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Gene

VDR

vitamin D receptor

Summary

Cytogenetic location
12q13.11
Coordinates
Chromosome 12: 47,841,537–47,904,994 (GRCh38)
Exons
10 exons across 63.5 kb
Protein
427 amino acids
Also known as
NR1I1, PPP1R163
MANE Select transcript
ENST00000549336.6NM_000376.3
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 report relevant to this gene

  • Hereditary Rickets (Hypophosphatemic and Vitamin D-Dependent)

    • Vitamin D-dependent rickets

      Inherited defects in activating vitamin D (CYP27B1, CYP2R1) or in the vitamin D receptor (VDR) that cause rickets in early childhood despite adequate vitamin D intake.

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

      Most types respond well to calcitriol, high-dose vitamin D or high-dose calcium, depending on the type.

Trait report that reads VDR

How VDR is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 12, with a bracket where VDR sits. VDR and 14 genes near it on chromosome 12, from 47,373,266 to 48,373,265.Chromosome 1212q13.11p13.33p13.32p13.31p13.2p13.1p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11q12q13.11q13.12q13.13q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.31q21.32q21.33q22q23.1q23.2q23.3q24.11q24.12q24.13q24.21q24.22q24.23q24.31q24.32q24.3347.4 Mb47.6 Mb47.8 Mb48 Mb48.2 MbRPAP3: 47,660,814–47,706,038, reverse strandRPAP3ENDOU: 47,709,734–47,725,567, reverse strandENDOURAPGEF3: 47,734,180–47,771,040, reverse strandRAPGEF3SLC48A1: 47,753,916–47,782,751, forward strandSLC48A1HDAC7: 47,782,722–47,833,132, reverse strandHDAC7VDR: 47,841,537–47,904,994, reverse strandVDRTMEM106C: 47,963,543–47,970,504, forward strandTMEM106CCOL2A1: 47,972,967–48,004,689, reverse strandCOL2A1SENP1: 48,039,784–48,106,316, reverse strandSENP1PFKM: 48,105,139–48,152,487, forward strandPFKMASB8: 48,147,789–48,181,213, reverse strandASB8CCDC184: 48,183,644–48,185,926, forward strandCCDC184OR10AD1: 48,202,339–48,203,292, reverse strandOR10AD1H1-7: 48,328,980–48,330,279, forward strandH1-7ZNF641: 48,337,180–48,351,414, reverse strandZNF641Diagram of VDR: 10 exons on the reverse strand of chromosome 12Exon 10: 5 known disease-causing sitesExon 9: 1 known disease-causing siteExon 8: 4 known disease-causing sitesExon 5: 1 known disease-causing siteExon 4: 3 known disease-causing sitesExon 3: 2 known disease-causing sitesExon 2: 1 known disease-causing siteExon 10: 47,841,537–47,845,005, 3,469 basesExon 9: 47,846,335–47,846,451, 117 basesExon 8: 47,846,657–47,846,808, 152 basesExon 7: 47,855,630–47,855,801, 172 basesExon 6: 47,857,129–47,857,249, 121 basesExon 5: 47,857,504–47,857,688, 185 basesExon 4: 47,865,047–47,865,177, 131 basesExon 3: 47,878,968–47,879,115, 148 basesExon 2: 47,882,694–47,882,774, 81 basesExon 1: 47,904,955–47,904,994, 40 bases10864215′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 4.6 kb of the gene's 63.5 kb; 1,284 of those bases code for the protein.

How a genome test reads VDR

20

positions in VDR 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 63.5 kb of VDR, introns included, not only the 4.6 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.). VDR gene: vitamin D receptor. Retrieved 16 October 2026, from https://dantelabs.com/genes/vdr

Vancouver

Dante Labs. VDR gene: vitamin D receptor [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/vdr

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