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CLEC3A C-type lectin domain family 3 member A [ Homo sapiens (human) ]

Gene ID: 10143, updated on 5-Mar-2024

Summary

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Official Symbol
CLEC3Aprovided by HGNC
Official Full Name
C-type lectin domain family 3 member Aprovided by HGNC
Primary source
HGNC:HGNC:2052
See related
Ensembl:ENSG00000166509 MIM:613588; AllianceGenome:HGNC:2052
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CLECSF1
Summary
Predicted to enable carbohydrate binding activity. Predicted to be involved in ossification. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in urinary bladder (RPKM 4.3), gall bladder (RPKM 1.0) and 1 other tissue See more
Orthologs
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Genomic context

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Location:
16q23.1
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (78022548..78032101)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (84078524..84088079)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (78056445..78065998)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene vesicle amine transport 1 like Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:77928177-77928677 Neighboring gene peptidylprolyl isomerase A pseudogene 50 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:77952963-77953462 Neighboring gene uncharacterized LOC105371351 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45464 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11154 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:78000722-78001339 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:78001340-78001958 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:78003196-78003813 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45488 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:78025071-78026270 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:78026297-78026990 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:78026991-78027683 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:78028377-78029069 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:78029289-78030488 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45524 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45539 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7735 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45548 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45593 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45596 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45605 Neighboring gene uncharacterized LOC107984897 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45663 Neighboring gene leucine rich repeat containing 59 pseudogene Neighboring gene keratin 8 pseudogene 22

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. C-type lectin domain-containing protein CLEC3A regulates proliferation, regeneration and maintenance of nucleus pulposus cells. Chen X, et al. Cell Mol Life Sci, 2022 Jul 21. PMID 35864364
  2. Suppression of CLEC3A inhibits osteosarcoma cell proliferation and promotes their chemosensitivity through the AKT1/mTOR/HIF1α signaling pathway. Ren C, et al. Mol Med Rep, 2020 Apr. PMID 32319617, Free PMC Article
  3. The cartilage-derived, C-type lectin (CLECSF1): structure of the gene and chromosomal location. Neame PJ, et al. Biochim Biophys Acta, 1999 Sep 3. PMID 10524194
  4. Matrilysin (MMP-7) cleaves C-type lectin domain family 3 member A (CLEC3A) on tumor cell surface and modulates its cell adhesion activity. Tsunezumi J, et al. J Cell Biochem, 2009 Mar 1. PMID 19173304
  5. CLEC3A, MMP7, and LCN2 as novel markers for predicting recurrence in resected G1 and G2 pancreatic neuroendocrine tumors. Miki M, et al. Cancer Med, 2019 Jul. PMID 31129920, Free PMC Article

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. C-type lectin domain-containing protein CLEC3A regulates proliferation, regeneration and maintenance of nucleus pulposus cells.
    Title: C-type lectin domain-containing protein CLEC3A regulates proliferation, regeneration and maintenance of nucleus pulposus cells.
  2. Suppression of CLEC3A inhibits osteosarcoma cell proliferation and promotes their chemosensitivity through the AKT1/mTOR/HIF1alpha signaling pathway.
    Title: Suppression of CLEC3A inhibits osteosarcoma cell proliferation and promotes their chemosensitivity through the AKT1/mTOR/HIF1α signaling pathway.
  3. we demonstrated that the recurrence potential in PNETs is characterized by the upregulation of genes related to ECM organization and cell adhesion. This study identified three genes-CLEC3, MMP7, and LCN2-that contribute to the prediction of postoperative recurrence of PNETs in clinical practice.
    Title: CLEC3A, MMP7, and LCN2 as novel markers for predicting recurrence in resected G1 and G2 pancreatic neuroendocrine tumors.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects.
  5. CLEC3A binds to heparan sulfate proteoglycans on cell surface, leading to the enhancement of cell adhesion to integrin ligands on ECM; cleavage of CLEC3A by MMP-7 weakens the stable adhesion of tumor cells to the matrix
    Title: Matrilysin (MMP-7) cleaves C-type lectin domain family 3 member A (CLEC3A) on tumor cell surface and modulates its cell adhesion activity.
Submit: New GeneRIF Correction

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
Gene-alcohol interactions identify several novel blood pressure loci including a promising locus near SLC16A9.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC129558, MGC129559

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables carbohydrate binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in ossification IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in skeletal system development TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
C-type lectin domain family 3 member A
Names
C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 1 (cartilage-derived)

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.

mRNA and Protein(s)

  1. NM_005752.6 → NP_005743.5  C-type lectin domain family 3 member A precursor

    Status: VALIDATED

    Source sequence(s)
    AC079414, AK313316, AY358376
    Consensus CDS
    CCDS10927.3
    UniProtKB/Swiss-Prot
    B2R8C4, O75596, Q3SX91, Q6UXF5
    UniProtKB/TrEMBL
    Q3SX92
    Related
    ENSP00000299642.5, ENST00000299642.10
    Conserved Domains (1) summary
    cd03596
    Location:68 → 193
    CLECT_tetranectin_like; C-type lectin-like domain (CTLD) of the type found in the tetranectin (TN), cartilage derived C-type lectin (CLECSF1), and stem cell growth factor (SCGF)

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    78022548..78032101
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    84078524..84088079
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001244755.1: Suppressed sequence

    Description
    NM_001244755.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75596.1 GenPept UniProtKB/Swiss-Prot:O75596

Gene LinkOut

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

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