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    COLEC12 collectin subfamily member 12 [ Homo sapiens (human) ]

    Gene ID: 81035, updated on 16-Apr-2024

    Summary

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    Official Symbol
    COLEC12provided by HGNC
    Official Full Name
    collectin subfamily member 12provided by HGNC
    Primary source
    HGNC:HGNC:16016
    See related
    Ensembl:ENSG00000158270 MIM:607621; AllianceGenome:HGNC:16016
    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
    CLP1; NSR2; SRCL; SCARA4
    Summary
    This gene encodes a member of the C-lectin family, proteins that possess collagen-like sequences and carbohydrate recognition domains. This protein is a scavenger receptor that displays several functions associated with host defense. It can bind to carbohydrate antigens on microorganisms, facilitating their recognition and removal. It also mediates the recognition, internalization, and degradation of oxidatively modified low density lipoprotein by vascular endothelial cells. [provided by RefSeq, May 2018]
    Expression
    Broad expression in placenta (RPKM 63.7), lung (RPKM 26.0) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    18p11.32
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (316737..500701, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (470846..654740, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (316737..500701, complement)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371951 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9236 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9237 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:185973-186474 Neighboring gene ubiquitin specific peptidase 14 Neighboring gene THO complex subunit 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13019 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9238 Neighboring gene uncharacterized LOC107985155 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:394012-395211 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:419844-420037 Neighboring gene OCT4 hESC enhancer GRCh37_chr18:420584-421135 Neighboring gene Sharpr-MPRA regulatory region 14658 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:505812-505991 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13020 Neighboring gene long intergenic non-protein coding RNA 1925 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:535941-536594 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:564852-565352 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:565353-565853 Neighboring gene centrin 1

    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. Identification of neutrophil granule glycoproteins as Lewis(x)-containing ligands cleared by the scavenger receptor C-type lectin. Graham SA, et al. J Biol Chem, 2011 Jul 8. PMID 21561871, Free PMC Article
    2. Expression and tissue localization of collectin placenta 1 (CL-P1, SRCL) in human tissues. Selman L, et al. Mol Immunol, 2008 Jun. PMID 18423602
    3. Selective binding of the scavenger receptor C-type lectin to Lewisx trisaccharide and related glycan ligands. Coombs PJ, et al. J Biol Chem, 2005 Jun 17. PMID 15845541
    4. SRCL/CL-P1 recognizes GalNAc and a carcinoma-associated antigen, Tn antigen. Yoshida T, et al. J Biochem, 2003 Mar. PMID 12761161
    5. Haplotype analysis of the human collectin placenta 1 (hCL-P1) gene. Ohmori H, et al. J Hum Genet, 2003. PMID 12601552

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Dysregulated AEBP1 and COLEC12 Genes in Late-Onset Alzheimer's Disease: Insights from Brain Cortex and Peripheral Blood Analysis.
      Title: Dysregulated AEBP1 and COLEC12 Genes in Late-Onset Alzheimer's Disease: Insights from Brain Cortex and Peripheral Blood Analysis.
    2. COLEC12 Promotes Tumor Progression and Is Correlated With Poor Prognosis in Gastric Cancer.
      Title: COLEC12 Promotes Tumor Progression and Is Correlated With Poor Prognosis in Gastric Cancer.
    3. COLEC12 regulates apoptosis of osteosarcoma through Toll-like receptor 4-activated inflammation.
      Title: COLEC12 regulates apoptosis of osteosarcoma through Toll-like receptor 4-activated inflammation.
    4. Soluble collectin-12 mediates C3-independent docking of properdin that activates the alternative pathway of complement.
      Title: Soluble collectin-12 mediates C3-independent docking of properdin that activates the alternative pathway of complement.
    5. COLEC12 integrates H. pylori, PGE2-EP2/4 axis and innate immunity in gastric diseases
      Title: Stromal C-type lectin receptor COLEC12 integrates H. pylori, PGE2-EP2/4 axis and innate immunity in gastric diseases.
    6. CL-P1 is a novel receptor involved in myelin uptake by phagocytes and likely plays a role in multiple sclerosis lesion development.
      Title: Scavenger receptor collectin placenta 1 is a novel receptor involved in the uptake of myelin by phagocytes.
    7. rs17684886 (ZNRF1) and rs599019 (COLEC12) are associated with diabetic retinopathy and rs6427247 (SCYL1BP1) and rs899036 (API5) are associated with severe diabetic retinopathy in Chinese patients with type 2 diabetes
      Title: Common variants in or near ZNRF1, COLEC12, SCYL1BP1 and API5 are associated with diabetic retinopathy in Chinese patients with type 2 diabetes.
    8. The common presence of Lewis(x) groups in granule protein glycans can thus target granule proteins for clearance by SRCL.
      Title: Identification of neutrophil granule glycoproteins as Lewis(x)-containing ligands cleared by the scavenger receptor C-type lectin.
    9. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    10. The Le(x) residues of both, CEACAM1 and CEA, interact with the human Le(x)-binding glycan receptors DC-SIGN and SRCL.
      Title: DC-SIGN and SRCL bind glycans of carcinoembryonic antigen (CEA) and CEA-related cell adhesion molecule 1 (CEACAM1): recombinant human glycan-binding receptors as analytical tools.
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    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
    Meta-analysis of genome-wide association data of bipolar disorder and major depressive disorder.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vif vif HIV-1 Vif downregulates the expression of collectin sub-family member 12 (COLEC12) in Vif-expression T cells PubMed

    Go to the HIV-1, Human Interaction Database

    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 galactose binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables low-density lipoprotein particle binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables low-density lipoprotein particle binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables pattern recognition receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables pattern recognition receptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables scavenger receptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables scavenger receptor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in carbohydrate mediated signaling NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    NOT involved_in cellular response to exogenous dsRNA IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cellular response to exogenous dsRNA IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in defense response TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in defense response to bacterium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in innate immune response TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in phagocytosis, recognition IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in phagocytosis, recognition IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_positive_effect plasma membrane raft organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in toll-like receptor 3 signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of collagen trimer IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endocytic vesicle membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    collectin-12
    Names
    collectin placenta protein 1
    collectin sub-family member 12
    hCL-P1
    nurse cell scavenger receptor 2
    scavenger receptor class A, member 4
    scavenger receptor with C-type lectin

    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_030342.2 RefSeqGene

      Range
      5000..188964
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_130386.3 → NP_569057.2  collectin-12

      Status: REVIEWED

      Source sequence(s)
      AP000915, AP005240
      Consensus CDS
      CCDS32782.1
      UniProtKB/Swiss-Prot
      Q5KU26, Q6P9F2, Q8TCR2, Q8WZA4, Q9BY85, Q9BYH7
      Related
      ENSP00000383115.3, ENST00000400256.5
      Conserved Domains (2) summary
      cd03590
      Location:607 → 732
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
      cl25732
      Location:77 → 350
      SMC_N; RecF/RecN/SMC N terminal domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      316737..500701 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011525741.3 → XP_011524043.1  collectin-12 isoform X1

      Conserved Domains (3) summary
      cd03590
      Location:590 → 715
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
      pfam05714
      Location:49 → 171
      Borrelia_lipo_1; Borrelia burgdorferi virulent strain associated lipoprotein
      cl02193
      Location:140 → 300
      VirB5_like; VirB5 protein family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      470846..654740 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319231.1 → XP_054175206.1  collectin-12 isoform X1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_030781.2: Suppressed sequence

      Description
      NM_030781.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5KU26.3 GenPept UniProtKB/Swiss-Prot:Q5KU26

    Gene LinkOut

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

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