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Gene

VPS11

VPS11 core subunit of CORVET and HOPS complexes

Summary

Cytogenetic location
11q23.3
Coordinates
Chromosome 11: 119,067,818–119,081,972 (GRCh38)
Exons
16 exons across 14.2 kb
Protein
941 amino acids
Inheritance
Autosomal recessive
Also known as
RNF108, PEP5
MANE Select transcript
ENST00000621676.5NM_021729.6
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

  • Pelizaeus-Merzbacher Disease & Hypomyelinating Leukodystrophies

    • Hypomyelinating leukodystrophy 12 (VPS11)Autosomal recessive

      A rare inherited form of hypomyelinating leukodystrophy, in which myelin in the brain does not form normally, causing delayed development and movement problems.

      • 2 GenCC submitters rate it definitive or strong

Broader groupings

  • Other Inherited Leukodystrophies

    • Leukodystrophy (other and unspecified types)

      One of 80 genes linked to it

      Inherited conditions that damage or prevent the normal formation of myelin, the white matter of the brain and spinal cord. Different types follow autosomal recessive, autosomal dominant or X-linked inheritance depending on the gene involved.

      • 2 GenCC submitters rate it definitive or strong
      What knowing changes

      Knowing the specific genetic cause can end a diagnostic search, guide supportive care and surveillance, show whether a specific treatment exists, and allow testing of relatives.

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 VPS11 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 11, with a bracket where VPS11 sits. VPS11 and 29 genes near it on chromosome 11, from 118,574,895 to 119,574,894.Chromosome 1111q23.3p15.5p15.4p15.3p15.2p15.1p14.3p14.2p14.1p13p12p11.2p11.12p11.11q11q12.1q12.2q12.3q13.1q13.2q13.3q13.4q13.5q14.1q14.2q14.3q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q25118.6 Mb118.8 Mb119 Mb119.2 Mb119.4 MbARCN1: 118,572,384–118,603,033, forward strandARCN1PHLDB1: 118,606,396–118,658,038, forward strandPHLDB1TREH: 118,657,265–118,679,694, reverse strandTREHDDX6: 118,747,763–118,791,226, reverse strandDDX6CXCR5: 118,883,868–118,897,787, forward strandCXCR5BCL9L: 118,893,875–118,925,926, reverse strandBCL9LUPK2: 118,925,164–118,958,559, forward strandUPK2FOXR1: 118,971,623–118,981,287, forward strandCENATAC: 118,998,051–119,015,811, forward strandRPS25: 119,014,665–119,018,724, reverse strandRPS25TRAPPC4: 119,018,733–119,025,454, forward strandTRAPPC4SLC37A4: 119,023,751–119,030,906, reverse strandSLC37A4HYOU1: 119,044,185–119,057,252, reverse strandHYOU1VPS11: 119,067,818–119,081,972, forward strandVPS11HMBS: 119,084,861–119,093,920, forward strandHMBSH2AX: 119,093,874–119,095,465, reverse strandH2AXDPAGT1: 119,095,979–119,108,331, reverse strandC2CD2L: 119,102,198–119,118,544, forward strandC2CD2LHINFP: 119,121,509–119,136,059, forward strandABCG4: 119,149,029–119,162,653, forward strandABCG4NLRX1: 119,166,481–119,184,017, forward strandNLRX1NHERF4: 119,185,457–119,190,227, forward strandNHERF4DRC12: 119,190,055–119,206,266, reverse strandDRC12CBL: 119,206,036–119,313,926, forward strandCBLMCAM: 119,307,972–119,321,521, reverse strandMCAMRNF26: 119,334,527–119,337,309, forward strandRNF26C1QTNF5: 119,338,942–119,340,940, reverse strandC1QTNF5MFRP: 119,338,942–119,346,705, reverse strandMFRPUSP2: 119,355,215–119,381,720, reverse strandUSP2THY1: 119,415,476–119,424,985, reverse strandTHY1Diagram of VPS11: 16 exons on the forward strand of chromosome 11Exon 15: 1 known disease-causing siteExon 1: 119,067,818–119,068,010, 193 basesExon 2: 119,069,196–119,069,344, 149 basesExon 3: 119,069,442–119,069,577, 136 basesExon 4: 119,070,234–119,070,397, 164 basesExon 5: 119,071,596–119,071,843, 248 basesExon 6: 119,073,198–119,073,399, 202 basesExon 7: 119,073,800–119,073,951, 152 basesExon 8: 119,076,897–119,077,083, 187 basesExon 9: 119,077,501–119,077,647, 147 basesExon 10: 119,077,878–119,078,066, 189 basesExon 11: 119,078,173–119,078,334, 162 basesExon 12: 119,078,565–119,078,704, 140 basesExon 13: 119,078,795–119,078,997, 203 basesExon 14: 119,079,129–119,079,300, 172 basesExon 15: 119,081,092–119,081,314, 223 basesExon 16: 119,081,459–119,081,972, 514 bases12468101214165′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 3.2 kb of the gene's 14.2 kb; 2,826 of those bases code for the protein.

How a genome test reads VPS11

1

position in VPS11 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 14.2 kb of VPS11, introns included, not only the 3.2 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.). VPS11 gene: VPS11 core subunit of CORVET and HOPS complexes. Retrieved 17 October 2026, from https://dantelabs.com/genes/vps11

Vancouver

Dante Labs. VPS11 gene: VPS11 core subunit of CORVET and HOPS complexes [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/vps11

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