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    GC GC vitamin D binding protein [ Homo sapiens (human) ]

    Gene ID: 2638, updated on 14-Nov-2024

    Summary

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    Official Symbol
    GCprovided by HGNC
    Official Full Name
    GC vitamin D binding proteinprovided by HGNC
    Primary source
    HGNC:HGNC:4187
    See related
    Ensembl:ENSG00000145321 MIM:139200; AllianceGenome:HGNC:4187
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DBP; VDB; GRD3; VDBG; VDBP; GcMAF; DBP/GC; Gc-MAF; DBP-maf; HEL-S-51
    Summary
    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.[provided by RefSeq, Feb 2011]
    Expression
    Restricted expression toward liver (RPKM 1264.0) See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    4q13.3
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (71741693..71805520, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (75084117..75147957, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (72607410..72671237, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:72458772-72459481 Neighboring gene uncharacterized LOC107986285 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:72479894-72481093 Neighboring gene uncharacterized LOC105377271 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:72519382-72520581 Neighboring gene RNA, 5S ribosomal pseudogene 163 Neighboring gene VISTA enhancer hs2570 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:72836369-72836534 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:72897326-72897928 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:72960191-72960690 Neighboring gene neuropeptide FF receptor 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:72977919-72979118 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:73019056-73019842 Neighboring gene ADAM metallopeptidase with thrombospondin type 1 motif 3 Neighboring gene Sharpr-MPRA regulatory region 5509

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Vitamin D-binding protein as a biomarker of active disease in acute intermittent porphyria. Serrano-Mendioroz I, et al. J Proteomics, 2015 Sep 8. PMID 25979770
    2. Genetic polymorphisms of the vitamin D binding protein and plasma concentrations of 25-hydroxyvitamin D in premenopausal women. Sinotte M, et al. Am J Clin Nutr, 2009 Feb. PMID 19116321
    3. Effects of vitamin D binding protein phenotypes and vitamin D supplementation on serum total 25(OH)D and directly measured free 25(OH)D. Sollid ST, et al. Eur J Endocrinol, 2016 Apr. PMID 26733479, Free PMC Article
    4. Characterization of mutants of the vitamin D-binding protein/group-specific component: molecular evolution of GC*1A2 and GC*1A3, common in some Asian populations. Yuasa I, et al. Hum Genet, 1995 May. PMID 7759070
    5. Genetic variants in the vitamin D pathway genes VDBP and RXRA modulate cutaneous melanoma disease-specific survival. Yin J, et al. Pigment Cell Melanoma Res, 2016 Mar. PMID 26575331, Free PMC Article

    See all (398) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Assessment of the contribution of VDR and VDBP/GC genes in the pathogenesis of celiac disease.
      Title: Assessment of the contribution of VDR and VDBP/GC genes in the pathogenesis of celiac disease.
    2. Association of rs4588 polymorphism in vitamin D binding protein gene with polycystic ovarian syndrome in Iranian women: a case-control study.
      Title: Association of rs4588 polymorphism in vitamin D binding protein gene with polycystic ovarian syndrome in Iranian women: a case-control study.
    3. Relationship between Vitamin D3 Deficiency, Metabolic Syndrome and VDR, GC, and CYP2R1 Gene Polymorphisms.
      Title: Relationship between Vitamin D3 Deficiency, Metabolic Syndrome and VDR, GC, and CYP2R1 Gene Polymorphisms.
    4. Association between the genetic variant in the vitamin D pathway (rs2282679), circulating 25-hydroxyvitamin D levels, insulin resistance and metabolic syndrome criteria.
      Title: Association between the genetic variant in the vitamin D pathway (rs2282679), circulating 25-hydroxyvitamin D levels, insulin resistance and metabolic syndrome criteria.
    5. Vitamin D receptor and binding protein genes variants in patients with migraine.
      Title: Vitamin D receptor and binding protein genes variants in patients with migraine.
    6. Vitamin D-Binding Protein and the Role of its Gene Polymorphisms in the Mortality of Sepsis Patients.
      Title: Vitamin D-Binding Protein and the Role of its Gene Polymorphisms in the Mortality of Sepsis Patients.
    7. Genetic influence on urinary vitamin D binding protein excretion and serum levels: a focus on rs4588 C>A polymorphism in the GC gene.
      Title: Genetic influence on urinary vitamin D binding protein excretion and serum levels: a focus on rs4588 C>A polymorphism in the GC gene.
    8. Vitamin D receptor rs3782905 and vitamin D binding protein rs7041 polymorphisms are associated with hepatocellular carcinoma susceptibility in cirrhotic HCV patients.
      Title: Vitamin D receptor rs3782905 and vitamin D binding protein rs7041 polymorphisms are associated with hepatocellular carcinoma susceptibility in cirrhotic HCV patients.
    9. The Molecular Aspects of Functional Activity of Macrophage-Activating Factor GcMAF.
      Title: The Molecular Aspects of Functional Activity of Macrophage-Activating Factor GcMAF.
    10. Sex-Specific Variations in Vitamin D and Vitamin D Binding Protein (Vdbp) and Flipped Pattern of their Association in Preeclamptic Women with Dyslipidemia.
      Title: Sex-Specific Variations in Vitamin D and Vitamin D Binding Protein (Vdbp) and Flipped Pattern of their Association in Preeclamptic Women with Dyslipidemia.
    Submit: New GeneRIF Correction See all GeneRIFs (310)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Association between liver-specific gene polymorphisms and their expression levels with nonalcoholic fatty liver disease.
    EBI GWAS Catalog
    Common genetic determinants of vitamin D insufficiency: a genome-wide association study.
    EBI GWAS Catalog
    Genome-wide association analysis of circulating vitamin D levels in children with asthma.
    EBI GWAS Catalog
    Genome-wide association study of circulating vitamin D levels.
    EBI GWAS Catalog
    Genome-wide association study of circulating vitamin D-binding protein.
    EBI GWAS Catalog
    Genome-wide association study of vitamin D levels in children: replication in the Western Australian Pregnancy Cohort (Raine) study.
    EBI GWAS Catalog
    Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
    EBI GWAS Catalog

    Variation

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    See Variation Viewer (GRCh37.p13)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables calcidiol binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables vitamin D binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables vitamin transmembrane transporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in vitamin D metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vitamin transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in vitamin transport TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in blood microparticle HDA PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in extracellular region NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular space HDA PubMed 
    located_in lysosomal lumen TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    vitamin D-binding protein
    Names
    epididymis secretory protein Li 51
    gc protein-derived macrophage activating factor
    gc-globulin
    group-specific component (vitamin D binding protein)
    vitamin D-binding alpha-globulin
    vitamin D-binding protein-macrophage activating factor
    NP_000574.2
    NP_001191235.1
    NP_001191236.1
    XP_006714240.1
    XP_054205648.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_012837.3 RefSeqGene

      Range
      26442..68824
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000583.4 → NP_000574.2  vitamin D-binding protein isoform 1 precursor

      See identical proteins and their annotated locations for NP_000574.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) is a predominant transcript. This variant and variant 2 encode the same isoform (1).
      Source sequence(s)
      AA702473, AK223458, X03178
      Consensus CDS
      CCDS3550.1
      UniProtKB/Swiss-Prot
      B4DPP2, D6RAK8, P02774, Q16309, Q16310, Q53F31, Q6GTG1
      UniProtKB/TrEMBL
      V9HWI6
      Related
      ENSP00000273951.8, ENST00000273951.13
      Conserved Domains (2) summary
      smart00103
      Location:19 → 201
      ALBUMIN; serum albumin
      pfam09164
      Location:405 → 469
      VitD-bind_III; Vitamin D binding protein, domain III

    2. NM_001204306.1 → NP_001191235.1  vitamin D-binding protein isoform 1 precursor

      See identical proteins and their annotated locations for NP_001191235.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has an alternate 5' UTR and encodes the same isoform 1, as compared to variant 1.
      Source sequence(s)
      AA702473, AK223458
      Consensus CDS
      CCDS3550.1
      UniProtKB/Swiss-Prot
      B4DPP2, D6RAK8, P02774, Q16309, Q16310, Q53F31, Q6GTG1
      UniProtKB/TrEMBL
      V9HWI6
      Conserved Domains (2) summary
      smart00103
      Location:19 → 201
      ALBUMIN; serum albumin
      pfam09164
      Location:405 → 469
      VitD-bind_III; Vitamin D binding protein, domain III

    3. NM_001204307.1 → NP_001191236.1  vitamin D-binding protein isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has an alternate 5' sequence which contains an upstream in-frame AUG start codon, as compared to variant 1. The resulting isoform (2) has a longer N-terminus, as compared to isoform 1.
      Source sequence(s)
      AA702473, AC024722, AK223458, AK309595, AK315853
      Consensus CDS
      CCDS56332.1
      UniProtKB/TrEMBL
      V9HWI6
      Related
      ENSP00000421725.1, ENST00000504199.5
      Conserved Domains (2) summary
      smart00103
      Location:38 → 220
      ALBUMIN; serum albumin
      pfam09164
      Location:424 → 488
      VitD-bind_III; Vitamin D binding protein, domain III

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      71741693..71805520 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006714177.3 → XP_006714240.1  vitamin D-binding protein isoform X1

      UniProtKB/TrEMBL
      V9HWI6
      Related
      ENSP00000422664.1, ENST00000509740.5
      Conserved Domains (1) summary
      smart00103
      Location:19 → 201
      ALBUMIN; serum albumin

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      75084117..75147957 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054349673.1 → XP_054205648.1  vitamin D-binding protein isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P02774.2 GenPept UniProtKB/Swiss-Prot:P02774

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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