CLEC3B C-type lectin domain family 3 member B [Homo sapiens (human)] - Gene

Summary

Official Symbol: CLEC3Bprovided by HGNC
Official Full Name: C-type lectin domain family 3 member Bprovided by HGNC
Primary source: HGNC:HGNC:11891
See related: Ensembl:ENSG00000163815 MIM:187520; AllianceGenome:HGNC:11891
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: TN; TNA; MCDR4
Summary: Enables calcium ion binding activity; heparin binding activity; and kringle domain binding activity. Involved in bone mineralization. Located in cytoplasm; extracellular space; and granular component. Implicated in osteoarthritis and retinal macular dystrophy 4. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Broad expression in spleen (RPKM 63.9), fat (RPKM 63.1) and 20 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p21.31

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (45026303..45036071)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (45042041..45051809)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (45067795..45077563)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Tetranectin as a potential novel prognostic biomarker in anthracycline-related cardiac dysfunction.
Title: Tetranectin as a potential novel prognostic biomarker in anthracycline-related cardiac dysfunction.
Down-regulation of CLEC3B facilitates epithelial-mesenchymal transition, migration and invasion of lung adenocarcinoma cells.
Title: Down-regulation of CLEC3B facilitates epithelial-mesenchymal transition, migration and invasion of lung adenocarcinoma cells.
CLEC3B p.S106G Mutant in a Caucasian Population of Successful Neurological Aging.
Title: CLEC3B p.S106G Mutant in a Caucasian Population of Successful Neurological Aging.
The In Vitro Biotransformation of the Fusion Protein Tetranectin-Apolipoprotein A1.
Title: The In Vitro Biotransformation of the Fusion Protein Tetranectin-Apolipoprotein A1.
CLEC3B alleviated the injury of hypoxic H9c2 cardiomyocytes via the PI3K/Akt pathway
Title: CLEC3B protects H9c2 cardiomyocytes from apoptosis caused by hypoxia via the PI3K/Akt pathway.
CLEC3B acts as a novel independent prognostic factor
Title: Downregulation of exosomal CLEC3B in hepatocellular carcinoma promotes metastasis and angiogenesis via AMPK and VEGF signals.
Integrative epigenomics, transcriptomics and proteomics of patients chondrocytes from hip or knee osteoarthritis (OA) identified AQP1, COL1A1 and CLEC3B as significantly and differentially regulated suggesting they play an important role in OA pathogenesis.
Title: Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis.
Low CLEC3B expression is associated with clear cell renal cell carcinoma.
Title: CLEC3B is downregulated and inhibits proliferation in clear cell renal cell carcinoma.
The present study identified the CLEC3B p.S106G as a novel longevity-associated variant, raising the novel hypothesis that tetranectin, encoded by CLEC3B, plays a role in human longevity and aging
Title: Exome-wide Association Study Identifies CLEC3B Missense Variant p.S106G as Being Associated With Extreme Longevity in East Asian Populations.
TMEM88, CCL14, and CLEC3B genes were stable and available in predicting the survival and palindromia time of hepatocellular carcinoma. These genes could function as potential prognostic genes contributing to improve patients' outcomes and survival
Title: TMEM88, CCL14 and CLEC3B as prognostic biomarkers for prognosis and palindromia of human hepatocellular carcinoma.

Submit: New GeneRIF Correction See all GeneRIFs (15)

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

Associated conditions

Description	Tests
Macular dystrophy, retinal, 4 MedGen: C5774187 OMIM: 619977 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-32929 (e-PCR)
- UniSTS:44510

RH70861 (e-PCR)
- UniSTS:27895

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables carbohydrate binding	IEA Inferred from Electronic Annotation more info
enables heparin binding	IDA Inferred from Direct Assay more info	PubMed
enables kringle domain binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in bone mineralization	IBA Inferred from Biological aspect of Ancestor more info
involved_in bone mineralization	IDA Inferred from Direct Assay more info	PubMed
involved_in ossification	IBA Inferred from Biological aspect of Ancestor more info
involved_in ossification	IEP Inferred from Expression Pattern more info	PubMed
involved_in positive regulation of plasminogen activation	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in collagen-containing extracellular matrix	HDA more info	PubMed
colocalizes_with collagen-containing extracellular matrix	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular region	HDA more info	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 more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in granular component	IDA Inferred from Direct Assay more info	PubMed
located_in platelet dense granule lumen	TAS Traceable Author Statement more info

General protein information

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Preferred Names: tetranectin

Names: plasminogen kringle 4-binding protein; tetranectin (plasminogen-binding protein)

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)

NM_001308394.2 → NP_001295323.1 tetranectin isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks a 5' exon and contains an alternate 5' terminal exon, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1.

Source sequence(s)

BI826174, BI826652, BM669340, CD616729

Consensus CDS

CCDS77730.1

UniProtKB/TrEMBL

E9PHK0, Q68DS3

Related

ENSP00000396013.1, ENST00000428034.1

Conserved Domains (1) summary

cd03596
Location:29 → 157

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)
NM_003278.3 → NP_003269.2 tetranectin isoform 1precursor

See identical proteins and their annotated locations for NP_003269.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC104165, BC011024, BI837909

Consensus CDS

CCDS2726.1

UniProtKB/Swiss-Prot

P05452, Q6FGX6

UniProtKB/TrEMBL

B2R582

Related

ENSP00000296130.4, ENST00000296130.5

Conserved Domains (1) summary

cd03596
Location:71 → 199

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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

45026303..45036071

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017007116.2 → XP_016862605.1 tetranectin isoform X1

UniProtKB/TrEMBL

B2R582

Conserved Domains (1) summary

cd03596
Location:38 → 166

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)