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Gene

VPS13D

vacuolar protein sorting 13 homolog D

Summary

Cytogenetic location
1p36.22-p36.21
Coordinates
Chromosome 1: 12,230,030–12,512,047 (GRCh38)
Exons
70 exons across 282 kb
Protein
4,388 amino acids
Inheritance
Autosomal recessive
Also known as
FLJ10619, KIAA0453, BLTP5D
MANE Select transcript
ENST00000620676.6NM_015378.4
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

    • Autosomal Recessive Cerebellar Ataxias (incl. CANVAS and AVED)

      • Autosomal Recessive Cerebellar AtaxiaAutosomal recessive

        One of 57 genes linked to it

        A group of recessively inherited ataxias caused by biallelic variants in genes such as RFC1, FXN, SACS, TTPA, SETX, APTX, PNKP, ANO10 and SYNE1.

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

        Ataxia with vitamin E deficiency (TTPA) is treatable with vitamin E supplements; other forms are managed with physiotherapy and symptom care, and relatives can be offered carrier testing.

    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 VPS13D is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    • Stretches short reads find hard
    Chromosome 1, with a bracket where VPS13D sits. VPS13D and 15 genes near it on chromosome 1, from 11,871,039 to 12,871,038.Chromosome 11p36.22-p36.21p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q4412 Mb12.2 Mb12.4 Mb12.6 Mb12.8 MbKIAA2013: 11,919,590–11,926,428, reverse strandKIAA2013PLOD1: 11,934,205–11,975,542, forward strandPLOD1MFN2: 11,980,181–12,015,211, forward strandMFN2MIIP: 12,019,466–12,032,048, forward strandMIIPTNFRSF8: 12,063,079–12,144,221, forward strandTNFRSF8TNFRSF1B: 12,166,970–12,209,228, forward strandTNFRSF1BVPS13D: 12,230,030–12,512,047, forward strandVPS13DDHRS3: 12,563,619–12,620,183, reverse strandDHRS3AADACL4: 12,644,085–12,667,076, forward strandAADACL4AADACL3: 12,716,109–12,728,760, forward strandAADACL3CFAP107: 12,746,194–12,763,699, forward strandCFAP107PRAMEF12: 12,773,738–12,777,906, forward strandPRAMEF12PRAMEF1: 12,791,397–12,796,628, forward strandPRAMEF1PRAMEF11: 12,824,605–12,831,410, reverse strandPRAMEF11HNRNPCL1: 12,847,377–12,848,720, reverse strandHNRNPCL1PRAMEF2: 12,857,086–12,861,909, forward strandPRAMEF2Diagram of VPS13D: 70 exons on the forward strand of chromosome 1Exon 10: 2 known disease-causing sitesExon 11: 1 known disease-causing siteExon 17: 1 known disease-causing siteExon 19: 1 known disease-causing siteExon 21: 1 known disease-causing siteExon 27: 1 known disease-causing siteExon 43: 1 known disease-causing siteExon 46: 1 known disease-causing siteExon 48: 1 known disease-causing siteExon 51: 1 known disease-causing siteExon 53: 1 known disease-causing siteExon 63: 1 known disease-causing siteExon 65: 1 known disease-causing siteExon 66: 5 known disease-causing sitesExon 67: 1 known disease-causing siteExon 68: 1 known disease-causing siteExon 69: 1 known disease-causing siteExon 1: 12,230,030–12,230,120, 91 basesExon 2: 12,234,191–12,234,363, 173 basesExon 3: 12,242,513–12,242,590, 78 basesExon 4: 12,244,246–12,244,436, 191 basesExon 5: 12,244,537–12,244,617, 81 basesExon 6: 12,249,223–12,249,339, 117 basesExon 7: 12,253,722–12,253,826, 105 basesExon 8: 12,256,333–12,256,503, 171 basesExon 9: 12,256,987–12,257,087, 101 basesExon 10: 12,257,935–12,258,103, 169 basesExon 11: 12,260,693–12,260,794, 102 basesExon 12: 12,260,948–12,261,149, 202 basesExon 13: 12,261,901–12,262,080, 180 basesExon 14: 12,266,881–12,267,011, 131 basesExon 15: 12,267,845–12,267,920, 76 basesExon 16: 12,268,706–12,268,876, 171 basesExon 17: 12,270,994–12,271,124, 131 basesExon 18: 12,273,003–12,273,135, 133 basesExon 19: 12,275,825–12,278,038, 2,214 basesExon 20: 12,279,499–12,279,650, 152 basesExon 21: 12,282,705–12,283,736, 1,032 basesExon 22: 12,288,223–12,288,313, 91 basesExon 23: 12,290,998–12,291,124, 127 basesExon 24: 12,293,524–12,293,704, 181 basesExon 25: 12,299,202–12,299,384, 183 basesExon 26: 12,304,506–12,304,728, 223 basesExon 27: 12,308,431–12,308,641, 211 basesExon 28: 12,311,454–12,311,625, 172 basesExon 29: 12,311,813–12,311,925, 113 basesExon 30: 12,314,115–12,314,327, 213 basesExon 31: 12,318,072–12,318,337, 266 basesExon 32: 12,319,497–12,319,630, 134 basesExon 33: 12,321,809–12,321,964, 156 basesExon 34: 12,322,536–12,322,746, 211 basesExon 35: 12,323,706–12,323,780, 75 basesExon 36: 12,327,648–12,327,854, 207 basesExon 37: 12,329,829–12,329,918, 90 basesExon 38: 12,333,226–12,333,366, 141 basesExon 39: 12,335,705–12,335,827, 123 basesExon 40: 12,338,231–12,338,305, 75 basesExon 41: 12,341,780–12,341,885, 106 basesExon 42: 12,342,899–12,343,051, 153 basesExon 43: 12,345,374–12,345,509, 136 basesExon 44: 12,346,605–12,346,652, 48 basesExon 45: 12,348,823–12,348,973, 151 basesExon 46: 12,349,164–12,349,374, 211 basesExon 47: 12,353,974–12,354,221, 248 basesExon 48: 12,355,899–12,356,090, 192 basesExon 49: 12,356,398–12,356,524, 127 basesExon 50: 12,358,459–12,358,601, 143 basesExon 51: 12,362,720–12,362,850, 131 basesExon 52: 12,363,072–12,363,247, 176 basesExon 53: 12,368,468–12,368,591, 124 basesExon 54: 12,369,467–12,369,702, 236 basesExon 55: 12,373,750–12,373,858, 109 basesExon 56: 12,378,428–12,378,591, 164 basesExon 57: 12,379,488–12,379,596, 109 basesExon 58: 12,382,976–12,383,155, 180 basesExon 59: 12,385,260–12,385,373, 114 basesExon 60: 12,386,185–12,386,334, 150 basesExon 61: 12,400,181–12,400,330, 150 basesExon 62: 12,401,608–12,401,704, 97 basesExon 63: 12,403,825–12,403,973, 149 basesExon 64: 12,415,087–12,415,221, 135 basesExon 65: 12,416,660–12,416,827, 168 basesExon 66: 12,455,998–12,456,130, 133 basesExon 67: 12,460,201–12,460,396, 196 basesExon 68: 12,497,500–12,497,631, 132 basesExon 69: 12,506,853–12,507,093, 241 basesExon 70: 12,508,893–12,512,047, 3,155 bases15101520253035404550556065705′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 16.4 kb of the gene's 282 kb; 13,167 of those bases code for the protein.

    How a genome test reads VPS13D

    28

    positions in VPS13D 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 282 kb of VPS13D, introns included, not only the 16.4 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.). VPS13D gene: vacuolar protein sorting 13 homolog D. Retrieved 17 October 2026, from https://dantelabs.com/genes/vps13d

    Vancouver

    Dante Labs. VPS13D gene: vacuolar protein sorting 13 homolog D [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/vps13d

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