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Gene

VPS13A

vacuolar protein sorting 13 homolog A

Summary

Cytogenetic location
9q21.2
Coordinates
Chromosome 9: 77,177,534–77,421,537 (GRCh38)
Exons
72 exons across 244 kb
Protein
3,174 amino acids
Also known as
KIAA0986, BLTP5A
Previous symbols
CHAC
MANE Select transcript
ENST00000360280.8NM_033305.3
Locus type
gene with protein product

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Neuroacanthocytosis and Huntington Disease Phenocopies

    • Neuroacanthocytosis

      A group of disorders with abnormally shaped red blood cells and neurodegeneration, including VPS13A-related chorea-acanthocytosis (recessive) and XK-related McLeod syndrome (X-linked).

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

      Neurological and psychiatric care; people with McLeod syndrome need Kell-compatible blood if transfused.

How VPS13A is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 9, with a bracket where VPS13A sits. VPS13A and 4 genes near it on chromosome 9, from 76,799,536 to 77,799,535.Chromosome 99q21.2p24.3p24.2p24.1p23p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q13q21.11q21.12q21.13q21.2q21.31q21.32q21.33q22.1q22.2q22.31q22.32q22.33q31.1q31.2q31.3q32q33.1q33.2q33.3q34.11q34.12q34.13q34.2q34.376.8 Mb77 Mb77.2 Mb77.4 Mb77.6 MbPRUNE2: 76,611,376–76,906,591, reverse strandPRUNE2FOXB2: 77,018,706–77,022,372, forward strandFOXB2VPS13A: 77,177,534–77,421,537, forward strandVPS13AGNA14: 77,423,079–77,649,210, reverse strandGNA14GNAQ: 77,716,097–78,032,500, reverse strandGNAQDiagram of VPS13A: 72 exons on the forward strand of chromosome 9Exon 1: 13 known disease-causing sitesExon 2: 2 known disease-causing sitesExon 3: 1 known disease-causing siteExon 4: 13 known disease-causing sitesExon 5: 5 known disease-causing sitesExon 6: 5 known disease-causing sitesExon 8: 2 known disease-causing sitesExon 9: 1 known disease-causing siteExon 10: 2 known disease-causing sitesExon 11: 9 known disease-causing sitesExon 12: 2 known disease-causing sitesExon 13: 14 known disease-causing sitesExon 14: 4 known disease-causing sitesExon 15: 9 known disease-causing sitesExon 16: 6 known disease-causing sitesExon 17: 5 known disease-causing sitesExon 18: 9 known disease-causing sitesExon 19: 6 known disease-causing sitesExon 20: 1 known disease-causing siteExon 21: 4 known disease-causing sitesExon 22: 6 known disease-causing sitesExon 23: 8 known disease-causing sitesExon 24: 2 known disease-causing sitesExon 25: 4 known disease-causing sitesExon 26: 9 known disease-causing sitesExon 27: 3 known disease-causing sitesExon 28: 2 known disease-causing sitesExon 29: 7 known disease-causing sitesExon 30: 1 known disease-causing siteExon 31: 2 known disease-causing sitesExon 32: 16 known disease-causing sitesExon 33: 6 known disease-causing sitesExon 34: 5 known disease-causing sitesExon 35: 5 known disease-causing sitesExon 36: 7 known disease-causing sitesExon 37: 10 known disease-causing sitesExon 38: 11 known disease-causing sitesExon 39: 8 known disease-causing sitesExon 40: 5 known disease-causing sitesExon 41: 11 known disease-causing sitesExon 42: 2 known disease-causing sitesExon 43: 2 known disease-causing sitesExon 44: 9 known disease-causing sitesExon 45: 10 known disease-causing sitesExon 46: 4 known disease-causing sitesExon 47: 15 known disease-causing sitesExon 48: 19 known disease-causing sitesExon 49: 8 known disease-causing sitesExon 50: 3 known disease-causing sitesExon 51: 6 known disease-causing sitesExon 52: 4 known disease-causing sitesExon 53: 7 known disease-causing sitesExon 54: 4 known disease-causing sitesExon 55: 6 known disease-causing sitesExon 56: 4 known disease-causing sitesExon 57: 2 known disease-causing sitesExon 58: 5 known disease-causing sitesExon 59: 5 known disease-causing sitesExon 60: 7 known disease-causing sitesExon 61: 5 known disease-causing sitesExon 62: 7 known disease-causing sitesExon 63: 4 known disease-causing sitesExon 65: 9 known disease-causing sitesExon 66: 2 known disease-causing sitesExon 67: 4 known disease-causing sitesExon 68: 3 known disease-causing sitesExon 69: 3 known disease-causing sitesExon 70: 5 known disease-causing sitesExon 71: 2 known disease-causing sitesExon 1: 77,177,534–77,177,804, 271 basesExon 2: 77,199,945–77,199,988, 44 basesExon 3: 77,201,365–77,201,407, 43 basesExon 4: 77,205,313–77,205,408, 96 basesExon 5: 77,205,978–77,206,079, 102 basesExon 6: 77,209,423–77,209,532, 110 basesExon 7: 77,210,616–77,210,675, 60 basesExon 8: 77,212,969–77,213,028, 60 basesExon 9: 77,213,234–77,213,314, 81 basesExon 10: 77,214,329–77,214,386, 58 basesExon 11: 77,219,954–77,220,081, 128 basesExon 12: 77,220,277–77,220,383, 107 basesExon 13: 77,221,185–77,221,356, 172 basesExon 14: 77,225,926–77,225,988, 63 basesExon 15: 77,226,466–77,226,598, 133 basesExon 16: 77,227,391–77,227,485, 95 basesExon 17: 77,228,122–77,228,264, 143 basesExon 18: 77,238,002–77,238,191, 190 basesExon 19: 77,238,272–77,238,386, 115 basesExon 20: 77,247,259–77,247,395, 137 basesExon 21: 77,250,097–77,250,229, 133 basesExon 22: 77,252,235–77,252,352, 118 basesExon 23: 77,260,086–77,260,224, 139 basesExon 24: 77,273,280–77,273,364, 85 basesExon 25: 77,275,498–77,275,652, 155 basesExon 26: 77,276,065–77,276,221, 157 basesExon 27: 77,280,159–77,280,238, 80 basesExon 28: 77,281,867–77,281,926, 60 basesExon 29: 77,282,121–77,282,274, 154 basesExon 30: 77,283,355–77,283,471, 117 basesExon 31: 77,283,547–77,283,650, 104 basesExon 32: 77,293,341–77,293,508, 168 basesExon 33: 77,295,542–77,295,846, 305 basesExon 34: 77,302,915–77,303,062, 148 basesExon 35: 77,307,945–77,308,098, 154 basesExon 36: 77,313,992–77,314,119, 128 basesExon 37: 77,314,495–77,314,664, 170 basesExon 38: 77,315,253–77,315,470, 218 basesExon 39: 77,316,174–77,316,406, 233 basesExon 40: 77,317,606–77,317,698, 93 basesExon 41: 77,318,235–77,318,591, 357 basesExon 42: 77,319,572–77,319,673, 102 basesExon 43: 77,321,169–77,321,327, 159 basesExon 44: 77,321,491–77,321,746, 256 basesExon 45: 77,323,067–77,323,227, 161 basesExon 46: 77,332,010–77,332,113, 104 basesExon 47: 77,337,255–77,337,537, 283 basesExon 48: 77,339,516–77,339,911, 396 basesExon 49: 77,340,178–77,340,282, 105 basesExon 50: 77,340,404–77,340,550, 147 basesExon 51: 77,344,153–77,344,281, 129 basesExon 52: 77,345,009–77,345,142, 134 basesExon 53: 77,351,317–77,351,446, 130 basesExon 54: 77,353,409–77,353,641, 233 basesExon 55: 77,356,714–77,356,867, 154 basesExon 56: 77,357,692–77,357,838, 147 basesExon 57: 77,358,357–77,358,438, 82 basesExon 58: 77,359,333–77,359,402, 70 basesExon 59: 77,360,536–77,360,641, 106 basesExon 60: 77,365,460–77,365,573, 114 basesExon 61: 77,366,727–77,366,872, 146 basesExon 62: 77,368,055–77,368,136, 82 basesExon 63: 77,369,299–77,369,412, 114 basesExon 64: 77,370,257–77,370,332, 76 basesExon 65: 77,370,415–77,370,578, 164 basesExon 66: 77,370,890–77,370,935, 46 basesExon 67: 77,371,026–77,371,149, 124 basesExon 68: 77,381,976–77,382,087, 112 basesExon 69: 77,403,236–77,403,321, 86 basesExon 70: 77,405,864–77,405,987, 124 basesExon 71: 77,407,533–77,407,607, 75 basesExon 72: 77,415,956–77,421,537, 5,582 bases110203040506070725′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 15.2 kb of the gene's 244 kb; 9,525 of those bases code for the protein.

How a genome test reads VPS13A

468

positions in VPS13A 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 244 kb of VPS13A, introns included, not only the 15.2 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.). VPS13A gene: vacuolar protein sorting 13 homolog A. Retrieved 17 October 2026, from https://dantelabs.com/genes/vps13a

Vancouver

Dante Labs. VPS13A gene: vacuolar protein sorting 13 homolog A [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/vps13a

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