chr12:47844974:A>G Detail (hg38) (VDR)

Information

Genome

Assembly Position
hg19 chr12:48,238,757-48,238,757 View the variant detail on this assembly version.
hg38 chr12:47,844,974-47,844,974

HGVS

Type Transcript Protein
RefSeq NM_001017535.1:c.1056T>C NP_001017535.1:p.Ile352=
NM_000376.2:c.1056T>C NP_000367.1:p.Ile352=
NM_001017536.1:c.1206T>C NP_001017536.1:p.Ile402=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.093
ToMMo:0.110
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.054

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 601769 OMIM
HGNC 12679 HGNC
Ensembl ENSG00000111424 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv45749333 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2021-12-05 criteria provided, multiple submitters, no conflicts Vitamin D-dependent rickets type II with alopecia germline Detail
Benign 2016-03-21 criteria provided, single submitter not specified germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Likely risk allele 2022-07-14 no assertion criteria provided hepatocellular carcinoma germline Detail
Benign 2023-04-20 no assertion criteria provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.001 melanoma In our hospital-based case-control study including 305 melanoma patients and 370... BeFree 22576141 Detail
<0.001 melanoma In our hospital-based case-control study including 305 melanoma patients and 370... BeFree 22576141 Detail
0.004 melanoma In our hospital-based case-control study including 305 melanoma patients and 370... BeFree 22576141 Detail
0.013 colorectal cancer Unadjusted and adjusted hazard ratios for all-cause mortality (469 events) and C... BeFree 24075799 Detail
0.012 colorectal carcinoma Unadjusted and adjusted hazard ratios for all-cause mortality (469 events) and C... BeFree 24075799 Detail
0.001 Diabetes Mellitus, Insulin-Dependent A total of 9, 5, 3, and 7 studies were finally included in the analyses for the ... BeFree 23209686 Detail
0.400 obesity Analysis of vitamin D receptor (VDR) TaqI (rs731236; T/C) and fat mass and obesi... BeFree 23103831 Detail
0.030 multiple sclerosis An association of two single-nucleotide polymorphisms (SNPs) of the vitamin D re... BeFree 19758194 Detail
0.007 mitral valve stenosis Analyses performed on HLA-DRB1*15-positive MS patients and HC alone confirmed th... BeFree 21664963 Detail
0.062 multiple sclerosis Analyses performed on HLA-DRB1*15-positive MS patients and HC alone confirmed th... BeFree 21664963 Detail
<0.001 Squamous cell carcinoma of the head and neck In a post-hoc analysis of our previous prospective cohort study, VDR polymorphis... BeFree 22242137 Detail
<0.001 Thyroid carcinoma Patients with thyroid carcinoma (n = 172) (n = 132 for papillary and n = 40 for ... BeFree 19499989 Detail
<0.001 schizophrenia Four single-nucleotide polymorphisms (SNPs; rs10735810/FokI, rs1544410/BsmI, rs7... BeFree 16634022 Detail
<0.001 Epithelial ovarian cancer The association of ovarian cancer risk with polymorphisms in the vitamin D recep... BeFree 18086759 Detail
0.003 Epithelial ovarian cancer The association of ovarian cancer risk with polymorphisms in the vitamin D recep... BeFree 18086759 Detail
<0.001 Thyroid carcinoma Patients with thyroid carcinoma (n = 172) (n = 132 for papillary and n = 40 for ... BeFree 19499989 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000376.3(VDR):c.1056T>C (p.Ile352=) AND Vitamin D-dependent rickets type II with alopecia ClinVar Detail
NM_000376.3(VDR):c.1056T>C (p.Ile352=) AND not specified ClinVar Detail
NM_000376.3(VDR):c.1056T>C (p.Ile352=) AND not provided ClinVar Detail
NM_000376.3(VDR):c.1056T>C (p.Ile352=) AND Hepatocellular carcinoma ClinVar Detail
NM_000376.3(VDR):c.1056T>C (p.Ile352=) AND Periodontitis ClinVar Detail
In our hospital-based case-control study including 305 melanoma patients and 370 healthy controls si... DisGeNET Detail
In our hospital-based case-control study including 305 melanoma patients and 370 healthy controls si... DisGeNET Detail
In our hospital-based case-control study including 305 melanoma patients and 370 healthy controls si... DisGeNET Detail
Unadjusted and adjusted hazard ratios for all-cause mortality (469 events) and CRC-specific mortalit... DisGeNET Detail
Unadjusted and adjusted hazard ratios for all-cause mortality (469 events) and CRC-specific mortalit... DisGeNET Detail
A total of 9, 5, 3, and 7 studies were finally included in the analyses for the associations between... DisGeNET Detail
Analysis of vitamin D receptor (VDR) TaqI (rs731236; T/C) and fat mass and obesity-associated (FTO) ... DisGeNET Detail
An association of two single-nucleotide polymorphisms (SNPs) of the vitamin D receptor (VDR) gene, A... DisGeNET Detail
Analyses performed on HLA-DRB1*15-positive MS patients and HC alone confirmed the protective role of... DisGeNET Detail
Analyses performed on HLA-DRB1*15-positive MS patients and HC alone confirmed the protective role of... DisGeNET Detail
In a post-hoc analysis of our previous prospective cohort study, VDR polymorphisms including Cdx2 G/... DisGeNET Detail
Patients with thyroid carcinoma (n = 172) (n = 132 for papillary and n = 40 for follicular) and HC (... DisGeNET Detail
Four single-nucleotide polymorphisms (SNPs; rs10735810/FokI, rs1544410/BsmI, rs7975232/ApaI, and rs7... DisGeNET Detail
The association of ovarian cancer risk with polymorphisms in the vitamin D receptor (VDR) gene, incl... DisGeNET Detail
The association of ovarian cancer risk with polymorphisms in the vitamin D receptor (VDR) gene, incl... DisGeNET Detail
Patients with thyroid carcinoma (n = 172) (n = 132 for papillary and n = 40 for follicular) and HC (... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs731236 dbSNP
Genome
hg38
Position
chr12:47,844,974-47,844,974
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1183
Mean of sample read depth (HGVD)
40.90
Standard deviation of sample read depth (HGVD)
17.89
Number of reference allele (HGVD)
2146
Number of alternative allele (HGVD)
220
Allele Frequency (HGVD)
0.09298393913778528
Gene Symbol (HGVD)
VDR
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs731236
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1103
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1849
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8636
East Asian Allele Counts (ExAC)
467
East Asian Heterozygous Counts (ExAC)
449
East Asian Homozygous Counts (ExAC)
9
East Asian Allele Frequency (ExAC)
0.05407596109309866
Chromosome Counts in All Race (ExAC)
121340
Allele Counts in All Race (ExAC)
40509
Heterozygous Counts in All Race (ExAC)
25499
Homozygous Counts in All Race (ExAC)
7505
Allele Frequency in All Race (ExAC)
0.33384704137135324
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