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

Gene ID: 81035, updated on 2-Nov-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
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Genomic context

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See COLEC12 in Genome Data Viewer
Location:
18p11.32
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (316737..500701, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (470846..654740, complement)
RS_2024_09 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 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. COLEC12 Promotes Tumor Progression and Is Correlated With Poor Prognosis in Gastric Cancer. Sun X, et al. Technol Cancer Res Treat, 2023 Jan-Dec. PMID 38112409, Free PMC Article
  2. Molecular cloning and functional characterization of a human scavenger receptor with C-type lectin (SRCL), a novel member of a scavenger receptor family. Nakamura K, et al. Biochem Biophys Res Commun, 2001 Feb 2. PMID 11162630
  3. Haplotype analysis of the human collectin placenta 1 (hCL-P1) gene. Ohmori H, et al. J Hum Genet, 2003. PMID 12601552
  4. SRCL/CL-P1 recognizes GalNAc and a carcinoma-associated antigen, Tn antigen. Yoshida T, et al. J Biochem, 2003 Mar. PMID 12761161
  5. 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

See all (40) 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_2024_08

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

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Chemical Information
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