Identification and analysis of 35 genes associated with vitamin D deficiency: A systematic review to identify genetic variants

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GeneAbstractsLvlCategorySub-CategoryNotes
VDR8859.9Experimental evidence of functional variant 12468277,
PTH1669.9Other evidence of a functional genetic variantGWAS/rs in intergenic regions or haplotypes26339419 Nearest gene ~4600 bp
GC1419.9Experimental evidence of functional variant22887780
CYP24A11409.9Experimental evidence of functional variant23001465 23293122 Related to vitamin D pathway (CYP24A1 is a vitamin D responsive gene) Associated with elevated serum levels of 1,25-dihydroxyvitamin D3
CYP2R11399.9Experimental evidence of functional variant15128933
CYP27B11159.9Experimental evidence of functional variant10566658 17488797 22588163
DHCR7799.9Other evidence of a functional genetic variantGWAS/rs within gen27732326 rs11603330
BGLAP689.9Biologically related but no mutation
DBP639.9Annotation errorDBP:D-box binding PAR bZIP transcription factor NOT vitamin D binding protein
CASR459.9Genetic variant in a related disease
CDX2419.9UnrelatedCDX2: enzyme
FGF23379.9Biologically related but no mutation
RXRA369.9Other evidence of a functional genetic variantGWAS/rs in intergenic regions or haplotypes20307661 Associated with circulating levels of vitamin D metabolites ~8 kb 28079136 Significantly associated with 25(OH)D dose-response
NADSYN1359.9Other evidence of a functional genetic variantGWAS/rs within gen20418485: rs3829251 22785457: rs10898191 26149120: rs12785878
CYP27A1279.9Other evidence of a functional genetic variantGWAS/rs within gen29153269 (rs933994) 26109216 (rs17470271) The genotype distributions of 13 SNPs (in the following genes: 7-dehydrocholesterol reductase NADSYN1/ DHCR7, vitamin D receptor VDR, group-specific component GC and CYP27A1) that showed a nominal association with 25-hydroxyvitamin D concentration (p<0.05) were compared between case and control families.
ESR1277.6Genetic variant in a related disease
ZNF410:Apa1(22)249.9Biologically related but no mutation
PHEX229.9Genetic variant in a related disease
SLC25A18:Gc2(13)209.9Annotation errorGc2 is isoform of GC not Glutamate Carrier 2
INS:insulin(26)190Biologically related but no mutation
CRP180Negative evidence29320465: No 25(OH)D-CRP genotype interactions were evident
IL6170Unrelated
HLA-DRB1145.8Genetic variant in a related disease
ALAD139.9Unrelated
ALPP:alkaline phosphatase(15)139.9Biologically related but no mutation
IGF1130.3Unrelated
IL10139.9Unrelated
TGFB1130Genetic variant in a related disease
CYP3A4112.8Experimental evidence of functional variant29461981
IFNL3:IL28B(9)119.9Negative evidenceNo relationships were found between 25(OH)D levels and biochemical liver tests, fibrosis stage and IL28B genotype (HCV infection)
LRP2119.9Other evidence of a functional genetic variantGWAS/rs in intergenic regions or haplotypes29153269: Haplotypes of GC and LRP2 genes shown significant associations with 25(OH)D levels among pregnant women, respectively. (Other evidence of genetic alteration).
TNFRSF11B116.8Genetic variant in a related disease
SLC25A22:Gc1(8)119.9Annotation errorGc1: isoform of GC not Glutamate Carrier 1
GNAS108.4Unrelated
COL1A197.7Unrelated
GALNT399.9Unrelated
APOE90.5Unrelated
IL490Genetic variant in a related disease(Undefined)21819409
TF:transferrin(7)90.3Unrelated
TNF99.9Unrelated
COL1A286Biologically related but no mutation
SLC34A389.9Genetic variant in a related disease
AR81.1Genetic variant in a related disease
CUBN89.9Experimental evidence of functional variant11717447 Human patients with mutations causing cubilin dysfunction exhibit urinary excretion of 25(OH) vitamin D(3).
KL88.9Genetic variant in a related disease26022923 Renal transplant (RT) recipients with FV phenotype had significantly lower levels of 1,25D compared to both recipients with FF phenotype and control subjects, whereas the level of 1,25D in RT recipients with FF phenotype was significantly higher than control subjects ( table 6 ). The level of 1,25D correlated negatively with KL polymorphism (r = _0.538, p = 0.006) in RT recipients
KLK3:prostate-specific antigen(4)70Biologically related but no mutation
LCT75.7Biologically related but no mutation
MC1R77.2Genetic variant in a related disease
SHBG72.2Unrelated
CTNNB160Negative evidence25396269
ACE60Genetic variant in a related disease
EGFR60Genetic variant in a related disease25030993
ALPL68.4Unrelated
IFNG60Biologically related but no mutation
KRAS60Biologically related but no mutation
MTHFR61.4Genetic variant in a related disease
TRPV669.1Biologically related but no mutation
SP161.1Unrelated
TNFSF1169.9Genetic variant in a related disease
CFTR59.9Biologically related but no mutation
FLG54.8Experimental evidence of functional variant23460889 FLG mutations is associated with increased serum 25-hydroxyvitamin D concentrations.
CXCL8:IL-8(3)50Biologically related but no mutation
IL17A50.2Biologically related but no mutation
ATHS:ALP(5)53.6Annotation errorALP: is refered to alkaline phosphatase (gene name: ALPL)
NELFCD:Th1(7)50Biologically related but no mutation
MED1:DRIP205(4)57.3Biologically related but no mutation
PTHLH:PTHrP(4)52.5Unrelated
CCL250Biologically related but no mutation
SPP1:osteopontin(5)51Biologically related but no mutation
BRAF50.1Genetic variant in a related disease
TP5350Biologically related but no mutation
CD459.9Biologically related but no mutation
CD8A:CD8(5)59.9Biologically related but no mutation
NCOA244.9Biologically related but no mutation
COX8A:Cox(3)40Annotation error
CYP17A142.4Unrelated
AGT40Unrelated
ERBB2:HER2(3)40Unrelated
GSTM141.2Unrelated
GSTP141.5Unrelated
HLA-DQB141Genetic variant in a related disease
IGHE:IgE(3)41.3Biologically related but no mutation
IRF443.9Genetic variant in a related disease
GSTK1:glutathione S-transferase(3)40.7Unrelated
LRP543.7Negative evidence
CYP4F3:cytochrome P450, family 2(2)40.2Annotation errorDescription of CYP2R1 not CYP4F3
MEFV42.5Genetic variant in a related disease
SERPINC140Biologically related but no mutation
NOS3:endothelial nitric oxide synthase(5)40.6Unrelated
VIT44.5Annotation errorVIT: is refered to Vitamin not Vitrin
SERPINA1:alpha-1-antitrypsin(2)40Unrelated
NOD242.1Genetic variant in a related disease
SLC34A147.9Unrelated
FTO42.7Genetic variant in a related disease
C10orf8849.9Negative evidence20418485
NCOA145.2Biologically related but no mutation
NR1I242.4Biologically related but no mutation
ADIPOQ40Unrelated
SLCO1B132.3Genetic variant in a related disease21547103 29420305
COL2A139.9Genetic variant in a related disease
AFP30Unrelated
DMP133.4Unrelated
EDN130Other evidence of a functional genetic variantGWAS/rs in intergenic regions or haplotypes25396269 Intergenic region
F2:METAVIR F0, F1 and F2(1)30Annotation errorMETAVIR F0, F1 and F2: Liver damage scale
GAPDH30.5Biologically related but no mutation
GATA331.4Unrelated
GH130Genetic variant in a related disease
GSTT131.1Unrelated
CFH31.2Genetic variant in a related disease
IGFBP330.2Biologically related but no mutation
IL2:IL-2(2)30Biologically related but no mutation
IL2RA30Biologically related but no mutation
IL12B33Genetic variant in a related disease
MYC:c-myc(3)30Biologically related but no mutation
ENPP133.6Unrelated
PIK3CA30.5Genetic variant in a related disease
PPARA:PPAR(5)30.1Biologically related but no mutation
PTPRN:IA-2(2)32.2Unrelated
CCND1:cyclin D1(2)30Biologically related but no mutation
REN:renin(5)39.9Biologically related but no mutation
RXRB34.8Genetic variant in a related disease
RXRG36.9Genetic variant in a related disease
CCL530.1Biologically related but no mutation
TYR30.5Unrelated
TYRP139.9Other evidence of a functional genetic variantGWAS/rs in intergenic regions or haplotypes
CALCR32.5Genetic variant in a related disease
SELENBP1:SBP(3)30.1Annotation errorSBP is refered to systolic blood pressure
GLYAT:GAT(1)22Annotation errorGAT is refered to nucleotide polymorphism not gene
TCIRG123.5Unrelated
SEC23A25.2Other evidence of a functional genetic variantGWAS/rs within gen
OLFM4:Gc1/1(1)23.5Annotation error
TXNIP22.3Negative evidence
RGS1424.7Unrelated
MGEA5:N-acetyl-beta-D-glucosaminidase(2)20.4Unrelated
CEACAM3:CEA(2)20Unrelated
APOA529.9Genetic variant in a related disease
CLU:clusterin(2)21.1Unrelated
CCR520Unrelated
CP:ceruloplasmin(2)20.1Unrelated
AMDHD128.2Other evidence of a functional genetic variantGWAS/rs within gen
ADRA1D:alpha-1(2)20.1Unrelated
CST3:cystatin C(1)20Unrelated
IL23R21.7Unrelated
CTLA420Unrelated
CYP19A120.4Unrelated
TMPRSS629.9Unrelated
DHX15:DBP1(1)24.3Annotation errorDBP: Vitamin D binding protein, not the gen
AHSG:fetuin-A(3)21.3Biologically related but no mutation
EPHB221.4Biologically related but no mutation
EPO20Biologically related but no mutation
MS4A223.9Genetic variant in a related disease
FGB:fibrinogen(2)20Unrelated
COG2:low-density lipoprotein-C(1)20.3Annotation error
DKK129.9Biologically related but no mutation
CLDN1424.7Unrelated
MTOR20Biologically related but no mutation
GAD2:GAD(65)(1)21.1Unrelated
COPD20Annotation errorCOPD: Chronic obstructive pulmonary disease not gene
SLC17A5:AST(2)29.9Annotation error
AMH20.4Biologically related but no mutation
GLI2:THP-1(2)20Biologically related but no mutation
GPT:alanine aminotransferase(2)20Unrelated
IGKV1D-17:L1-4(2)29.9Annotation errorL1-4
HBA120Biologically related but no mutation
HFE20.6Unrelated
HLA-B20Other evidence of a functional genetic variantGWAS/rs within gen27623983
HRAS20.2Unrelated
IL4R21.1Unrelated
IL1320Genetic variant in a related disease
ACADSB25.9Negative evidence
INSR20Unrelated
ARMS222.7Biologically related but no mutation
LMNA29.9Unrelated
LTA:TNFB(1)20.8Unrelated
SMAD320.4Genetic variant in a related disease
MEN120.6Unrelated
KITLG20Negative evidence
MITF21.2Negative evidence
MMP920Biologically related but no mutation
COX220Unrelated
NF120Unrelated
NFKB1:NF-kappaB(1)20Biologically related but no mutation
OCRL23.2Unrelated
PDE3B22.7Other evidence of a functional genetic variantGWAS/rs within gen25208829
IL23A:IL-23(2)29.9Biologically related but no mutation
ABCB1:MDR1(2)20Genetic variant in a related disease
ATP7B21.6Unrelated
POMC20Unrelated
CHD729.9Unrelated
ST6GALNAC1:StyI(2)24.2Unrelated
B2M:beta(2)-microglobulin(1)20Unrelated
MEPE23.7Unrelated
FAM20C24.4Unrelated
PTGS220Unrelated
PTH1R21.9Genetic variant in a related disease
RARA:RAR(2)20.5Biologically related but no mutation
RARB21.2Genetic variant in a related disease
BCL2:bcl-2(3)20Biologically related but no mutation
RET29.9Unrelated
SHMT1:SHMT(2)23Biologically related but no mutation
SRD5A222.5Genetic variant in a related disease
BRCA120Unrelated
SSTR423.7Other evidence of a functional genetic variantGWAS/rs in intergenic regions or haplotypes
SULT2A120.9Other evidence of a functional genetic variantGWAS/rs within gen29343609 Further analysis revealed a significant association between a common SNV within intron-1 of SULT2A1 (rs296361; MAF = 15% in Whites) and liver cytosolic SULT2A1 content as well as 25OHD3-3-O-sulfate formation rate, suggesting that variation in the SULT2A1 gene contributes importantly to inter-individual differences in vitamin D homeostasis.
TBX1:TGA(2)20.5Annotation errorTGA: stop codon, no the gene
BTF3P11:OPG(2)21.7Unrelated
TLR2:TLR-2(2)20Genetic variant in a related disease
TMPRSS221.7Unrelated
UPP124.5Genetic variant in a related disease
WT120.3Genetic variant in a related disease
CALB121.7Genetic variant in a related disease
ANKRD5526.2Unrelated
PNPLA322.1Genetic variant in a related disease
AAAS23.6Unrelated
APOL122.4Unrelated
CAV120.1Unrelated
RUNX220.1Biologically related but no mutation
STX1624.2Biologically related but no mutation
SQSTM121.2Unrelated
CD2829.9Biologically related but no mutation
NCOR1:N-CoR(2)21.8Unrelated
NCOR222.1Biologically related but no mutation
NR1I321.5Unrelated
CDH120Biologically related but no mutation
NAT210Unrelated
C20orf181:insulin growth factor-1, tissue plasminogen activator(1)10Biologically related but no mutation
TRAP10Unrelated
MAMLD1:F-18(1)10Unrelated
SNHG1610Unrelated
ABCB6:ABC(1)10Annotation error
CDKN2B10Biologically related but no mutation
TUBB310Negative evidence
GNB2L1:RACK1(1)10Negative evidence
LYPLA1:i(2)10Annotation error
SLC9A610Unrelated
CARM1:CARM-1(1)10Negative evidence
CEBPA:C/EBP(1)10Unrelated
MYBBP1A:p160(2)10Unrelated
NEBL10Other evidence of a functional genetic variantGWAS/rs within gen27579147 rs10828183
BATF10Unrelated
AGPAT210Genetic variant in a related disease
IFI44:p44(1)10Unrelated
SLC34A210Unrelated
EBP10Unrelated
HCP5:P5; -1,85 SD(1)10Annotation error
RAB3210Unrelated
IMMT:HMP(1)10Annotation errorHMP: homozygous for the major polymorphisms
IL24:IL-24(1)10Unrelated
CHGA:CGA(1)10Annotation errorCGA stop codon not gene
BAZ1A10Genetic variant in a related disease
PKP310Genetic variant in a related disease
IL17F:IL-17F(2)10Unrelated
CHRM3:Pb-S(1)10Annotation errorPb: lead no the gene
SLC46A1:PCFT(1)10Unrelated
NLRP310Unrelated
TIRAP10Biologically related but no mutation
PGLYRP2:Tagl(1)10Unrelated
MOGAT1:DC2(1)10Annotation errorCD2: dendritic cells not the gene
TAGAP10Biologically related but no mutation
AP2S110Genetic variant in a related disease
CLCN510Unrelated
SLC24A410Negative evidence
ABCC210Biologically related but no mutation
FAM210A10Genetic variant in a related disease
CNR110Negative evidence
PROKR210Unrelated
COMT10Unrelated
IL31RA10Unrelated
CLDN410Unrelated
CLDN310Unrelated
CREBBP:CBP(1)10Biologically related but no mutation
CRIP2:CRP2(1)10Negative evidence
CHODL10Unrelated
PARP1:poly(ADP ribose) polymerase-1, haeme oxygenase-1(1)10Biologically related but no mutation
SESN310Biologically related but no mutation
CTNS:cystinosin(1)10Unrelated
CTSB:cathepsin B(1)10Biologically related but no mutation
CTSD:cathepsin D(2)10Unrelated
CYP1A110Genetic variant in a related disease
CYP1B110Genetic variant in a related disease(Undefined)
ADRB3:beta 3 adrenergic receptor(1)10Unrelated
CYP2C810Unrelated
CYP2C910Genetic variant in a related disease
CYP2D610Genetic variant in a related disease
CYP11A110Biologically related but no mutation
DAB110Other evidence of a functional genetic variantGWAS/rs within gen26704534 rs6680429
DBH10Unrelated
DCT:dopachrome tautomerase(1)10Negative evidence
HFM1:helicase(1)10Unrelated
DDB210Genetic variant in a related disease
DDC:L-amino acid decarboxylase(1)10Unrelated
DEFB4A:defensin beta2(2)10Biologically related but no mutation
DHFR10Biologically related but no mutation
DIO210Unrelated
DIO3:D(3)(1)10Annotation error
DSC3:dsc-4(1)10Unrelated
DSPP10Unrelated
AGTR110Unrelated
EDN310Negative evidence
EDNRB10Negative evidence
EGR1:Egr-1(1)10Unrelated
ANO610Other evidence of a functional genetic variantGWAS/rs in intergenic regions or haplotypes
ARID210Other evidence of a functional genetic variantGWAS/rs in intergenic regions or haplotypes
CRYGEP:G0, G1, or G2(1)10Unrelated
ENG:endoglin(2)10Unrelated
ENO2:NSE(1)10Unrelated
ENPEP:Apa(1)10Unrelated
ERCC210Genetic variant in a related disease
AKT1:AKT(1)10Unrelated
ESR2:estrogen receptor beta(2)10Biologically related but no mutation
ETS1:Ets-1(2)10Unrelated
ETS210Genetic variant in a related disease
ETV1:ETS variant 1(1)10Biologically related but no mutation
ALB10Biologically related but no mutation
EXT110Genetic variant in a related disease
EXT210Genetic variant in a related disease
FABP210Unrelated
TPCN210Negative evidence
FBN110Genetic variant in a related disease
FCER1A10Genetic variant in a related disease
FCER1G10Genetic variant in a related disease
FCGR2A:FC gamma receptor IIA(1)10Unrelated
FCGR3A:CD16(1)10Unrelated
SCUBE310Genetic variant in a related disease
FDX110Biologically related but no mutation
FDXR:adrenodoxin reductase(1)10Unrelated
FECH:ferrochelatase(1)10Unrelated
FEN1:flap endonuclease 1(1)10Biologically related but no mutation
FGF210Negative evidence
FGF810Unrelated
FGFR110Unrelated
FGFR310Genetic variant in a related disease
ZNF36510Unrelated
SNW1:SKIIP(1)10Biologically related but no mutation
FOXO110Biologically related but no mutation
FOXO3:FoxO3a(1)10Biologically related but no mutation
PLCB110Genetic variant in a related disease
CLEC16A10Unrelated
SIRT310Unrelated
FOLR1:folate receptor alpha(1)10Unrelated
CLEC5A10Unrelated
ALOX5:5-lipoxygenase(2)10Biologically related but no mutation
ALPI10Biologically related but no mutation
GAST:gastrin(1)10Unrelated
FUT210Unrelated
ST6GALNAC310Biologically related but no mutation
GALT10Unrelated
ASPM10Unrelated
NSMF:NELF(1)10Unrelated
ABCA1210Unrelated
PTPN2210Unrelated
GATA1:GATA-1(1)10Unrelated
BLOC1S6:PLDN(1)10Negative evidence
ERAL1:era(2)10Annotation error
BSCL2:seipin(1)10Unrelated
GFAP10Unrelated
GGCX10Unrelated
GHSR10Unrelated
ATP2C110Unrelated
DIEXF:DEF(1)10Annotation error
RSPH14:RTDR1(1)10Unrelated
GLB1:beta-galactosidase(1)10Biologically related but no mutation
SULT1C410Unrelated
SESN110Biologically related but no mutation
SULT1B110Unrelated
TOX310Unrelated
GNA1110Unrelated
GNRH110Unrelated
GNRHR10Unrelated
ABO10Unrelated
GPR3:ACCA(1)10Annotation errorhaplotypes ACCA, not gene
LINC0034610Genetic variant in a related disease
IGHV3-69-1:immunoglobulin heavy chain variable (IGHV)(1)10Genetic variant in a related disease
KIF4B10Other evidence of a functional genetic variantGWAS/rs in intergenic regions or haplotypes
ANK310Unrelated
GRB1010Genetic variant in a related disease
IGKV1D-8:L2-4(1)10Annotation errorvertebrae L2-4 not gene
PDIA310Biologically related but no mutation
GSTM2:GSTM(1)10Unrelated
GZMA:granzyme A(2)10Biologically related but no mutation
HADHA:Long-chain 3-hydroxyacyl-CoA dehydrogenase(1)10Unrelated
HGF10Annotation errorHGF: Human gingival fibroblasts, not the gen
CD20910Unrelated
HLA-A10Unrelated
HMOX110Unrelated
NR4A1:hormone receptor(1)10Unrelated
FOXA210Other evidence of a functional genetic variantGWAS/rs in intergenic regions or haplotypes
HNF4A:TCF(1)10Biologically related but no mutation
APC10Biologically related but no mutation
HP:haptoglobin(1)10Biologically related but no mutation
AIRE10Unrelated
HSD17B4:17beta-HSD IV(1)10Unrelated
HSPA4:hsp-70(1)10Biologically related but no mutation
APOA1:Apolipoprotein A-I(1)10Unrelated
HTR2A10Other evidence of a functional genetic variantGWAS/rs in intergenic regions or haplotypes
APOA4:apolipoprotein A-IV(1)10Unrelated
CHSY3:N-acetyl galactosaminyl transferase 3(1)10Unrelated
APOB:apolipoprotein B(1)10Unrelated
ANO9:TMEM16J(2)10Genetic variant in a related disease
ID110Biologically related but no mutation
NACA2:ANAC(1)10Annotation errorANAC: cardiac autonomic nervous not the gene
CFI10Genetic variant in a related disease
IGFBP1:IGFBP-1(1)10Unrelated
APP10Biologically related but no mutation
IL1A10Unrelated
IL1B:interleukin-1beta(1)10Unrelated
IL1RN10Unrelated
IL5:IL-5(1)10Biologically related but no mutation
IL6ST10Unrelated
IL7R:IL7RA(1)10Unrelated
IL12A10Unrelated
IL1810Unrelated
CXCL10:IP-10(1)10Unrelated
INSL3:INSL-3(1)10Unrelated
INSM1:IA1(2)10Annotation errorIA1: Collagen type not the gene
IRF110Unrelated
ITGA4:CD49d(1)10Biologically related but no mutation
ABCC610Unrelated
ITGB210Unrelated
IVL10Other evidence of a functional genetic variantGWAS/rs in intergenic regions or haplotypes
JUN:activation protein-1(1)10Unrelated
KAL110Unrelated
NDUFS7:confidence interval (CI) 20(1)10Annotation errorCI: Confidence interval not gene
KCNJ110Genetic variant in a related disease
MALAT110Genetic variant in a related disease
KISS110Unrelated
KIT10Negative evidence
KRT17:CK17(1)10Unrelated
KRT19:CK19(1)10Unrelated
LBP10Genetic variant in a related disease
LEP:Leptin(2)10Unrelated
LEPR10Unrelated
LGALS3:galectin 3(1)10Unrelated
LGALS4:Gal4(1)10Unrelated
LINC0051110Genetic variant in a related disease
LPL:lipoprotein lipase(1)10Unrelated
CIMT10Annotation errorCIMT not gene (surrogate marker of coronary artery disease)
MIRLET7B:let-7b(1)10Biologically related but no mutation
LYZ10Unrelated
HPC3:HPC20(1)10Unrelated
MXD110Other evidence of a functional genetic variantGWAS/rs in intergenic regions or haplotypes
MARK310Unrelated
MATN310Genetic variant in a related disease
MBL210Unrelated
MBP10Unrelated
MC4R10Unrelated
MCM610Negative evidence
MDM210Biologically related but no mutation
MECP210Unrelated
MAP3K510Biologically related but no mutation
MEP1A10Unrelated
MGAT310Negative evidence
CXCL9:MIG(1)10Unrelated
ACHE10Biologically related but no mutation
FOXO410Biologically related but no mutation
MMP2:matrix metalloproteinase 2(1)10Unrelated
ASIP10Negative evidence
MS:MULTIPLE SCLEROSIS(1)10Annotation errorMS: disease not gene
MSX2:MSH(1)10Unrelated
MYO5A10Negative evidence
ATF1:[ATF1(1)10Negative evidence
NCAM1:CD56(1)10Unrelated
NDUFB3:B12(1)10Annotation errorVitamin B12 not the gene
NFE2L2:Nrf2(1)10Unrelated
NFKBIA10Negative evidence
NOS2:inducible nitric oxide synthase(1)10Biologically related but no mutation
NPAS210Unrelated
NPHS1:nephrin(1)10Unrelated
ATP2A210Unrelated
NPR1:natriuretic peptide receptor-A(1)10Biologically related but no mutation
NRAS10Genetic variant in a related disease
ATP2B1:PMCA1(1)10Biologically related but no mutation
NT5E10Unrelated
OGG1:8-oxoguanine DNA glycosylase(1)10Biologically related but no mutation
ORM1:AGP-A(1)10Biologically related but no mutation
FURIN10Unrelated
SERPINE1:PAI-1(2)10Unrelated
IL22:IL-22(1)10Biologically related but no mutation
PARK210Unrelated
PAX310Negative evidence
PAX5:BSAP(1)10Unrelated
SOST10Genetic variant in a related disease
MLXIPL:carbohydrate response element-binding protein(1)10Unrelated
ABHD510Unrelated
SBDS10Unrelated
PHF11:PHF-11(1)10Genetic variant in a related disease
INSIG210Unrelated
SLC45A210Negative evidence
KLF3:klf-3(2)10Biologically related but no mutation
WNT1610Genetic variant in a related disease
PEX5L:pxr*2(1)10Unrelated
ERAP1:ALAP(1)10Unrelated
PER110Unrelated
PF410Unrelated
PGR:progesterone receptor(1)10Unrelated
PIM1:Pim-1(1)10Unrelated
TPCN1:TPC1(1)10Unrelated
BCO1:beta-carotene 15,15'-monooxygenase 1(1)10Unrelated
ATP7A10Negative evidence
ACP5:TRACP5b(1)10Unrelated
CYCS:cytochrome C(1)10Biologically related but no mutation
TREM110Unrelated
WNT410Biologically related but no mutation
PON110Genetic variant in a related disease
POR:NADPH-cytochrome P450 oxidoreductase(2)10Unrelated
POU1F1:Pit-1(2)10Unrelated
UGT1A410Biologically related but no mutation
UGT1A310Biologically related but no mutation
PPARD10Genetic variant in a related disease
PPARG10Genetic variant in a related disease
FAM20A10Unrelated
TRPM710Unrelated
PPP1CC:PP1G(1)10Unrelated
ATG16L110Unrelated
FEZF2:MALDI-TOF(1)10Annotation errorMALDI-TOF: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, not gene
QRSL1:GATA(1)10Genetic variant in a related disease
PPP3R110Genetic variant in a related disease
SLC30A1010Biologically related but no mutation
PRKACB10Negative evidence
PRKACG10Other evidence of a functional genetic variantGWAS/rs in intergenic regions or haplotypes
PRKAR1A10Negative evidence
CDK5RAP2:c48(1)10Annotation error
PRKAR2A10Negative evidence
PRKAR2B10Negative evidence
EXOC210Negative evidence
PRKCB10Genetic variant in a related disease
PRKCH10Genetic variant in a related disease
PRKDC:DNA-PK(1)10Biologically related but no mutation
MAPK1:ERK(1)10Unrelated
MAPK3:extracellular signal-regulated kinase 2(1)10Biologically related but no mutation
MAP2K7:MEK(1)10Unrelated
ANKH10Unrelated
CRTAM10Genetic variant in a related disease
TRPV510Unrelated
HTRA110Unrelated
BAAT:bAt(2)10Genetic variant in a related disease
PTEN10Biologically related but no mutation
PTGER1:EP1(1)10Biologically related but no mutation
PTGER2:EP2(1)10Biologically related but no mutation
PTGER3:EP3(1)10Unrelated
PTGER4:EP4(1)10Biologically related but no mutation
MIB1:MIB-1(1)10Unrelated
PEX5:Pxr*1(1)10Unrelated
RAB27A10Negative evidence
RAD5110Unrelated
BCHE:butyrylcholinesterase(1)10Biologically related but no mutation
SIGIRR10Genetic variant in a related disease
RCN210Unrelated
ACTB10Unrelated
PROK210Unrelated
RORA:RORalpha(2)10Unrelated
S100A6:calcyclin(1)10Unrelated
S100P10Unrelated
SCN9A10Unrelated
CCL20:chemokine ligand (CCL)-20(1)10Unrelated
CXCL510Unrelated
BLOC1S510Other evidence of a functional genetic variantGWAS/rs within genrs9328451
SELP:P-selectin(1)10Unrelated
SNHG610Genetic variant in a related disease
SFRP4:sFRP-4(1)10Unrelated
SRSF110Unrelated
SRSF2:SC-35(1)10Unrelated
SFTPB:Surfactant protein B(1)10Unrelated
H3F3AP6:p21(1)10Unrelated
FNDC3B10Genetic variant in a related disease
CYP3A4310Other evidence of a functional genetic variantGWAS/rs within gendbSNP ID rs680055 (Ala340Pro)
PMEL10Negative evidence
BMP210Unrelated
SLC2A2:Glut 2(1)10Genetic variant in a related disease
BMP4:Bone Morphogenetic Protein-4(1)10Unrelated
SLC5A1:SGLT1(1)10Genetic variant in a related disease
ZSWIM410Biologically related but no mutation
SLC6A4:Serotonin Transporter(1)10Genetic variant in a related disease
GGTLC5P:gGT(1)10Unrelated
SLC10A110Unrelated
SLC12A310Unrelated
SLC19A1:RFC(2)10Unrelated
SLCO1A210Biologically related but no mutation
SMPD1:acid-sphingomyelinase(1)10Biologically related but no mutation
SMPD2:neutral sphingomyelinase(1)10Biologically related but no mutation
SNAI1:Snail1(2)10Biologically related but no mutation
SOD110Unrelated
SOD210Unrelated
SOX1010Negative evidence
SRC:SRC-1(1)10Unrelated
BRCA210Unrelated
STAT110Unrelated
STC110Unrelated
SULT1E110Unrelated
SULT1A110Unrelated
SULT2B110Unrelated
TAC310Unrelated
KLF910Unrelated
TACR310Unrelated
TAF7:TAF(II)55(2)10Biologically related but no mutation
TCF4:TCF-4(2)10Biologically related but no mutation
HNF1B10Unrelated
TCF7L210Unrelated
TRA:TRalpha(1)10Biologically related but no mutation
TRB:TR beta(1)10Unrelated
TFAP2A:AP-2(1)10Unrelated
TGM1:transglutaminase-1(1)10Unrelated
THRA10Unrelated
THRB10Unrelated
THRSP:S14(1)10Unrelated
TLR110Biologically related but no mutation
TLR410Unrelated
CCT3:CCTG(1)10UnrelatedCCTG: not the gene
TRPM2:TRPM-2(1)10Biologically related but no mutation
TSHB:TSH beta(1)10Unrelated
TSHR:thyrotropin receptor(1)10Unrelated
C5AR1:C5a(1)10Unrelated
CCR210Unrelated
TXN:thioredoxin(1)10Unrelated
UCP110Unrelated
UGT2B1710Unrelated
VDAC3:voltage-dependent anion-selective channel protein 3(1)10Unrelated
VEGFA:VEGF(1)10Genetic variant in a related disease
VTN:vitronectin(1)10Unrelated
ZAP70:ZAP-70(1)10Biologically related but no mutation
CACNA1C10Genetic variant in a related disease
CACNA1E10Biologically related but no mutation
SLC30A210Unrelated
NPHS2:podocin(1)10Unrelated
PAX810Unrelated
VKORC1:Vitamin K Epoxide Reductase(1)10Genetic variant in a related disease
MLPH10Other evidence of a functional genetic variantGWAS/rs in intergenic regions or haplotypes
GNPTAB10Unrelated
S100G:calbindin-D9k(1)10Biologically related but no mutation
CDC73:HRPT2(1)10Unrelated
CALCA:Calcitonin(1)10Biologically related but no mutation
HDAC11:HD-11(1)10Annotation errorHD-11: cell line
ADAM1210Unrelated
QTRT1:TGT(1)10Genetic variant in a related disease
CAMP:LL-37(2)10Biologically related but no mutation
NCOA310Genetic variant in a related disease
SESN210Biologically related but no mutation
DTNBP110Negative evidence
CASP8:caspase 8(1)10Biologically related but no mutation
DHX16:DBP-2(1)10Annotation errorDBP: Vitamin D binding protein not the gene
ZNF46910Unrelated
CILP10Unrelated
ENC1:ectodermal-neural cortex-1(1)10Biologically related but no mutation
KRT88P:HBc(1)10Annotation erroranti-HBc not gene
ABCB1110Unrelated
SERPINA6:Transcortin(1)10Unrelated
TNFRSF25:DR3(1)10Biologically related but no mutation
TNFRSF11A10Unrelated
TRIM24:TIF1alpha(2)10Biologically related but no mutation
CCAL1:CPDD(1)10Annotation errorCPDD: calcium pyrophosphate deposition disease, not the gene
WISP110Biologically related but no mutation
HDAC310Biologically related but no mutation
HERC210Biologically related but no mutation
HAP110Unrelated
IL33:IL-33(1)10Unrelated
IL1RL110Biologically related but no mutation
GCM210Unrelated
CD1410Biologically related but no mutation
CD1910Unrelated
HS6ST110Unrelated
RECQL410Unrelated
CD8610Unrelated
ABCG210Unrelated
CD3410Unrelated
THEMIS2:icb-1(2)10Unrelated
CD3610Unrelated
SLC4A710Unrelated
CD3810Biologically related but no mutation
CHD1L:cHDL(1)10Annotation errorcHDL: cholesterol HDL, not the gene
BCAR1:CAS(2)10Unrelated
HPCX10Unrelated
PRDX6:peroxiredoxin-6(1)10Unrelated
CD4410Biologically related but no mutation
CD53:cell-surface antigen(1)10Unrelated
CD59:min-1(1)10Unrelated
CD8110Biologically related but no mutation
CDC610Biologically related but no mutation
KIAA0020:PUFA(1)10Annotation errorPUFA:Polyunsaturated fatty acids, not the gene
FGF1910Unrelated
MED1210Genetic variant in a related disease
The data shown here is supplementary for the research publication Identification and analysis of 35 genes associated with vitamin D deficiency: A systematic review to identify genetic variants. Maricruz Sepulveda-Villegas, Leticia Elizondo-Montemayor, Victor Trevino. PMID:31678109.

Abstract


Vitamin D deficiency is a public health concern associated with, but not limited to, skeletal anomalies, chronic diseases, immune conditions, and cancer, among others. Hypovitaminosis D is mainly associated with en- vironmental and lifestyle factors that affect sunlight exposure. However, genetic factors also influence 25-hy- droxyvitamin D (25[OH]D) serum concentration. Although there is available information of genes with clear biological relevance or markers identified by Genome-Wide Association Studies, an overall view and screening tool to identify known genetic causes of altered serum levels of 25(OH)D is lacking. Moreover, there are no studies including the total genetic evidence associated with abnormal serum concentration of 25(OH)D. Therefore, we conducted a de-novo systematic literature review to propose a set of genes comprehensive of all genetic variants reported to be associated with deficiency of vitamin D. Abstracts retrieved from PubMed search were organized by gene and curated one-by-one using the PubTerm web tool. The genes identified were clas- sified according to the type of genetic evidence associated with serum 25(OH)D levels and were also compared with the few commonly screened genes related to vitamin D status. This strategy allowed the identification of 35 genes associated with serum 25(OH)D concentrations, 27 (75%) of which are not commercially available and are not, therefore, analyzed in clinical practice for genetic counseling, nor are they sufficiently studied for research purposes. Functional analysis of the genes identified confirmed their role in vitamin D pathways and diseases. Thus, the list of genes is an important source to understand the genetic determinants of 25(OH)D levels. To further support our findings, we provide a map of the reported functional variants and SNPs not included in ClinVar, minor allelic frequencies, SNP effect sizes, associated diseases, and an integrated overview of the biological role of the genes. In conclusion, we identified a comprehensive candidate list of genes associated with serum 25(OH)D concentrations, most of which are not commercially available, but would prove of importance in clinical practice in screening for patients that should respond to supplementation because of alterations in ab- sorption, patients that would have little benefit because alterations in the downstream metabolism of vitamin D, and to study non-responsiveness to supplementation with vitamin D.