chr12:47879112:A>C Detail (hg38) (VDR)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
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Information

Genome

Assembly	Position
hg19	chr12:48,272,895-48,272,895 View the variant detail on this assembly version.
hg38	chr12:47,879,112-47,879,112

HGVS

Type	Transcript	Protein
RefSeq	NM_001017535.1:c.2T>G	NP_001017535.1:p.?
	NM_000376.2:c.2T>G	NP_000367.1:p.?
	NM_001017536.1:c.152T>G	NP_001017536.1:p.Met51Arg
Ensemble	ENST00000229022.9:c.2T>G	ENST00000229022.9:p.?
	ENST00000395324.6:c.2T>G	ENST00000395324.6:p.?
	ENST00000549336.6:c.2T>G	ENST00000549336.6:p.?
	ENST00000550325.5:c.152T>G	ENST00000550325.5:p.Met51Arg

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

[No Data.]

Prediction

ClinVar

Clinical Significance	Uncertain significance
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
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Uncertain significance		no assertion criteria provided	Vitamin D-dependent rickets type II with alopecia	unknown	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.371	Diabetes Mellitus, Insulin-Dependent	Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs115...	BeFree	22960018	Detail
0.013	colorectal cancer	Unadjusted and adjusted hazard ratios for all-cause mortality (469 events) and C...	BeFree	24075799	Detail
0.020	Diabetes Mellitus, Insulin-Dependent	Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs115...	BeFree	22960018	Detail
0.012	colorectal carcinoma	Unadjusted and adjusted hazard ratios for all-cause mortality (469 events) and C...	BeFree	24075799	Detail
0.008	coronary artery disease	The aim of this study was to investigate the association between FokI (rs2228570...	BeFree	19563249	Detail
0.014	breast carcinoma	Two common single nucleotide polymorphisms (SNP) in the VDR gene (VDR), rs154441...	BeFree	19124512	Detail
0.066	Malignant neoplasm of breast	Two common single nucleotide polymorphisms (SNP) in the VDR gene (VDR), rs154441...	BeFree	19124512	Detail
0.061	Osteoporosis, Postmenopausal	The present study investigated the effect of two single nucleotide polymorphisms...	BeFree	25764158	Detail
<0.001	Acute Q fever	Single nucleotide polymorphisms (SNPs) in the IFNG (rs2430561/rs1861493), STAT1 ...	BeFree	25577174	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
0.126	Hypertensive disease	Our findings suggest that VDR genetic polymorphism rs2228570 is significantly as...	BeFree	25196087	Detail
0.018	hepatitis B	We conclude that the VDR rs2228570 and DBP rs7041 polymorphisms may contribute t...	BeFree	25541958	Detail
0.030	multiple sclerosis	The aim of this study is to measure plasma levels of OPG and RANKL as well as to...	BeFree	22805623	Detail
<0.001	diabetes mellitus	Logistic analysis confirmed that diabetes duration (odds ratio (OR) 1.108, P<...	BeFree	25899017	Detail
0.002	Diabetes	Logistic analysis confirmed that diabetes duration (odds ratio (OR) 1.108, P<...	BeFree	25899017	Detail
<0.001	Diabetes	Logistic analysis confirmed that diabetes duration (odds ratio (OR) 1.108, P<...	BeFree	25899017	Detail
<0.001	mitral valve stenosis	The aim of this study is to measure plasma levels of OPG and RANKL as well as to...	BeFree	22805623	Detail
0.003	Malignant neoplasm of breast	For example, breast cancer risk was associated with the GC rs7041 TT genotype (a...	BeFree	21693626	Detail
0.002	diabetes mellitus	Logistic analysis confirmed that diabetes duration (odds ratio (OR) 1.108, P<...	BeFree	25899017	Detail
0.016	Malignant neoplasm of ovary	[This pooled analysis provides further evidence that the VDR rs2228570 polymorph...	GAD	20473893	Detail
<0.001	breast carcinoma	For example, breast cancer risk was associated with the GC rs7041 TT genotype (a...	BeFree	21693626	Detail
0.016	Malignant neoplasm of ovary	The association of invasive ovarian carcinoma risk with the functional polymorph...	BeFree	20473893	Detail
0.002	ovarian carcinoma	The association of invasive ovarian carcinoma risk with the functional polymorph...	BeFree	20473893	Detail
0.003	Epithelial ovarian cancer	The association of invasive ovarian carcinoma risk with the functional polymorph...	BeFree	20473893	Detail

Annotation

Annotations

Descrption	Source	Links
NM_000376.3(VDR):c.2T>G (p.Met1Arg) AND Vitamin D-dependent rickets type II with alopecia	ClinVar	Detail
Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs11568820, PTPN2 rs18932...	DisGeNET	Detail
Unadjusted and adjusted hazard ratios for all-cause mortality (469 events) and CRC-specific mortalit...	DisGeNET	Detail
Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs11568820, PTPN2 rs18932...	DisGeNET	Detail
Unadjusted and adjusted hazard ratios for all-cause mortality (469 events) and CRC-specific mortalit...	DisGeNET	Detail
The aim of this study was to investigate the association between FokI (rs2228570) and BsmI (rs154441...	DisGeNET	Detail
Two common single nucleotide polymorphisms (SNP) in the VDR gene (VDR), rs1544410 (BsmI), and rs2228...	DisGeNET	Detail
Two common single nucleotide polymorphisms (SNP) in the VDR gene (VDR), rs1544410 (BsmI), and rs2228...	DisGeNET	Detail
The present study investigated the effect of two single nucleotide polymorphisms (SNPs) of the vitam...	DisGeNET	Detail
Single nucleotide polymorphisms (SNPs) in the IFNG (rs2430561/rs1861493), STAT1 (rs1914408), and VDR...	DisGeNET	Detail
A total of 9, 5, 3, and 7 studies were finally included in the analyses for the associations between...	DisGeNET	Detail
Our findings suggest that VDR genetic polymorphism rs2228570 is significantly associated with the de...	DisGeNET	Detail
We conclude that the VDR rs2228570 and DBP rs7041 polymorphisms may contribute to increased suscepti...	DisGeNET	Detail
The aim of this study is to measure plasma levels of OPG and RANKL as well as to analyze VDR FokI po...	DisGeNET	Detail
Logistic analysis confirmed that diabetes duration (odds ratio (OR) 1.108, P<0.01), SBP (OR 1.022...	DisGeNET	Detail
Logistic analysis confirmed that diabetes duration (odds ratio (OR) 1.108, P<0.01), SBP (OR 1.022...	DisGeNET	Detail
Logistic analysis confirmed that diabetes duration (odds ratio (OR) 1.108, P<0.01), SBP (OR 1.022...	DisGeNET	Detail
The aim of this study is to measure plasma levels of OPG and RANKL as well as to analyze VDR FokI po...	DisGeNET	Detail
For example, breast cancer risk was associated with the GC rs7041 TT genotype (age-adjusted odds rat...	DisGeNET	Detail
Logistic analysis confirmed that diabetes duration (odds ratio (OR) 1.108, P<0.01), SBP (OR 1.022...	DisGeNET	Detail
[This pooled analysis provides further evidence that the VDR rs2228570 polymorphism might influence ...	DisGeNET	Detail
For example, breast cancer risk was associated with the GC rs7041 TT genotype (age-adjusted odds rat...	DisGeNET	Detail
The association of invasive ovarian carcinoma risk with the functional polymorphism rs2228570 (aka r...	DisGeNET	Detail
The association of invasive ovarian carcinoma risk with the functional polymorphism rs2228570 (aka r...	DisGeNET	Detail
The association of invasive ovarian carcinoma risk with the functional polymorphism rs2228570 (aka r...	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: rs2228570 dbSNP
Genome: hg38
Position: chr12:47,879,112-47,879,112
Variant Type: snv
Reference Allele: A
Alternative Allele: C

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