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Gene

VPS53

VPS53 subunit of GARP complex

Summary

Cytogenetic location
17p13.3
Coordinates
Chromosome 17: 508,668–714,839 (GRCh38)
Exons
22 exons across 206.2 kb
Protein
832 amino acids
Also known as
FLJ10979, HCCS1
MANE Select transcript
ENST00000437048.7NM_001128159.3
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 VPS53 yet. The test sequences your whole genome, so your data includes it all the same.

How VPS53 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 17, with a bracket where VPS53 sits. VPS53 and 12 genes near it on chromosome 17, from 111,754 to 1,111,753.Chromosome 1717p13.3p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12q21.1q21.2q21.31q21.32q21.33q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.30.2 Mb0.4 Mb0.6 Mb0.8 Mb1 MbSCGB1C2: 137,569–139,067, forward strandSCGB1C2DOC2B: 142,789–181,691, reverse strandDOC2BRPH3AL: 210,130–386,376, reverse strandRPH3ALLIAT1: 410,302–431,062, forward strandLIAT1RFLNB: 439,978–445,939, reverse strandRFLNBVPS53: 508,668–714,839, reverse strandVPS53TLCD3A: 732,412–743,009, forward strandTLCD3AGEMIN4: 742,840–753,999, reverse strandGEMIN4GLOD4: 757,097–782,341, reverse strandGLOD4MRM3: 782,342–792,510, forward strandMRM3NXN: 799,310–979,816, reverse strandNXNTIMM22: 997,090–1,003,671, forward strandTIMM22ABR: 1,003,519–1,229,738, reverse strandABRDiagram of VPS53: 22 exons on the reverse strand of chromosome 17Exon 19: 1 known disease-causing siteExon 18: 3 known disease-causing sitesExon 16: 2 known disease-causing sitesExon 15: 2 known disease-causing sitesExon 14: 4 known disease-causing sitesExon 13: 2 known disease-causing sitesExon 11: 1 known disease-causing siteExon 10: 7 known disease-causing sitesExon 9: 2 known disease-causing sitesExon 8: 2 known disease-causing sitesExon 6: 1 known disease-causing siteExon 5: 2 known disease-causing sitesExon 4: 2 known disease-causing sitesExon 22: 508,668–519,298, 10,631 basesExon 21: 519,826–519,930, 105 basesExon 20: 521,601–521,738, 138 basesExon 19: 532,842–532,911, 70 basesExon 18: 537,028–537,176, 149 basesExon 17: 551,872–551,950, 79 basesExon 16: 553,380–553,462, 83 basesExon 15: 560,426–560,573, 148 basesExon 14: 562,503–562,745, 243 basesExon 13: 586,270–586,364, 95 basesExon 12: 601,795–601,896, 102 basesExon 11: 623,533–623,674, 142 basesExon 10: 627,174–627,316, 143 basesExon 9: 628,088–628,231, 144 basesExon 8: 631,550–631,628, 79 basesExon 7: 653,291–653,410, 120 basesExon 6: 655,838–655,953, 116 basesExon 5: 661,809–661,895, 87 basesExon 4: 697,418–697,484, 67 basesExon 3: 699,331–699,380, 50 basesExon 2: 710,533–710,613, 81 basesExon 1: 714,623–714,839, 217 bases22201816141210864215′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 13.1 kb of the gene's 206.2 kb; 2,499 of those bases code for the protein.

How a genome test reads VPS53

38

positions in VPS53 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 206.2 kb of VPS53, introns included, not only the 13.1 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.). VPS53 gene: VPS53 subunit of GARP complex. Retrieved 16 October 2026, from https://dantelabs.com/genes/vps53

Vancouver

Dante Labs. VPS53 gene: VPS53 subunit of GARP complex [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/vps53

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