Important Variant Information for VDR
Submitted by: Audrey H. Poon, Charlotte Brasch-Andersen, Augusto A. Litonjua, Benjamin A. Raby, Scott T. Weiss (PHAT)
Reviewed by: Reviewed
Submitted date: May 22, 2006
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- VDR Overview
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There are Nine Important Variants for VDR.
- VDR: Cdx2 (rs11568820)
- VDR: FokI (rs10735810)
- VDR: rs3782905
- VDR: rs2239179
- VDR: rs1540339
- VDR: rs2239185
- VDR: BsmI (rs1544410)
- VDR: ApaI (rs7975232)
- VDR: TaqI (rs731236)
| Gene HGNC Name: | VDR |
|---|---|
| Variant Summary: | This variant is commonly known as Cdx2 due to its location in the binding site of transcription factor Cdx2. It is located in the promoter region, upstream of exon 1e [PMID: 9933478]. Functional analyses showed that the A to G base substitution (referring to the minus strand) eliminates the Cdx binding site and reduces transcriptional activity of VDR to 70% of the A allele [PMID: 11450701]. There have been reports of the A allele being associated with fracture protection and prostate cancer risk [PMID: 12968672, 14991752]; however, confirmations await. |
| Key PubMed IDs: | 9933478, 11450701, 12968672, 14991752 |
| Genomic Variant & GenBank ID: | 10,445,851 C>T on NT_029419 |
| mRNA Variant & GenBank ID: | NA |
| Protein Variant & GenBank ID: | NA |
| dbSNP rs#: | rs11568820 |
| GoldenPath Position: | chr12:46,588,812 (hg18) |
| Key Drugs/Substrates: | This variant is located at the binding site for the intestine-specific transcription factor Cdx2 [PMID: 11450701]. Refer to VDR Overview for information on drugs/substrates which interact with VDR. |
| Key Phenotypes/Diseases: | Hip fracture incidence [PMID: 12968672], and prostate cancer [PMID: 14991752]. |
| Gene HGNC Name: | VDR |
|---|---|
| Variant Summary: | This variant is commonly known as FokI [PMID: 1652893 (PS203466)]. The base change eliminates the translation start site in exon 2 and the encoded protein is shortened by 3 amino acids. The smaller protein exhibits greater transcription activity due to its greater binding efficiency to transcription factor IIB [PMID: 10707958]. Allele C(referring to the minus strand) is associated with greater baseline airways obstruction [PMID: 15282200]. The same allele is also associated with prostate cancer risk in African Americans [PMID: 15298953]. Allele T is associated with pulmonary TB risk in Chinese [PMID: 15141734 ] and breast cancer in Caucasian women [PMID: 16214913]. In an Australian study of postmenopausal women, in the presence of calcium therapy, allele T confers fracture risk [PMID: 15861036 (PA135307235)]. |
| Key PubMed IDs: | 15282200, 10707958, 15298953, 15141734, 16214913 , 15861036 |
| Genomic Variant & GenBank ID: | 10,416,201 A > G on NT_029419 |
| mRNA Variant & GenBank ID: | 162 T > C on NM_000376 |
| Protein Variant & GenBank ID: | 1 Met > Thr on NP_000367 |
| dbSNP rs#: | rs10735810 |
| GoldenPath Position: | chr12:46,559,162 (hg18) |
| Key Drugs/Substrates: | Refer to VDR Overview for information on drugs/substrates which interact with VDR. |
| Key Phenotypes/Diseases: | Baseline airways obstruction [PMID: 15282200], prostate cancer [PMID: 15298953], TB [PMID: 15141734], breast cancer [PMID: 16214913], and fracture risk [PMID: 15861036 (PA135307235)] |
| Phenotype Data Sets: | PA136096708 and PA126753360 |
3. VDR: rs3782905
| Gene HGNC Name: | VDR |
|---|---|
| Variant Summary: | This variant is located in intron 2. Allele C (referring to the minus strand) is associated with asthma susceptibility in childhood and adult asthma [PMID: 15282199, 15282200]. |
| Key PubMed IDs: | 15282199, 15282200 |
| Genomic Variant & GenBank ID: | 10,409,473 G>C on NT_029419 |
| mRNA Variant & GenBank ID: | NA |
| Protein Variant & GenBank ID: | NA |
| dbSNP rs#: | rs3782905 |
| GoldenPath Position: | chr12:46,552,434 (hg18) |
| Key Drugs/Substrates: | Refer to VDR Overview for information on drugs/substrates which interact with VDR. |
| Key Phenotypes/Diseases: | Asthma [PMID: 15282199, 15282200], and allergy skin test [PMID: 15282199] |
| Gene HGNC Name: | VDR |
|---|---|
| Variant Summary: | This variant is located in intron 3. Allele G(referring to the minus strand) is associated with lower bronchodilator responsiveness [PMID: 15282200]. |
| Key PubMed IDs: | 15282200 |
| Genomic Variant & GenBank ID: | 10,401,072 T>C on NT_029419 |
| mRNA Variant & GenBank ID: | NA |
| Protein Variant & GenBank ID: | NA |
| dbSNP rs#: | rs2239179 |
| GoldenPath Position: | chr12:46,544,033 (hg18) |
| Key Drugs/Substrates: | Refer to VDR Overview for information on drugs/substrates which interact with VDR |
| Key Phenotypes/Diseases: | Bronchodilator responsiveness [PMID: 15282200] |
| Gene HGNC Name: | VDR |
|---|---|
| Variant Summary: | This variant is located in intron 3. Allele G (referring to the minus strand) is associated with asthma susceptibility [PMID: 15282199] and lower bronchodilator responsiveness [PMID: 15282200]. |
| Key PubMed IDs: | 15282199, 15282200 |
| Genomic Variant & GenBank ID: | 10,400,632 C>T on NT_029419 |
| mRNA Variant & GenBank ID: | NA |
| Protein Variant & GenBank ID: | NA |
| dbSNP rs#: | rs1540339 |
| GoldenPath Position: | chr12:46,543,593 (hg18) |
| Key Drugs/Substrates: | Refer to VDR Overview for information on drugs/substrates which interact with VDR |
| Key Phenotypes/Diseases: | Bronchodilator responsiveness [PMID: 15282200] |
| Gene HGNC Name: | VDR |
|---|---|
| Variant Summary: | This variant is located in intron 6. Allele C (referring to the minus strand) is associated with (1) asthma susceptibility in childhood and adult asthma [PMID: 15282199, 15282200], (2) high IgE level in a French Canadian childhood asthma cohort [PMID: 15282199], and (3) low IgE level in an American childhood asthma cohort after stratification by gender where association was observed in girls [PMID: 15282200]. |
| Key PubMed IDs: | 15282199, 15282200 |
| Genomic Variant & GenBank ID: | 10,387,865 G>A on NT_029419 |
| mRNA Variant & GenBank ID: | NA |
| Protein Variant & GenBank ID: | NA |
| dbSNP rs#: | rs2239185 |
| GoldenPath Position: | chr12:46,530,826 (hg18) |
| Key Drugs/Substrates: | Refer to VDR Overview for information on drugs/substrates which interact with VDR |
| Key Phenotypes/Diseases: | Asthma [PMID: 15282199, 15282200], serum total IgE level [PMID: 15282199, 15282200], and allergy skin test response [PMID: 15282199]. |
| Gene HGNC Name: | VDR |
|---|---|
| Variant Summary: | This variant is commonly known as BsmI and it is located in intron 8. Inconsistent findings of its genetic effects in BMD exist (reviewed in [PMID: 15225770]); however, a meta analysis concluded that allele A(referring to the minus strand) is associated with lower spine BMD and greater bone loss at lumbar spine in postmenopausal women [PMID: 15040830]. Similarly, its genetic effect on IDDM [PMID: 12843155, 10792336, 9267994] and breast cancer [PMID: 16214913, 15328186] are also unclear. Genotype AA is associated with greater improvement in BMD after alendronate plus raloxifene therapy [PMID: 15739035]. Genotype AA is associated with myocardial infarction in a German study [PMID: 16207551]. Allele G is associated with prostate cancer in Japanese [PMID: 10667581]. Genotype GG is associated with greater improvement in bone turnover markers after administration of alendronate plus raloxifene therapy [PMID: 15739035]. Allele G is also associated with hyperparathyroidism in Japanese and Caucasians [PMID: 9740163, 9070272]. The genetic effect of BsmI in breast cancer risk is unclear. |
| Key PubMed IDs: | 15225770, 15040830, 12843155, 10792336, 9267994, 16214913, 15328186, 15739035, 10667581, 15739035, 9740163, 9070272 |
| Genomic Variant & GenBank ID: | 10,438,141 C>T on NT_029419 |
| mRNA Variant & GenBank ID: | NA |
| Protein Variant & GenBank ID: | NA |
| dbSNP rs#: | rs1544410 |
| GoldenPath Position: | chr12:46,526,102 (hg18) |
| Key Drugs/Substrates: | Refer to VDR Overview for information on drugs/substrates which interact with VDR. |
| Key Phenotypes/Diseases: | Bronchodilator responsiveness [PMID: 15282200], prostate cancer [PMID: 10667581, 15050735], breast cancer [PMID: 16214913], BMD [PMID: 8703580, 9200004], IDDM [PMID: 10792336, 10868975, 10792336] and osteoporosis therapy efficacy [PMID: 15739035]. |
| Phenotype Data Sets: | PA136096708 and PA126753360 |
8. VDR: ApaI (rs7975232)
| Gene HGNC Name: | VDR |
|---|---|
| Variant Summary: | This variant is commonly known as ApaI and is located in intron 8. Allele C(referring to the plus strand) is associated with (1) asthma susceptibility in childhood and adult asthma [PMID: 15282200], (2) high IgE level in childhood asthma [PMID: 15282199], and (3) atopy [PMID: 15282199]. In a global haplotype containing allele C of the FokI, allele A of ApaI is associated with pulmonary TB in West Africans [PMID: 15478069]. Allele A is also found to be associated with psoriasis occurrence in Koreans [PMID: 9886274]. |
| Key PubMed IDs: | 15282200, 15282199, 15478060, 9886274 |
| Genomic Variant & GenBank ID: | 10,382,143 C>A on NT_029419 |
| mRNA Variant & GenBank ID: | NA |
| Protein Variant & GenBank ID: | NA |
| dbSNP rs#: | rs7975232 |
| GoldenPath Position: | chr12:46,525,104 (hg18) |
| Key Drugs/Substrates: | Refer to VDR Overview for information on drugs/substrates which interact with VDR. |
| Key Phenotypes/Diseases: | Asthma [PMID: 15282200], serum total IgE level [PMID: 15282199, 15282200], allergy skin test response [PMID: 15282199] and TB [PMID: 15478069] |
| Gene HGNC Name: | VDR |
|---|---|
| Variant Summary: | This variant is commonly known as TaqI and it is located in exon 9. Allele T(referring to the minus strand) is associated with (1) asthma susceptibility in childhood and adult asthma [PMID: 15282199, 15282200], and (2) high IgE level in a French Canadian childhood asthma cohort [PMID: 15282199]. Allele C is associated with low IgE level in an American childhood asthma cohort after stratification by gender where association was observed in girls [PMID: 15282200] . The TT genotype is associated with TB susceptibility, and the TT and TC genotypes, in the presence of vitamin D3 deficiency confer risk for TB in Gujarati Asians living in the United Kingdom [PMID: 10696983] . Genotype CC has been found to be a protective factor for TB in Africans [PMID: 9952386] . In a multivariate study investigating the interaction between therapy and VDR variants, in the presence of calcium treatment, allele C confers risk to new fracture in a postmenopausal women study in Australia [PMID: 15861036 (PA135307235 )]. The direction of association with prostate cancer is unclear [PMID: 8797574, 12181642]. |
| Key PubMed IDs: | 15282199, 15282200, 10696983, 9952386, 15861036, 8797574, 12181642 |
| Genomic Variant & GenBank ID: | 10,382,063 A>G on NT_029419 |
| mRNA Variant & GenBank ID: | 1216 T>C on NM_000376 |
| Protein Variant & GenBank ID: | 352 Ile>Ile on NP_000367 |
| dbSNP rs#: | rs731236 |
| GoldenPath Position: | chr12:46,525,024 (hg18) |
| Key Drugs/Substrates: | Refer to VDR Overview for information on drugs/substrates which interact with VDR. |
| Key Phenotypes/Diseases: | Asthma [PMID: 15282199, 15282200], serum total IgE level [PMID: 15282199, 15282200], atopy [PMID: 15282199], TB [PMID: 10696983, 9952386], osteoporosis [PMID: 15861036(PA135307235 )], and prostate cancer [PMID: 8797574, 12181642]. |