rs12794714

This is a synonymous variant in the CYP2R1 gene — it does not change the protein's amino acid sequence.

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GWAS Catalog Trait Associations (3)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

vitamin D level

Revez JA et al. “Genome-wide association study identifies 143 loci associated with 25 hydroxyvitamin D concentration.” Nature Communications 11(1):1647 (2020)
Allele G
OR —
β 0.089
p 1.0e-300
N 417,580
Large GWAS
European

vitamin deficiency disorder

Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)
Allele G
OR 0.11
p 4.0e-111
N 577,973
Major Consortium StudyLarge GWAS
multi-ancestry

vitamin D deficiency

Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)
Allele G
OR 0.12
p 2.0e-16
N 54,105
Major Consortium StudyLarge GWAS
Hispanic or Latin American
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ClinVar annotation

Benign★★★☆
7 submitters2 publications

Pulmonary disease, chronic obstructive, susceptibility to; not specified

View on ClinVar →
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Research that mentions this SNP (2)

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Association between variants in vitamin D‐binding protein gene and vitamin D deficiency among pregnant women in china
AssociationN=815Jinju Dong et al.(2020)· Journal of Clinical Laboratory Analysis

This case-control association study of 815 Chinese pregnant women identified five SNPs in the GC (vitamin D-binding protein) gene significantly associated with serum 25-hydroxyvitamin D concentration: rs17467825, rs4588, rs2282679, rs2298850, and rs1155563. Mean 25(OH)D level was 15.67±7.98 ng/mL with 75% prevalence of deficiency. An XGBoost model incorporating these SNPs plus environmental factors achieved AUC 0.828 for predicting 25(OH)D deficiency risk. The study suggests maternal vitamin D deficiency may increase macrosomia risk (12 of 16 macrosomic infants had deficient mothers).

Traits studied:25-hydroxyvitamin D concentrationMacrosomiaVitamin D deficiency
PubMedDOIMetascience Observatory
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An analysis of the association between the vitamin D pathway and serum 25-hydroxyvitamin D levels in a healthy Chinese population
AssociationN=1,924Zeng Zhang et al.(2013)· Journal of Bone and Mineral Research

A cohort study of 1,924 very low birth weight preterm infants examined whether genetic predisposition for vitamin D deficiency (based on three SNPs: rs12794714, rs7944926, and rs2282679) was associated with adverse outcomes. The study found no significant associations between low genetic vitamin D level estimates and prematurity complications (IVH, PVL, BPD, NEC, sepsis, ROP), growth parameters, or bone fractures at age 5 years.

Traits studied:Bone fracturesBronchopulmonary dysplasia (BPD)Growth parametersIntraventricular hemorrhage (IVH)Necrotizing enterocolitis (NEC)Periventricular leukomalacia (PVL)Preterm birth outcomesRetinopathy of prematurity (ROP)SepsisVitamin D deficiency
PubMedDOIMetascience Observatory

About CYP2R1

This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This enzyme is a microsomal vitamin D hydroxylase that converts vitamin D into the active ligand for the vitamin D receptor. A mutation in this gene has been associated with selective 25-hydroxyvitamin D deficiency. [provided by RefSeq, Jul 2008]

View all CYP2R1 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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