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GC

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Also known as DBPVDBPhDBP

Summary

GC (GC vitamin D binding protein, HGNC:4187) is a protein-coding gene on chromosome 4q13.3, encoding Vitamin D-binding protein (P02774). Involved in vitamin D transport and storage, scavenging of extracellular G-actin, enhancement of the chemotactic activity of C5 alpha for neutrophils in inflammation and macrophage activation.

The protein encoded by this gene belongs to the albumin gene family. It is a multifunctional protein found in plasma, ascitic fluid, cerebrospinal fluid and on the surface of many cell types. It binds to vitamin D and its plasma metabolites and transports them to target tissues. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 2638 — RefSeq curated summary.

At a glance

  • GWAS associations: 43 (top 2% of genes corpus-wide)
  • Clinical variants (ClinVar): 74 total
  • GTEx eGene: eQTL in 3 tissues, sQTL in 2 (q < 0.05)
  • ChEMBL bioactivity: 1 clinical-phase molecule tested; no curated mechanism-of-action drug
  • Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.49 (unconstrained)
  • MANE Select transcript: NM_000583
  • Notable: 74 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4187
Approved symbolGC
NameGC vitamin D binding protein
Location4q13.3
Locus typegene with protein product
StatusApproved
AliasesDBP, VDBP, hDBP
Ensembl geneENSG00000145321
Ensembl biotypeprotein_coding
OMIM139200
Entrez2638

Gene structure

Transcript identifiers

Ensembl transcripts: 39 — 27 protein_coding, 9 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

MANE Select: ENST00000273951

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 2, TSL 2: 1, TSL 3: 2, TSL 5: 3

ENST00000273951, ENST00000503364, ENST00000503472, ENST00000504199, ENST00000505234, ENST00000506245, ENST00000509740, ENST00000513476, ENST00000882421, ENST00000882422, ENST00000882423, ENST00000882424, ENST00000882425, ENST00000882426, ENST00000882427, ENST00000882428, ENST00000882429, ENST00000882430, ENST00000882431, ENST00000882432, ENST00000941117, ENST00000941118, ENST00000994914, ENST00000994916, ENST00000994917, ENST00000994918, ENST00000994919, ENST00000994926, ENST00000994927, ENST00000994931, ENST00000994935, ENST00000994936, ENST00000994941, ENST00000994944, ENST00000994948, ENST00000994949, ENST00001096554, ENST00001096555, ENST00001096556

RefSeq mRNA: 4 — MANE Select: NM_000583 NM_000583, NM_001204306, NM_001204307, NM_001440458

CCDS: CCDS3550, CCDS56332

Canonical transcript exons

ENST00000273951 — 13 exons

ExonStartEnd
ENSE000011386317178396171784079
ENSE000020222287174169771741870
ENSE000034625797176933171769400
ENSE000034931897175671271756914
ENSE000035410727176830171768433
ENSE000035462537176340871763502
ENSE000035552157175497871755107
ENSE000035942087174615171746205
ENSE000036377787175441171754508
ENSE000036472507176543271765643
ENSE000036768747176380471763936
ENSE000036808997175804271758171
ENSE000036929877175251871752650

Expression profiles

Bgee: expression breadth ubiquitous, 144 present calls, max score 99.79.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 18.8028 / max 7858.0246, expressed in 38 samples.

Highest expression (Bgee): liver, lobe of liver, gall bladder, pancreatic ductal cell, type B pancreatic cell.

Genetic regulation across tissues (GTEx eQTL / sQTL)

GC is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 3 tissues and its splicing (sQTL) in 2 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

5 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Liversqtl2.3e-41+1.364:71752606:G:T
Stomacheqtl2.9e-07+0.264:71858001:C:T
Pancreassqtl2.6e-03+0.454:71749645:A:G
Colon Transverseeqtl4.3e-02-0.314:71582240:G:A
Esophagus Mucosaeqtl4.4e-02+1.014:72733211:A:AAC

FANTOM5 promoters

1 alternative TSS:

Promoter IDTPM avgSamples expressed
5245718.802838

Top tissues by expression

showing 100 of 287 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
liverUBERON:000210799.79gold quality
right lobe of liverUBERON:000111499.72gold quality
gall bladderUBERON:000211099.62gold quality
pancreatic ductal cellCL:000207999.32gold quality
type B pancreatic cellCL:000016998.64gold quality
islet of LangerhansUBERON:000000698.45gold quality
epithelial cell of pancreasCL:000008397.28gold quality
pancreasUBERON:000126491.66gold quality
duodenumUBERON:000211489.87gold quality
body of pancreasUBERON:000115089.54gold quality
jejunal mucosaUBERON:000039984.85gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047381.90silver quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099179.95gold quality
body of stomachUBERON:000116174.71gold quality
stomachUBERON:000094574.19gold quality
cardia of stomachUBERON:000116273.94gold quality
fundus of stomachUBERON:000116073.30gold quality
adult mammalian kidneyUBERON:000008269.24gold quality
jejunumUBERON:000211567.14gold quality
colonic epitheliumUBERON:000039765.58silver quality
kidneyUBERON:000211364.08gold quality
nephron tubuleUBERON:000123163.92gold quality
adrenal tissueUBERON:001830362.96gold quality
kidney epitheliumUBERON:000481962.61silver quality
right coronary arteryUBERON:000162560.00gold quality
metanephric glomerulusUBERON:000473659.44silver quality
middle frontal gyrusUBERON:000270259.25gold quality
renal glomerulusUBERON:000007458.82silver quality
metanephrosUBERON:000008158.19gold quality
metanephros cortexUBERON:001053357.72gold quality
lower esophagus mucosaUBERON:003583453.87gold quality
cortex of kidneyUBERON:000122553.71gold quality
oocyteCL:000002353.29gold quality
frontal poleUBERON:000279550.41gold quality
paraflocculusUBERON:000535150.18gold quality
Brodmann (1909) area 10UBERON:001354150.18gold quality
quadriceps femorisUBERON:000137750.06gold quality
ectocervixUBERON:001224949.85gold quality
descending thoracic aortaUBERON:000234549.53gold quality
vastus lateralisUBERON:000137949.50gold quality
Brodmann (1909) area 46UBERON:000648349.30gold quality
blood vessel layerUBERON:000479749.29gold quality
cerebellar vermisUBERON:000472049.25gold quality
cervix squamous epitheliumUBERON:000692249.20gold quality
hair follicleUBERON:000207349.18gold quality
thymusUBERON:000237049.13gold quality
olfactory bulbUBERON:000226448.92gold quality
choroid plexus epitheliumUBERON:000391148.89gold quality
myocardiumUBERON:000234948.87gold quality
cardiac muscle of right atriumUBERON:000337948.55gold quality
CA1 field of hippocampusUBERON:000388148.50gold quality
uterine cervixUBERON:000000248.31gold quality
lymph nodeUBERON:000002948.27gold quality
left ventricle myocardiumUBERON:000656648.24gold quality
tibialis anteriorUBERON:000138548.21silver quality
oviduct epitheliumUBERON:000480448.21gold quality
orbitofrontal cortexUBERON:000416748.20gold quality
deltoidUBERON:000147648.06gold quality
upper arm skinUBERON:000426348.06gold quality
cervix epitheliumUBERON:000480148.04gold quality
tongue squamous epitheliumUBERON:000691947.92gold quality
mucosa of urinary bladderUBERON:000125947.80gold quality
nasal cavity epitheliumUBERON:000538447.70gold quality
layer of synovial tissueUBERON:000761647.54gold quality
pylorusUBERON:000116647.42silver quality
periodontal ligamentUBERON:000826647.14gold quality
diaphragmUBERON:000110347.05gold quality
gluteal muscleUBERON:000200047.03gold quality
triceps brachiiUBERON:000150947.01gold quality
endometrium epitheliumUBERON:000481146.85gold quality
right adrenal glandUBERON:000123346.78gold quality
small intestineUBERON:000210846.59gold quality
upper leg skinUBERON:000426246.32silver quality
left uterine tubeUBERON:000130345.96gold quality
lower esophagusUBERON:001347345.40gold quality
dorsal motor nucleus of vagus nerveUBERON:000287045.35gold quality
lower esophagus muscularis layerUBERON:003583345.29gold quality
muscle tissueUBERON:000238545.23gold quality
inferior olivary complexUBERON:000212745.14gold quality
esophagusUBERON:000104344.53gold quality
skeletal muscle tissueUBERON:000113444.44gold quality
squamous epitheliumUBERON:000691444.20gold quality
bloodUBERON:000017844.17gold quality
endocervixUBERON:000045844.14gold quality
epithelium of esophagusUBERON:000197643.98gold quality
esophagus mucosaUBERON:000246943.76gold quality
urinary bladderUBERON:000125543.66gold quality
tracheaUBERON:000312643.44gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451143.37gold quality
epithelium of bronchusUBERON:000203142.95gold quality
right ovaryUBERON:000211842.88gold quality
bronchusUBERON:000218542.82gold quality
secondary oocyteCL:000065542.57gold quality
spleenUBERON:000210642.49gold quality
coronary arteryUBERON:000162142.33gold quality
intestineUBERON:000016042.11gold quality
esophagogastric junction muscularis propriaUBERON:003584142.05gold quality
cartilage tissueUBERON:000241842.04gold quality
adrenal glandUBERON:000236941.99gold quality
right lungUBERON:000216741.98gold quality

Single-cell (SCXA)

Detected in 11 experiment(s), a significant marker in 11.

ExperimentMarker?Max mean expression
E-GEOD-81547yes5201.74
E-MTAB-7407yes2459.51
E-CURD-98yes1948.37
E-MTAB-5061yes1530.54
E-GEOD-81608yes1334.71
E-ENAD-27yes1110.10
E-GEOD-83139yes1092.55
E-HCAD-31yes67.76
E-HCAD-9yes58.22
E-MTAB-10553yes34.22
E-ANND-3no0.00

HPA expression

RNA tissue specificity: Tissue enriched

showing 60 of 64 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Livertissue7722.0low
Gallbladdertissue465.2medium
Duodenumtissue56.8medium
Stomach 1tissue48.8medium
Kidneytissue43.0medium
Pancreastissue41.9medium
Small intestinetissue7.5low
Cerebral cortextissue0.7low
Basal gangliatissue0.7not detected
Amygdalatissue0.7
Cerebellumtissue0.7not detected
Hippocampal formationtissue0.7
Entorhinal cortextissue0.7
Retrosplenial and cingulate cortextissue0.7
Periaqueductal graytissue0.7
Olfactory bulbtissue0.7
Retrosplenial cortextissue0.7
Insular cortextissue0.7
Prefrontal cortextissue0.6
Motor cortextissue0.6
Hypothalamustissue0.6
Spinal cordtissue0.6
Corpus callosumtissue0.6
Ventral forebraintissue0.6
Septumtissue0.6
Somatosensory cortextissue0.6
Temporal cortextissue0.6
Occipital cortextissue0.6
Epididymistissue0.5not detected
Putamentissue0.5
Substantia nigratissue0.5
Midbraintissue0.4
Medulla oblongatatissue0.4
Thalamustissue0.4
Superior colliculitissue0.4
Skin 1tissue0.3low
Ponstissue0.3
Adipose tissuetissue0.3low
Lymph nodetissue0.2not detected
Caudate putamentissue0.2
Heart muscletissue0.1low
Esophagustissue0.1not detected
Colontissue0.1low
Spleentissue0.1not detected
Bone marrowtissue0.1not detected
Postcentral gyrustissue0.1
Cervixtissue0.0low
Breasttissue0.0medium
Testistissue0.0medium
Ovarytissue0.0low
Vaginatissue0.0low
Seminal vesicletissue0.0low
Rectumtissue0.0low
Parathyroid glandtissue0.0low
Smooth muscletissue0.0low
Urinary bladdertissue0.0low
Endometrium 1tissue0.0medium
Placentatissue0.0low
Lungtissue0.0low
Prostatetissue0.0medium

Brain sub-regions (HPA Brain Atlas): detected in 40; highest nTPM — Superior vestibular nucleus (0.8), Dorsal hippocampus (0.6), Ventral spinal cord (0.6), White matter (0.6), Dorsal spinal cord (0.5).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AP1, AR, GCFC2, HIF1A, HNF1A, JUN, KLF5, NFATC3, NR4A1, RELA, SP1, SP3, TBP, TP53, WT1

miRNA regulators (miRDB)

Targeting GC by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

16 miRNAs:

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-806799.8669.592260
HSA-MIR-6885-3P99.7570.363187
HSA-MIR-29799.4069.581418
HSA-MIR-19A-5P99.3666.931675
HSA-MIR-19B-1-5P99.3667.071669
HSA-MIR-19B-2-5P99.3667.071669
HSA-MIR-314998.7767.131639
HSA-MIR-1-5P98.7068.661017
HSA-MIR-3928-5P98.5067.48980
HSA-MIR-6806-3P98.5067.31980
HSA-MIR-6764-3P98.4467.641153
HSA-MIR-6824-3P98.4467.621154
HSA-MIR-616-3P96.8266.99784
HSA-MIR-584-5P95.8268.05848
HSA-MIR-675-3P95.7769.27675

Functional genomics

gnomAD constraint: pLI 2.29e-07, LOEUF 1.49, missense Z 0.308 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000273951 — one region, missense o/e 0.97.

Literature-anchored findings (GeneRIF, showing 40)

  • GC*IF gene polymorphism of Gc-globulin may be one of the risk factors for chronic obstructive pulmonary disease. However, no association between this polymorphism of Gc-globulin and susceptibility to diffuse panbronchiolitis was found. (PMID:11757623)
  • crystal structure in complex with 25-hydroxyvitamin D3, a vitamin D3 metabolite, which reveals the vitamin D-binding site in the N-terminal part of domain I; crystal structure in complex with a vitamin D3 analog (PMID:11799400)
  • A polymorphism within the vitamin D-binding protein gene is associated with Graves’ disease but not with Hashimoto’s thyroiditis. (PMID:12050214)
  • Although binding of 25-OH-D(3) to DBP might result in discrete conformational changes in the holo-protein to influence actin-binding, these binding processes are largely independent of each other in solution. (PMID:12051678)
  • gene and genetic susceptibility to type 2 diabetes mellitus in a Polish population. (PMID:12062854)
  • crystal structure of complex with actin (PMID:12119014)
  • function in macrophage tumoricidal activity (PMID:12580408)
  • Data show that vitamin D-binding protein-macrophage-activating factor (DBP-maf) induces apoptosis in macrophages via a p38 and jun kinase 1/2 pathway. (PMID:12938159)
  • The analysis involved the data on nine polymorphic codominant loci: HP, GC, TF, PI, PGM1, GLO1, C3, ACP1, and ESD. The loci were selected by significance of differences in genotype frequencies between tuberculosis patients and healthy controls (PMID:12942785)
  • complex combined effect of several SNPs within the DBP gene that might underlie susceptibility to low radial BMD and osteoporosis (PMID:12968673)
  • Gc-globulin polymorphism is significantly associated with susceptibility to COPD (PMID:14718422)
  • Chronic liver patients showed increased levels of Gc globulin following transplantation (PMID:15115254)
  • Association was found between frequencies of genotypes SS, 2F and FS, F allele of GC gene with osteoporosis. (PMID:15230135)
  • a 20-amino-acid sequence (residues 130-149, 5’-EAFRKDPKEYANQFMWEYST-3’) in domain I of DBP is essential for its C5a chemotactic cofactor function (PMID:15485893)
  • single nucleotide polymorphisms (SNPs) within the transcriptional regulatory regions of the VDR and DBP are associated with prostate cancer risk (PMID:15717311)
  • The decreased level of DBPE in the peritoneal fluid but not in plasma of women with untreated endometriosis suggests that this molecule may be relevant in the pathogenesis of this disease (PMID:15866120)
  • The active form of Vitamin D (1,25(OH)2D3) completely eliminated the chemotactic cofactor function of DBP (Vitamin B binding protein). (PMID:16115686)
  • vitamin D binding sites are important for initiating the activities of vitamin D-binding protein on vascular smooth muscle cells (PMID:16269129)
  • No major effect of (TAAA)(n)-Alu repeat DBP-polymorphism was demonstrated on BMD, bone turnover markers or body composition. (PMID:16309986)
  • Inhibits angiogenesis by blocking critical steps such as endothelial cell proliferation, migration, tube formation and microvessel sprouting. (PMID:16400520)
  • A model is proposed in which the DBP gene is independently regulated by dedicated locus control regions. (PMID:16648359)
  • These results indicate that fusion of granules with the plasma membrane forms heavy plasma membrane that contains DBP binding sites. (PMID:17113648)
  • Polymorphisms of vitamin D-binding protein (DBP) gene were significantly association with human percentage of fat mass, especially in female, suggesting the importance of DBP gene in the pathogenesis of human obesity. (PMID:17342072)
  • C5 gene variants and Gc-globulin levels co-define the proinflammatory and profibrogenic effects of C5 in patients at-risk for progression of liver fibrosis (PMID:17428459)
  • Free Gc-globulin provides prognostic information in acute liver fafilure. (PMID:17763387)
  • A prognostic marker for liver transplantation after acute liver failure. (PMID:17763397)
  • *mportance of acute liver failure Gc reductions in the development of multiple organ dysfunction in acute liver failure and cirrhosis. (PMID:17763400)
  • These data demonstrate a critical role for elements within intron 1 in the establishment of an autonomous and productive hDBP chromatin locus and suggest that this function is dependent upon C/EBPalpha. (PMID:17785430)
  • results provide a direct evidence of cross-talk among the structural domains of DBP (PMID:18035050)
  • There was a relationship between DBP Alu genotype and BMD, suggesting that DBP-Alu genotype may influence fracture risk. This effect may be mediated by changes in the circulating concentrations of DBP which influences free concentrations of vitamin D. (PMID:18038108)
  • Serum VDBP can be considered a nutritional marker for lipids in cystic fibrosis. (PMID:18303991)
  • Serum and peritoneal DBP concentrations are not affected in women with endometriosis. (PMID:18334925)
  • the micro-environment of the fatty acid-binding domains of DBP and albumin may be different; and DBP may not replace ALB as a transporter of fatty acids. (PMID:18374965)
  • A significantly reduced risk of postmenopausal breast cancer in homozygote carriers of the Gc2 allele in the vitamin D binding protein was observed, independent of serum 25(OH)D. (PMID:18559548)
  • SNPs in the DBP are associated with levels of 25(OH)D and 1,25(OH)2D in hispanics and African americans. (PMID:18593774)
  • characterization of genotype-dependent glycosylation patterns for the 3 major allele products of DBP (PMID:18686987)
  • No evidence that DBP polymorphisms were associated with mammographic breast density among Caucasian premenopausal women of French descent. (PMID:18768522)
  • These results support a correlation between the level of DBP and MS. DBP may be a potential useful biomarker for diagnosis or a medicine target for treatment of MS. (PMID:18807170)
  • Data show that vitamin D-binding protein (DBP) is elevated in the CSF of temporal lobe epilepsy patients. (PMID:19109932)
  • Circulating 25(OH)D concentrations in premenopausal women are strongly related to DBP polymorphisms (PMID:19116321)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriogcENSDARG00000089310
mus_musculusGcENSMUSG00000035540
rattus_norvegicusGcENSRNOG00000003119

Paralogs (3): AFM (ENSG00000079557), AFP (ENSG00000081051), ALB (ENSG00000163631)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:95669) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 11 distinct phenotype terms.

Mouse phenotype (MP)Records
decreased circulating HDL cholesterol level1
decreased circulating triglyceride level1
abnormal bone mineralization1
increased circulating alanine transaminase level1
abnormal bone remodeling1
increased activity of parathyroid1
abnormal osteoblast physiology1
decreased circulating cholesterol level1
decreased circulating glucose level1
decreased circulating total protein level1
abnormal vitamin D level1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

OrganismUniProtIdentityMethod
Oryctolagus cuniculusP5378982.5%Diamond
Bos taurusQ3MHN580.3%Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
NPFFR2protein-coding10886
ADAMTS3protein-coding9508
SLC4A4protein-coding8671

Protein

Protein identifiers

Vitamin D-binding protein — P02774 (reviewed: P02774)

Alternative names: Gc protein-derived macrophage activating factor, Gc-globulin, Group-specific component, Vitamin D-binding protein-macrophage activating factor

All UniProt accessions (4): D6RBJ7, D6RF20, D6RF35, P02774

UniProt curated annotations — full annotation on UniProt →

Function. Involved in vitamin D transport and storage, scavenging of extracellular G-actin, enhancement of the chemotactic activity of C5 alpha for neutrophils in inflammation and macrophage activation.

Subunit / interactions. Associates with membrane-bound immunoglobulin on the surface of B-lymphocytes and with IgG Fc receptor on the membranes of T-lymphocytes. Interacts with LRP2; the interaction is required for renal uptake of GC in complex with 25-hydroxyvitamin D3.

Subcellular location. Secreted.

Tissue specificity. Expressed in the liver. Found in plasma, ascites, cerebrospinal fluid and urine.

Post-translational modifications. Allele GC*1S is O-glycosylated at Thr-436. The trisaccharide sugar moiety can be modified by the successive removal of neuraminic acid and galactose leaving an O-mceeN-acetyl-galactosamine. This conversion is thought to produce a macrophage-activating factor (Gc-MAF). Only a minor proportion of plasma GC is O-glycosylated. The potential N-glycosylation site predicted at Asn-288 is thought to be nonglycosylated.

Polymorphism. Over 80 variants of human DBP have been identified. The three most common alleles are called GC1F, GC1S, and GC2. The sequence shown is that of the GC1A1 allele.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the ALB/AFP/VDB family.

Isoforms (3)

UniProt IDNamesCanonical?
P02774-11yes
P02774-22
P02774-33

RefSeq proteins (4): NP_000574, NP_001191235, NP_001191236, NP_001427387 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000213VitD-bdFamily
IPR000264ALB/AFP/VDBFamily
IPR014760Serum_albumin_NDomain
IPR015247VitD-bind_IIIDomain
IPR020857Serum_albumin_CSConserved_site
IPR020858Serum_albumin-likeHomologous_superfamily

Pfam: PF00273, PF09164

UniProt features (64 total): helix 27, disulfide bond 14, strand 5, sequence variant 4, turn 4, domain 3, sequence conflict 3, splice variant 2, signal peptide 1, chain 1

Structure

Experimental structures (PDB)

6 structures by resolution:

PDBTitleMethodResolution (Å)
1KXPCRYSTAL STRUCTURE OF HUMAN VITAMIN D-BINDING PROTEIN IN COMPLEX WITH SKELETAL ACTINX-RAY DIFFRACTION2.1
1KW2CRYSTAL STRUCTURE OF UNCOMPLEXED VITAMIN D-BINDING PROTEINX-RAY DIFFRACTION2.15
1J78Crystallographic analysis of the human vitamin D binding proteinX-RAY DIFFRACTION2.31
1MA9Crystal structure of the complex of human vitamin D binding protein and rabbit muscle …X-RAY DIFFRACTION2.4
1LOTCRYSTAL STRUCTURE OF THE COMPLEX OF ACTIN WITH VITAMIN D-BINDING PROTEINX-RAY DIFFRACTION2.5
1J7EA Structural Basis for the Unique Binding Features of the Human Vitamin D-binding ProteinX-RAY DIFFRACTION2.55

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P02774-F192.810.89

Human Protein Atlas

Protein class: Metabolic proteins, Predicted secreted proteins, Plasma proteins

Protein evidence: Evidence at protein level

Antibody reliability (HPA): IH supported

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (14)

TypePositions
Disulfide bond189–198, 220–266, 265–273, 286–300, 299–311, 335–376, 375–384, 407–453, 452–462, 29–75, 74–83, 96–112, 111–122, 145–190

Function

Pathways and Gene Ontology

Reactome pathways

1 curated (TAS) of 4; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

4 pathways:

IDPathwayEvidence
R-HSA-196791Vitamin D (calciferol) metabolismcurated
R-HSA-1430728Metabolism—
R-HSA-556833Metabolism of lipids—
R-HSA-8957322Metabolism of steroids—

MSigDB gene sets: 386 (showing top): RNGTGGGC_UNKNOWN, MODULE_93, MODULE_52, GOBP_HEPATICOBILIARY_SYSTEM_DEVELOPMENT, WANG_CLIM2_TARGETS_UP, MYOGENIN_Q6, RORA1_01, YAO_HOXA10_TARGETS_VIA_PROGESTERONE_UP, HNF1_Q6, MODULE_404, MODULE_503, chr4q13, MODULE_66, MODULE_118, CAIRO_HEPATOBLASTOMA_CLASSES_DN

GO Biological Process (4): response to nutrient levels (GO:0031667), vitamin D metabolic process (GO:0042359), vitamin transport (GO:0051180), vitamin transmembrane transport (GO:0035461)

GO Molecular Function (5): actin binding (GO:0003779), vitamin D binding (GO:0005499), vitamin transmembrane transporter activity (GO:0090482), molecular carrier activity (GO:0140104), calcidiol binding (GO:1902118)

GO Cellular Component (6): extracellular region (GO:0005576), cytosol (GO:0005829), lysosomal lumen (GO:0043202), extracellular exosome (GO:0070062), blood microparticle (GO:0072562), cytoplasm (GO:0005737)

Reactome top-level categories

3 top-level categories:

CategoryPathways
Metabolism of steroids1
Metabolism1
Metabolism of lipids1

GO top-level categories

20 GO namespaces:

CategoryTerms
cellular anatomical structure4
response to stimulus1
steroid metabolic process1
transport1
vitamin transport1
transmembrane transport1
cytoskeletal protein binding1
steroid binding1
vitamin binding1
transmembrane transporter activity1
vitamin transmembrane transport1
molecular_function1
binding1
D3 vitamins binding1
cytoplasm1
lysosome1
vacuolar lumen1
extracellular vesicle1
extracellular region1
intracellular anatomical structure1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 4 of 16 annotations. The rest are phylogenetic / computational / electronic (IEA).

4 experimentally-supported GO terms:

GO termNSEvidence
blood microparticleCChigh-throughput assay
extracellular exosomeCChigh-throughput assay
actin bindingMFphysical interaction
calcidiol bindingMFdirect assay

Protein interactions and networks

STRING

showing 15 of 1,314 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
GCCYP2R1Q6VVX0913
GCSLC25A18Q9H1K4894
GCCYP24A1Q07973860
GCCYP27B1O15528858
GCLRP2P98164852
GCCUBNO60494839
GCPTHP01270786
GCSCINQ9Y6U3782
GCAHSGP02765768
GCGSNP06396746
GCST6GALNAC1Q9NSC7738
GCAMBPP00977732
GCDHCR7Q9UBM7723
GCHPP00737708
GCGSRP00390696

IntAct

Human interaction partners of GC in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

10 partners by confidence:

PartnerInteraction typeMIscoreRecords
POTEFassociation0.5304
HYCC1association0.5302
NR2F2association0.5302
ACTA1direct interaction0.4401
CCND3physical association0.3701
CDC73physical association0.0001
GRB2physical association0.0001
PIK3R3physical association0.0001
RIF1physical association0.0001
SERF2physical association0.0001

BioGRID (77 interactions; top human partners by supporting records): ACTA2 (Affinity Capture-MS; 2 records), ACTB (Affinity Capture-MS; 2 records), ACTBL2 (Affinity Capture-MS; 2 records), DDX31 (Affinity Capture-MS; 2 records), FAM126A (Affinity Capture-MS; 2 records), NR2F2 (Affinity Capture-MS; 2 records), POTEF (Affinity Capture-MS; 2 records), POTEI (Affinity Capture-MS; 2 records), POTEKP (Affinity Capture-MS; 2 records), ACTA1 (Co-crystal Structure), AGPAT1 (Affinity Capture-MS), BUB1B (Affinity Capture-MS), CCND3 (Two-hybrid), CCR1 (Affinity Capture-MS), CDC73 (Two-hybrid)

SIGNOR signaling

1 signaling interactions:

AEffectBMechanism
GC“up-regulates quantity”“vitamin D”relocalization

Disease & clinical

Genetic variants

Variant evidence for GC: 74 ClinVar records (0 pathogenic / likely pathogenic); 1 PharmGKB clinical annotation; 43 GWAS associations.

ClinVar

74 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance44
Likely benign7
Benign9

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 32 predictions of 755):

Position(s)EffectΔscoreSites
4:71754409–71754410donor_loss1.00006
4:71754509–71754510acceptor_loss1.00004
4:71754982donor_gain1.0000
4:71756715donor_gain1.0000
4:71756872acceptor_gain1.0000
4:71756915–71756916acceptor_loss1.00005
4:71758040–71758041donor_loss1.00005
4:71763802–71763803donor_loss1.00003
4:71765457donor_gain1.0000
4:71768299–71768300donor_loss1.00005

AlphaMissense

583 missense substitutions predicted likely pathogenic (of 3,098 scored), across 180 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
F19980.9070.993
C14570.9840.991
C19070.9800.989
C18970.9780.988
C7470.9760.990
C7570.9750.988
C9670.9750.988
C2970.9730.989
C12270.9720.988
C8370.9710.983
C19870.9670.979
C11170.9630.985
C22070.9600.979
C11270.9570.974
C28670.9360.969
C26670.9330.963
F4070.9290.983
F5270.9270.980
C46270.9250.959
C45370.9160.955

HPA cancer prognostics

RNA cancer specificity: Cancer enriched (Liver Hepatocellular Carcinoma)

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

CancerPrognosticp-value
Liver Hepatocellular Carcinoma (TCGA)favorable0.000866
Prostate Adenocarcinoma (TCGA)unfavorable0.00099

Disease associations

OMIM: gene MIM:139200 | disease phenotypes:

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (1 panels, 0 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

1 panels:

PanelRating
COVID-19 researchamber

GWAS associations

showing 30 of 43 associations:

StudyTraitp-value
GCST005367_3Vitamin D levels0.000000e+00
GCST002414_1Serum vitamin D-binding protein levels1e-246
GCST005366_1Vitamin D levels (dietary vitamin D intake interaction)1e-187
GCST000697_2Vitamin D insufficiency2e-109
GCST002414_3Serum vitamin D-binding protein levels5e-91
GCST012426_1Serum vitamin D-binding protein levels in type 2 diabetes9e-86
GCST005782_4Serum 25-Hydroxyvitamin D levels4e-63
GCST005782_11Serum 25-Hydroxyvitamin D levels4e-62
GCST000664_1Vitamin D levels2e-49
GCST012426_2Serum vitamin D-binding protein levels in type 2 diabetes5e-43
GCST90002407_75White blood cell count1e-40
GCST005729_1Serum 25-Hydroxyvitamin D levels5e-38
GCST90002398_294Neutrophil count4e-33
GCST012014_1Serum 25-Hydroxyvitamin D levels2e-25
GCST012425_1Bioavailable vitamin D levels in type 2 diabetes3e-19
GCST001639_31Metabolite levels1e-14
GCST012426_3Serum vitamin D-binding protein levels in type 2 diabetes1e-14
GCST001560_1Vitamin D levels2e-14
GCST005782_15Serum 25-Hydroxyvitamin D levels6e-13
GCST005782_1Serum 25-Hydroxyvitamin D levels1e-12
GCST009240_166Serum metabolite levels (CMS)3e-12
GCST009671_1Serum 25-Hydroxyvitamin D levels1e-11
GCST004610_143White blood cell count2e-11
GCST90002400_440Plateletcrit2e-11
GCST90002388_143Lymphocyte count4e-11
GCST004626_103Myeloid white cell count5e-11
GCST004614_93Granulocyte count1e-10
GCST004620_83Sum basophil neutrophil counts1e-10
GCST004613_100Sum neutrophil eosinophil counts2e-10
GCST004629_14Neutrophil count2e-10

EFO canonical traits (from GWAS)

12 canonical traits:

EFO IDTrait name
EFO:0003762vitamin D deficiency
EFO:0004723coronary artery calcification
EFO:0005675vitamin D-binding protein measurement
EFO:0004833neutrophil count
EFO:0004842eosinophil count
EFO:0007987granulocyte count
EFO:0005090basophil count
EFO:0008539vitamin D dietary intake measurement
EFO:0004587lymphocyte count
EFO:0005091monocyte count
EFO:0007985platelet crit
EFO:0004309platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2259 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

Phase ≥1, by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 29,883 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

1 molecules by phase:

MoleculeNamePhasePatents
CHEMBL846CALCITRIOL429,883

PharmGKB: 1 entry (CPIC guideline: no)

PharmGKB clinical annotations

1 annotations by evidence level (1 strongest → 4):

VariantAssociationLevelDrugsPhenotypes
rs7041Efficacy3deferasiroxBeta-thalassemia and related diseases

PharmGKB variants

1 variants:

VariantGenesLevelScore#Clin annotsDrugs
rs7041GC32.001deferasirox

PharmGKB variant annotations

Per-publication pharmacogenomic findings for this gene (significant associations).

3 published findings:

VariantDrug(s)CategoryFindingPMID
rs4588bevacizumabEfficacyGenotype TT is associated with decreased overall survival when treated with bevacizumab in people with Colorectal Neoplasms and Neoplasm Metastasis as compared to genotypes GG + GT.PMID:29208668
rs4588cetuximabEfficacyGenotype TT is associated with increased overall survival when treated with cetuximab in people with Colorectal Neoplasms and Neoplasm Metastasis as compared to genotypes GG + GT.PMID:29208668
rs7041deferasiroxEfficacyGenotype AA is associated with increased response to deferasirox in people with beta-Thalassemia as compared to genotypes AC + CC.PMID:30651574

ChEMBL bioactivities

1 potent at pChembl≥5 of 1 total, top 1 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.62Kd24nMCALCITRIOL

PubChem BioAssay actives

1 with measured affinity, of 57 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
Calcitriol472017: Binding affinity to human vitamin D binding proteinkd0.0240uM

CTD chemical–gene interactions

30 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Calcitriolaffects binding, affects abundance, affects transport3
25-hydroxyvitamin Daffects abundance2
Acetaminophendecreases expression2
Benzo(a)pyreneaffects methylation, decreases expression2
Vitamin Daffects binding2
Cyclosporinedecreases expression2
Aflatoxin B1affects expression, decreases methylation2
methyleugenoldecreases expression1
bisphenol Aaffects binding1
potassium persulfateincreases expression1
terbufosaffects response to substance1
sodium arsenitedecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, increases expression1
(+)-JQ1 compounddecreases expression1
Olanzapineaffects phosphorylation1
Zoledronic Acidincreases expression1
Ethanoldecreases expression1
Vehicle Emissionsdecreases methylation1
Cadmiumaffects binding1
Carbonaffects response to substance1
Copperaffects binding1
Leadaffects binding1
Lipopolysaccharidesaffects cotreatment, increases expression1
N-Nitrosopyrrolidinedecreases expression1
Nickelaffects binding1
Ouabainaffects expression1
Parathionaffects response to substance1
Tobacco Smoke Pollutionaffects expression1
Tretinoinincreases expression1
Okadaic Aciddecreases expression1

ChEMBL screening assays

13 unique, capped per target: 13 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL1014566BindingBinding affinity to human DBP at EC50 in 4 degC relative to 1-alpha,25-(OH)2D3Synthesis and biological activity of previtamin D(3) analogues with A-ring modifications. — *Bioorg Med Chem*

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

showing 60 of 300 trials:

NCTPhaseStatusTitle
NCT00296881Phase 4UNKNOWNSRP in Combination With PERIOWAVE in Comparison to SRP Alone in Chronic Periodontitis
NCT00297518Phase 4COMPLETEDStudy of Scaling and Root Planing (SRP) With PerioWave vs. SRP Alone in Chronic Periodontitis
NCT00297531Phase 4UNKNOWNStudy of Scaling and Root Planing With PerioWave Versus Scaling and Root Planing Alone in Chronic Periodontitis
NCT00668746Phase 4COMPLETEDLong-term Safety of Minocycline in Patients With Gum Disease
NCT00707369Phase 4COMPLETEDAdjunctive Antimicrobial Therapy of Periodontitis: Long-Term Effects on Disease Progression and Oral Microbiological Colonization
NCT01030666Phase 4TERMINATEDEffect of Postsurgical Systemic Doxycycline After Regenerative Periodontal Therapy
NCT01538927Phase 4COMPLETEDEffect of Fibrin Sealant on Early Wound Healing
NCT01548469Phase 4COMPLETEDStudy to Evaluate Clinical Efficacy and Safety of Bio Mineral Toothpaste in Patients With Mild Periodontitis
NCT01593540Phase 4COMPLETEDClinical Examination of Metal Free Interdental Brushes
NCT01806974Phase 4TERMINATEDConsequences of Anti-interleukin 6 Immunotherapy Treatment for Rheumatoid Arthritis on Periodontium
NCT02030470Phase 4COMPLETEDEvaluation of Photodynamic Treatment FOTOSAN® Efficacy in Periodontology
NCT02062047Phase 4COMPLETEDFull-mouth and Partial-mouth Scaling and Root Planing in Type 2 Diabetic Subjects
NCT02124655Phase 4COMPLETEDAntiplaque Effect of Essential Oils and 0.2% Chlorhexidine on an in Situ Model of Oral Biofilm Growth.
NCT02135952Phase 4UNKNOWNMetronidazole and Amoxicillin for the Treatment of Type 2 Diabetic Subjects With Periodontitis
NCT02149758Phase 4COMPLETEDEFFECT OF SELECTIVE COX-2 INHIBITOR (ETORICOXIB) ALONG WITH SCALING AND ROOT PLANING (SRP) ON CLINICAL PARAMETERS AND SALIVARY LEVEL OF SUPEROXIDE DISMUTASE IN CHRONIC GENERALIZED PERIODONTITIS A DOUBLE-BLIND, PLACEBO-CONTROLLED, DOUBLE-MASKED RANDOMIZED CONTROLLED TRIAL (RCT).
NCT02215460Phase 4COMPLETEDTreatment of Periodontitis by Conventional 4 Weekly Sections or Within 24 Hours
NCT02215473Phase 4COMPLETEDBacteremia in Periodontal Patients
NCT02267239Phase 4UNKNOWNMethodology Antiseptic Application, Influence on Oral Biofilm.
NCT02359721Phase 4COMPLETEDClarithromycin is an Adjunct to Scaling and Root Planing
NCT02470611Phase 4COMPLETEDSodium Alendronate in Non Surgical Periodontal Therapy
NCT02794506Phase 4COMPLETEDPropolis Improves Glycemic Control in Subjects With Type 2 Diabetes and Chronic Periodontitis
NCT02921165Phase 4COMPLETEDComparison of Topical Analgesic With Saline Rinses in Post Extraction Healing
NCT02946801Phase 4UNKNOWNAntiplaque Effect of Essential Oils With and Without Alcochol on an in Situ Model of Oral Biofilm Growth
NCT03103204Phase 4COMPLETEDTreatment of Periodontitis in Obese Individuals
NCT03146390Phase 4UNKNOWNEssential Oils With and Without Alcohol: Substantivity and Antiplaque Effect
NCT03176537Phase 4WITHDRAWNPeriodontal Profile of Hypogonadic Men
NCT03311906Phase 4COMPLETEDEvaluation of the Efficacy of 0.8% Hyaluronic Acid Gel
NCT03354312Phase 4COMPLETEDAcceptance and Preference of Lidocaine Gel Compared to Injection Anesthesia After Non Surgical Periodontal Treatment
NCT04027179Phase 4UNKNOWNTongue Dysbiosis Effects on Arterial Pressure of Periodontitis Patients
NCT04032132Phase 4COMPLETEDCurcumin Paste as an Adjunctive Therapy in Periodontitis
NCT04036890Phase 4COMPLETEDLocal Minocycline in Patients Under Supportive Periodontal Therapy
NCT04044417Phase 4COMPLETEDCurcumin-Simvastatin-EDTA in the Treatment of Periodontitis
NCT04149405Phase 4COMPLETEDAlterations of GCF Levels of Sclerostin and DKK-1 in Postmenopausal Osteoporosis
NCT04178590Phase 4COMPLETEDEffect of Injectable Platelet-Rich Fibrin (i-PRF) in Initial Treatment of Chronic Periodontitis
NCT04223076Phase 4UNKNOWNClinical Effect of Chlorhexidine Mouthwash After Periodontal Surgery
NCT04353362Phase 4COMPLETEDAlternative Antibiotic Regimen in Periodontitis Treatment
NCT04964167Phase 4COMPLETEDIndocyanine-green Mediated Photosensitizer VS Aloe Vera Gel: Adjunct Therapy to Scaling and Root Planing in Patients With Chronic Periodontitis
NCT04983849Phase 4COMPLETEDEvaluation of Metronidazole Hydrogel 25% in Stage II and III Periodontitis
NCT05530252Phase 4COMPLETEDEffects of AMP Application After Non-surgical Periodontal Therapy on Treatment of Periodontitis
NCT05657015Phase 4COMPLETEDLepidium Sativum Extract Versus Simvastatin as an Adjunctive Local Delivery Agents to Non-Surgical Periodontal Therapy
NCT05834517Phase 4COMPLETED‘‘Efficacy of Locally Delivered Hyaluronic Acid Gel as an Adjunctive to Non-Surgical Management of Periodontitis
NCT05870358Phase 4COMPLETEDMelatonin Supports Non Surgical Periodontal Treatment in Patients With Type 2 Diabetes and Periodontitis
NCT05936450Phase 4COMPLETEDAssessment Of Healing After Periodontal Flap Surgery With And Without The Use Of Placental Extracts
NCT07316582Phase 4ENROLLING_BY_INVITATIONMelatonin Loaded in Injectable Platelet-Rich Fibrin in the Management Periodontitis
NCT07402694Phase 4NOT_YET_RECRUITINGOral Health Outcomes With Amphion Mouthwash as an Adjunct to Non-Surgical Periodontal Therapy
NCT07459049Phase 4RECRUITINGEffect of Ibuprofen on Acute Inflammatory Response After One-Stage Periodontal Therapy
NCT07707063Phase 4RECRUITINGThis a Clinical Trial to Evaluate the Efficacy of I-PRF, Povidone-Iodine and Laser as Adjuncts to Non-surgical Periodontal Treatment in Smokers and Non-Smokers Periodontitis Patients
NCT00066027Phase 3COMPLETEDEffects of Low-Dose Doxycycline on Oral Bone Loss
NCT00066131Phase 3COMPLETEDObstetrics and Periodontal Therapy (OPT) Study
NCT00327561Phase 3COMPLETEDEffect of Intensive Periodontal Therapy on Vascular Function
NCT00336661Phase 3COMPLETEDPerioWave Re-Treatment Protocol Compared to Scaling and Root Planing (SRP) and a Single Treatment With PerioWave
NCT00371332Phase 3COMPLETEDEffect of Adjunctive Treatment With Arestin on the Subgingival Microflora in Patients With Moderate to Advanced Periodontitis
NCT00662532Phase 3COMPLETEDAntibiotic Study for Dental Implants
NCT00681564Phase 3COMPLETEDPeriodontal Infection and Endothelial Dysfunction
NCT00734708Phase 3COMPLETEDPhase 3 Clinical Trial of Periodontal Tissue Regeneration Using Fibroblast Growth Factor-2(Trafermin)
NCT00762762Phase 3COMPLETEDEffectiveness of a Triclosan Containing Toothpaste in Maintaining Periodontal Health in a Type 2 Diabetic Population
NCT01015404Phase 3COMPLETEDA Study to Assess the Safety of Using Fibroblast Growth Factor-2 With Periodontal Surgery in Japan (Phase 3)
NCT01098448Phase 3COMPLETEDControl of Periodontal Infections
NCT01503593Phase 3UNKNOWNUsing Combination of Synthetic Bone Substitutes During Extractions
NCT01750801Phase 3UNKNOWNEfficacy of a Mouthwash Containing Propolis

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for GC across ~30M SureChEMBL compounds — explore on Sugi Predict.