLZTS3DDRGK1: 3,188,734–3,204,700, reverse strandDDRGK1ITPA: 3,208,868–3,227,446, forward strandITPASLC4A11: 3,227,417–3,239,580, reverse strandSLC4A11DNAAF9: 3,249,295–3,407,942, reverse strandDNAAF9Diagram of VPS16: 24 exons on the forward strand of chromosome 20Exon 6: 2 known disease-causing sitesExon 11: 1 known disease-causing siteExon 14: 1 known disease-causing siteExon 15: 1 known disease-causing siteExon 16: 1 known disease-causing siteExon 18: 1 known disease-causing siteExon 19: 1 known disease-causing siteExon 20: 2 known disease-causing sitesExon 21: 2 known disease-causing sitesExon 1: 2,840,745–2,840,827, 83 basesExon 2: 2,859,719–2,859,807, 89 basesExon 3: 2,860,054–2,860,151, 98 basesExon 4: 2,860,239–2,860,367, 129 basesExon 5: 2,860,449–2,860,593, 145 basesExon 6: 2,860,748–2,860,863, 116 basesExon 7: 2,860,970–2,861,092, 123 basesExon 8: 2,861,225–2,861,280, 56 basesExon 9: 2,861,615–2,861,704, 90 basesExon 10: 2,861,805–2,861,899, 95 basesExon 11: 2,862,054–2,862,130, 77 basesExon 12: 2,862,579–2,862,710, 132 basesExon 13: 2,862,807–2,862,934, 128 basesExon 14: 2,863,065–2,863,100, 36 basesExon 15: 2,863,290–2,863,398, 109 basesExon 16: 2,863,949–2,864,083, 135 basesExon 17: 2,864,179–2,864,287, 109 basesExon 18: 2,864,365–2,864,462, 98 basesExon 19: 2,864,547–2,864,654, 108 basesExon 20: 2,864,978–2,865,055, 78 basesExon 21: 2,865,148–2,865,317, 170 basesExon 22: 2,865,399–2,865,495, 97 basesExon 23: 2,866,212–2,866,315, 104 basesExon 24: 2,866,430–2,866,732, 303 bases15101520245′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 2.7 kb of the gene's 26 kb; 2,520 of those bases code for the protein.

Sequencing VPS16

15

positions in VPS16 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 VPS16, introns included, not only the 2.7 kb of exons.

Genes linked to the same conditions

Traits linked to VPS16

The Human Phenotype Ontology lists these as features of the rare conditions VPS16 can cause. Each trait's page lists the other genes linked to it.

External links

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 2026-10-17: 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 2026.10.17-8666dff2.

Cite this page

APA

Dante Labs. (n.d.). VPS16 gene: VPS16 core subunit of CORVET and HOPS complexes. Retrieved 17 October 2026, from https://dantelabs.com/genes/vps16

Vancouver

Dante Labs. VPS16 gene: VPS16 core subunit of CORVET and HOPS complexes [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/vps16

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