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Aliases for COLEC12 Gene

Aliases for COLEC12 Gene

  • Collectin Subfamily Member 12 2 3 5
  • Scavenger Receptor With C-Type Lectin 3 4
  • Nurse Cell Scavenger Receptor 2 3 4
  • Collectin Placenta Protein 1 3 4
  • SCARA4 3 4
  • HCL-P1 3 4
  • CLP1 3 4
  • NSR2 3 4
  • SRCL 3 4
  • Scavenger Receptor Class A, Member 4 3
  • Scavenger Receptor Class A Member 4 4
  • Collectin Sub-Family Member 12 3
  • Collectin-12 3
  • CL-P1 4

External Ids for COLEC12 Gene

Previous GeneCards Identifiers for COLEC12 Gene

  • GC18M000603
  • GC18M000306

Summaries for COLEC12 Gene

Entrez Gene Summary for COLEC12 Gene

  • 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]

GeneCards Summary for COLEC12 Gene

COLEC12 (Collectin Subfamily Member 12) is a Protein Coding gene. Diseases associated with COLEC12 include Syndromic X-Linked Intellectual Disability Snyder Type and Background Diabetic Retinopathy. Among its related pathways are Phagosome and Binding and Uptake of Ligands by Scavenger Receptors. Gene Ontology (GO) annotations related to this gene include scavenger receptor activity and signaling pattern recognition receptor activity. An important paralog of this gene is SCARA3.

UniProtKB/Swiss-Prot for COLEC12 Gene

  • Scavenger receptor that displays several functions associated with host defense. Promotes binding and phagocytosis of Gram-positive, Gram-negative bacteria and yeast. Mediates the recognition, internalization and degradation of oxidatively modified low density lipoprotein (oxLDL) by vascular endothelial cells. Binds to several carbohydrates including Gal-type ligands, D-galactose, L- and D-fucose, GalNAc, T and Tn antigens in a calcium-dependent manner and internalizes specifically GalNAc in nurse-like cells. Binds also to sialyl Lewis X or a trisaccharide and asialo-orosomucoid (ASOR). May also play a role in the clearance of amyloid-beta in Alzheimer disease.

Additional gene information for COLEC12 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COLEC12 Gene

Genomics for COLEC12 Gene

GeneHancer (GH) Regulatory Elements for COLEC12 Gene

Promoters and enhancers for COLEC12 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH18J000498 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 650.7 +0.9 900 2.3 PKNOX1 FOXA2 FEZF1 GLI4 ZNF2 GLIS2 ZNF213 KLF7 SP3 TSHZ1 COLEC12 LINC01925 RN7SKP146 ENSG00000265671 LOC105371950 IL9RP4 LOC105371953 ENSG00000263396 SLC25A3P3 GC18P000435
GH18J000392 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 11.3 +105.8 105821 4.8 PKNOX1 ARNT FEZF1 ZNF2 GLIS2 ZNF213 FOS SP3 REST TSHZ1 THOC1 LINC01925 RN7SKP146 IL9RP4 LOC105371950 ENSG00000265671 LOC105371953 SLC25A3P3 ENSG00000263396 COLEC12
GH18J000360 Enhancer 1.3 Ensembl ENCODE dbSUPER 11.1 +137.6 137641 4.8 FOXA2 MLX ARID4B FEZF1 ZNF2 ZNF48 ETS1 ZNF213 KLF7 TSHZ1 COLEC12 CETN1 GC18P000404 ENSG00000264514
GH18J000331 Enhancer 0.9 FANTOM5 Ensembl ENCODE 15.5 +168.3 168274 2.8 CTCF IKZF1 CBFA2T3 COLEC12 CLUL1 ENSG00000264514 GC18P000404
GH18J000474 Enhancer 1.1 Ensembl ENCODE dbSUPER 12.4 +25.2 25168 2.4 CTCF ZBTB6 ZNF792 SAP130 JUN RARA ZNF7 ETS1 TEAD3 POLR2A COLEC12 THOC1 CLUL1 CETN1 USP14 GC18P000435
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around COLEC12 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the COLEC12 gene promoter:

Genomic Locations for COLEC12 Gene

Genomic Locations for COLEC12 Gene
chr18:316,740-500,729
(GRCh38/hg38)
Size:
183,990 bases
Orientation:
Minus strand
chr18:319,355-500,729
(GRCh37/hg19)

Genomic View for COLEC12 Gene

Genes around COLEC12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COLEC12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COLEC12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COLEC12 Gene

Proteins for COLEC12 Gene

  • Protein details for COLEC12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5KU26-COL12_HUMAN
    Recommended name:
    Collectin-12
    Protein Accession:
    Q5KU26
    Secondary Accessions:
    • Q6P9F2
    • Q8TCR2
    • Q8WZA4
    • Q9BY85
    • Q9BYH7

    Protein attributes for COLEC12 Gene

    Size:
    742 amino acids
    Molecular mass:
    81515 Da
    Quaternary structure:
    • The extracellular domain forms a stable trimer. The extracellular domain interacts with fibrillar amyloid-beta peptide.
    SequenceCaution:
    • Sequence=BAB39148.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for COLEC12 Gene

neXtProt entry for COLEC12 Gene

Post-translational modifications for COLEC12 Gene

  • Glycosylation at posLast=271271, posLast=168168, posLast=159159, and Asn67
  • Modification sites at PhosphoSitePlus

Other Protein References for COLEC12 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for COLEC12 Gene

Domains & Families for COLEC12 Gene

Gene Families for COLEC12 Gene

Suggested Antigen Peptide Sequences for COLEC12 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with COLEC12: view

No data available for UniProtKB/Swiss-Prot for COLEC12 Gene

Function for COLEC12 Gene

Molecular function for COLEC12 Gene

UniProtKB/Swiss-Prot Function:
Scavenger receptor that displays several functions associated with host defense. Promotes binding and phagocytosis of Gram-positive, Gram-negative bacteria and yeast. Mediates the recognition, internalization and degradation of oxidatively modified low density lipoprotein (oxLDL) by vascular endothelial cells. Binds to several carbohydrates including Gal-type ligands, D-galactose, L- and D-fucose, GalNAc, T and Tn antigens in a calcium-dependent manner and internalizes specifically GalNAc in nurse-like cells. Binds also to sialyl Lewis X or a trisaccharide and asialo-orosomucoid (ASOR). May also play a role in the clearance of amyloid-beta in Alzheimer disease.

Phenotypes From GWAS Catalog for COLEC12 Gene

Gene Ontology (GO) - Molecular Function for COLEC12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005044 scavenger receptor activity TAS 11162630
GO:0005534 galactose binding NAS 11564734
GO:0008329 signaling pattern recognition receptor activity IDA 11564734
GO:0030169 low-density lipoprotein particle binding IDA 11564734
GO:0030246 carbohydrate binding IEA --
genes like me logo Genes that share ontologies with COLEC12: view
genes like me logo Genes that share phenotypes with COLEC12: view

Animal Model Products

  • Taconic Biosciences Mouse Models for COLEC12

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for COLEC12 Gene

Localization for COLEC12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COLEC12 Gene

Membrane; Single-pass type II membrane protein. Note=Forms clusters on the cell surface.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for COLEC12 gene
Compartment Confidence
plasma membrane 5
extracellular 5
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
cytosol 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (2)
  • Golgi apparatus (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for COLEC12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005581 collagen trimer IEA --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane TAS 11162630
GO:0030666 endocytic vesicle membrane TAS --
genes like me logo Genes that share ontologies with COLEC12: view

Pathways & Interactions for COLEC12 Gene

genes like me logo Genes that share pathways with COLEC12: view

Pathways by source for COLEC12 Gene

Gene Ontology (GO) - Biological Process for COLEC12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006898 receptor-mediated endocytosis TAS --
GO:0006910 phagocytosis, recognition IDA 11564734
GO:0006952 defense response TAS 11162630
GO:0006955 immune response IEA --
GO:0009756 carbohydrate mediated signaling NAS 11564734
genes like me logo Genes that share ontologies with COLEC12: view

No data available for SIGNOR curated interactions for COLEC12 Gene

Drugs & Compounds for COLEC12 Gene

(2) Drugs for COLEC12 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Galactose Approved, Investigational Pharma 0
calcium Approved Nutra 0

(2) Additional Compounds for COLEC12 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Lewis X trisaccharide
  • 3-Fucosyl-N-acetyllactosamine
  • FAL
  • Lewis X
  • Lex
  • Lex tri
71208-06-5
genes like me logo Genes that share compounds with COLEC12: view

Transcripts for COLEC12 Gene

mRNA/cDNA for COLEC12 Gene

Unigene Clusters for COLEC12 Gene

Collectin sub-family member 12:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for COLEC12 Gene

No ASD Table

Relevant External Links for COLEC12 Gene

GeneLoc Exon Structure for
COLEC12
ECgene alternative splicing isoforms for
COLEC12

Expression for COLEC12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for COLEC12 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for COLEC12 Gene

This gene is overexpressed in Placenta (16.6) and Cerebrospinal fluid (15.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for COLEC12 Gene



NURSA nuclear receptor signaling pathways regulating expression of COLEC12 Gene:

COLEC12

SOURCE GeneReport for Unigene cluster for COLEC12 Gene:

Hs.464422

mRNA Expression by UniProt/SwissProt for COLEC12 Gene:

Q5KU26-COL12_HUMAN
Tissue specificity: Expressed in perivascular macrophages. Expressed in plaques-surrounding reactive astrocytes and in perivascular astrocytes associated with cerebral amyloid angiopathy (CAA) in the temporal cortex of Alzheimer patient (at protein level). Strongly expressed in placenta. Moderately expressed in heart, skeletal muscle, small intestine and lung. Weakly expressed in brain, colon, thymus and kidney. Expressed in nurse-like cells. Expressed in reactive astrocytes and vascular/perivascular cells in the brain of Alzheimer patient.

Evidence on tissue expression from TISSUES for COLEC12 Gene

  • Lung(4.3)
  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with COLEC12: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for COLEC12 Gene

Orthologs for COLEC12 Gene

This gene was present in the common ancestor of animals.

Orthologs for COLEC12 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia COLEC12 34 33
  • 99.37 (n)
OneToOne
dog
(Canis familiaris)
Mammalia COLEC12 34 33
  • 91.11 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia COLEC12 34
  • 89 (a)
OneToOne
cow
(Bos Taurus)
Mammalia COLEC12 34 33
  • 88.36 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Colec12 33
  • 87.87 (n)
mouse
(Mus musculus)
Mammalia Colec12 16 34 33
  • 87.69 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia COLEC12 34
  • 85 (a)
OneToOne
chicken
(Gallus gallus)
Aves COLEC12 34 33
  • 76.03 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia COLEC12 34
  • 76 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia colec12 33
  • 67.31 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.19955 33
zebrafish
(Danio rerio)
Actinopterygii colec12 34 33
  • 57.06 (n)
OneToOne
idibd2826 33
worm
(Caenorhabditis elegans)
Secernentea col-187 34
  • 29 (a)
ManyToMany
col-118 34
  • 29 (a)
ManyToMany
col-148 34
  • 27 (a)
ManyToMany
col-89 34
  • 26 (a)
ManyToMany
col-149 34
  • 25 (a)
ManyToMany
col-176 34
  • 25 (a)
ManyToMany
col-150 34
  • 25 (a)
ManyToMany
col-145 34
  • 24 (a)
ManyToMany
col-144 34
  • 24 (a)
ManyToMany
col-10 34
  • 24 (a)
ManyToMany
col-126 34
  • 24 (a)
ManyToMany
col-127 34
  • 24 (a)
ManyToMany
col-61 34
  • 23 (a)
ManyToMany
col-177 34
  • 19 (a)
ManyToMany
Species where no ortholog for COLEC12 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for COLEC12 Gene

ENSEMBL:
Gene Tree for COLEC12 (if available)
TreeFam:
Gene Tree for COLEC12 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for COLEC12: view image

Paralogs for COLEC12 Gene

Paralogs for COLEC12 Gene

(5) SIMAP similar genes for COLEC12 Gene using alignment to 1 proteins:

  • COL12_HUMAN
genes like me logo Genes that share paralogs with COLEC12: view

Variants for COLEC12 Gene

Sequence variations from dbSNP and Humsavar for COLEC12 Gene

SNP ID Clin Chr 18 pos Variation AA Info Type
rs1000014768 -- 454,009(-) C/T intron_variant
rs1000018784 -- 365,972(-) G/A intron_variant
rs1000028344 -- 459,996(-) G/T intron_variant
rs1000085093 -- 413,039(-) A/G intron_variant
rs1000096828 -- 399,330(-) GG/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for COLEC12 Gene

Variant ID Type Subtype PubMed ID
dgv3301n100 CNV gain 25217958
dgv3306n100 CNV loss 25217958
dgv3307n100 CNV gain 25217958
dgv5810n54 CNV gain 21841781
dgv594e214 CNV gain 21293372
esv3554937 CNV deletion 23714750
esv3582928 CNV loss 25503493
esv3582929 CNV loss 25503493
esv3582930 CNV loss 25503493
esv3641472 CNV loss 21293372
esv3641473 CNV gain 21293372
esv3641484 CNV gain 21293372
esv3641486 CNV loss 21293372
esv3641488 CNV gain 21293372
esv3641490 CNV loss 21293372
esv3641491 CNV loss 21293372
esv3641492 CNV loss 21293372
esv3641495 CNV gain 21293372
esv3893055 CNV gain 25118596
esv3893056 CNV gain 25118596
nsv1064150 CNV gain 25217958
nsv1066129 CNV gain 25217958
nsv1066337 CNV gain 25217958
nsv1066822 CNV gain 25217958
nsv1070858 CNV deletion 25765185
nsv1109117 CNV deletion 24896259
nsv1138591 CNV deletion 24896259
nsv2177 CNV insertion 18451855
nsv457977 CNV gain 19166990
nsv475138 CNV novel sequence insertion 20440878
nsv477785 CNV novel sequence insertion 20440878
nsv482935 CNV loss 15286789
nsv510444 OTHER sequence alteration 20534489
nsv517980 CNV loss 19592680
nsv518642 CNV gain 19592680
nsv522804 CNV loss 19592680
nsv576227 CNV gain 21841781
nsv576228 CNV loss 21841781
nsv576235 CNV gain 21841781
nsv576236 CNV gain 21841781
nsv576238 CNV loss 21841781
nsv576239 CNV gain 21841781

Variation tolerance for COLEC12 Gene

Residual Variation Intolerance Score: 75.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.03; 92.12% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for COLEC12 Gene

Human Gene Mutation Database (HGMD)
COLEC12
SNPedia medical, phenotypic, and genealogical associations of SNPs for
COLEC12

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COLEC12 Gene

Disorders for COLEC12 Gene

MalaCards: The human disease database

(2) MalaCards diseases for COLEC12 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
syndromic x-linked intellectual disability snyder type
  • srs
background diabetic retinopathy
  • non proliferative diabetic retinopathy
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for COLEC12

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with COLEC12: view

No data available for UniProtKB/Swiss-Prot and Genatlas for COLEC12 Gene

Publications for COLEC12 Gene

  1. Molecular cloning and functional characterization of a human scavenger receptor with C-type lectin (SRCL), a novel member of a scavenger receptor family. (PMID: 11162630) Nakamura K … Nakamura T (Biochemical and biophysical research communications 2001) 2 3 4 22 58
  2. Selective binding of the scavenger receptor C-type lectin to Lewisx trisaccharide and related glycan ligands. (PMID: 15845541) Coombs PJ … Taylor ME (The Journal of biological chemistry 2005) 3 4 22 58
  3. Haplotype analysis of the human collectin placenta 1 (hCL-P1) gene. (PMID: 12601552) Ohmori H … Hata A (Journal of human genetics 2003) 3 4 22 58
  4. The membrane-type collectin CL-P1 is a scavenger receptor on vascular endothelial cells. (PMID: 11564734) Ohtani K … Wakamiya N (The Journal of biological chemistry 2001) 3 4 22 58
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58

Products for COLEC12 Gene

Sources for COLEC12 Gene

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