Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	10332
Gene name	C-type lectin domain family 4 member M
Gene symbol	CLEC4M
Synonyms (NCBI Gene)	CD209LCD299DC-SIGN2DC-SIGNRDCSIGNRHP10347L-SIGNLSIGN
Chromosome	19
Chromosome location	19p13.2
Summary	This gene encodes a C-type lectin that functions in cell adhesion and pathogen recognition. This receptor recognizes a wide range of evolutionarily divergent pathogens with a large impact on public health, including tuberculosis mycobacteria, and viruses

Show/Hide all (18)

miRTarBase ID	miRNA	Experiments
MIRT896132	hsa-miR-2392	CLIP-seq
MIRT896133	hsa-miR-297	CLIP-seq
MIRT896134	hsa-miR-3149	CLIP-seq
MIRT896135	hsa-miR-3151	CLIP-seq
MIRT896136	hsa-miR-3190	CLIP-seq
MIRT896137	hsa-miR-4447	CLIP-seq
MIRT896138	hsa-miR-4472	CLIP-seq
MIRT896139	hsa-miR-4640-5p	CLIP-seq
MIRT896140	hsa-miR-4651	CLIP-seq
MIRT896141	hsa-miR-4726-5p	CLIP-seq
MIRT896142	hsa-miR-4731-3p	CLIP-seq
MIRT896143	hsa-miR-4801	CLIP-seq
MIRT896144	hsa-miR-4802-5p	CLIP-seq
MIRT896145	hsa-miR-491-5p	CLIP-seq
MIRT896146	hsa-miR-608	CLIP-seq
MIRT896147	hsa-miR-7	CLIP-seq
MIRT2504475	hsa-miR-4468	CLIP-seq
MIRT2504475	hsa-miR-4468	CLIP-seq

Show/Hide all (43)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001618	Function	Virus receptor activity	IDA	15496474, 24623090
GO:0001618	Function	Virus receptor activity	IEA
GO:0001618	Function	Virus receptor activity	IMP	15496474
GO:0002250	Process	Adaptive immune response	IEA
GO:0002376	Process	Immune system process	IEA
GO:0005515	Function	Protein binding	IPI	32296183, 32607506, 32766577, 33961781, 34015061, 34341769
GO:0005537	Function	D-mannose binding	IBA
GO:0005537	Function	D-mannose binding	IEA
GO:0005576	Component	Extracellular region	IEA
GO:0005737	Component	Cytoplasm	NAS	11337487
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS	10072769
GO:0006897	Process	Endocytosis	IEA
GO:0006955	Process	Immune response	IBA
GO:0007159	Process	Leukocyte cell-cell adhesion	NAS	11337487
GO:0009897	Component	External side of plasma membrane	IBA
GO:0009988	Process	Cell-cell recognition	IEA
GO:0009988	Process	Cell-cell recognition	TAS	11337487
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	TAS	11337487
GO:0019062	Process	Virion attachment to host cell	IEA
GO:0019062	Process	Virion attachment to host cell	TAS	11337487
GO:0019065	Process	Receptor-mediated endocytosis of virus by host cell	NAS	15479853, 32766577
GO:0019079	Process	Viral genome replication	NAS	11337487
GO:0019882	Process	Antigen processing and presentation	NAS	11337487
GO:0030246	Function	Carbohydrate binding	IEA
GO:0030246	Function	Carbohydrate binding	NAS	11337487
GO:0030369	Function	ICAM-3 receptor activity	NAS	11257134
GO:0035556	Process	Intracellular signal transduction	NAS	11337487
GO:0038023	Function	Signaling receptor activity	NAS	11257134
GO:0038187	Function	Pattern recognition receptor activity	IBA
GO:0042605	Function	Peptide antigen binding	NAS	11337487
GO:0043657	Component	Host cell	IEA
GO:0045087	Process	Innate immune response	IEA
GO:0046718	Process	Symbiont entry into host cell	IDA	15479853, 24623090, 32766577
GO:0046790	Function	Virion binding	IEA
GO:0046790	Function	Virion binding	TAS	11337487
GO:0046813	Process	Receptor-mediated virion attachment to host cell	IDA	15479853, 32766577
GO:0046872	Function	Metal ion binding	IEA
GO:0046968	Process	Peptide antigen transport	NAS	11337487
GO:0048306	Function	Calcium-dependent protein binding	IPI	12609975
GO:0075733	Process	Intracellular transport of virus	IEA
GO:0075733	Process	Intracellular transport of virus	TAS	11337487

MIM	HGNC	e!Ensembl
605872	13523	ENSG00000104938

Q9H2X3

Protein name

C-type lectin domain family 4 member M (CD209 antigen-like protein 1) (DC-SIGN-related protein) (DC-SIGNR) (Dendritic cell-specific ICAM-3-grabbing non-integrin 2) (DC-SIGN2) (Liver/lymph node-specific ICAM-3-grabbing non-integrin) (L-SIGN) (CD antigen CD

Protein function

Probable pathogen-recognition receptor involved in peripheral immune surveillance in liver. May mediate the endocytosis of pathogens which are subsequently degraded in lysosomal compartments. Is a receptor for ICAM3, probably by binding to manno

PDB

1K9J , 1SL6 , 1XAR , 1XPH , 3JQH , 8RCY

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00059	Lectin_C	285 → 391	Lectin C-type domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Predominantly highly expressed in liver sinusoidal endothelial cells and in lymph node. Found in placental endothelium but not in macrophages. Expressed in type II alveolar cells and lung endothelial cells. {ECO:0000269|PubMed:11226297

Sequence

MSDSKEPRVQQLGLLEEDPTTSGIRLFPRDFQFQQIHGHKSSTGCLGHGALVLQLLSFML
LAGVLVAILVQVSKVPSSLSQEQSEQDAIYQNLTQLKAAVGELSEKSKLQEIYQELTQLK
AAVGELPEKSKLQEIYQELTRLKAAVGELPEKSKLQEIYQELTRLKAAVGELPEKSKLQE
IYQELTRLKAAVGELPEKSKLQEIYQELTELKAAVGELPEKSKLQEIYQELTQLKAAVGE
LPDQSKQQQIYQELTDLKTAFERLCRHCPKDWTFFQGNCYFMSNSQRNWHDSVTACQEVR
AQLVVIKTAEEQNFLQLQTSRSNRFSWMGLSDLNQEGTWQWVDGSPLSPSFQRYWNSGEP
NNSGNEDCAEFSGSGWNDNRCDVDNYWICKKPAACFRDE

Sequence length

399

Interactions

View interactions

	KEGG
	Virion - Human immunodeficiency virus Virion - Flavivirus and Alphavirus Virion - Ebolavirus, Lyssavirus and Morbillivirus Virion - Lassa virus and SFTS virus Phagosome C-type lectin receptor signaling pathway Tuberculosis Measles

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (3)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
CARCINOMA, HEPATOCELLULAR	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
VENOUS THROMBOEMBOLISM	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (22)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	32705212	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiovascular Diseases	Cardiovascular disease	Pubtator	32970391	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colon Carcinoma	Colon Carcinoma	BEFREE	28109307, 31766099		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	25504222, 31766099	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital Hemidysplasia with Ichthyosiform Erythroderma and Limb Defects	Congenital hemidysplasia with ichthyosiform erythroderma and limb defects	Pubtator	19809496	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes mellitus	Pubtator	32970391	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	CTD_human_DG	28284560		★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver Diseases	Liver disease	Pubtator	14693842	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	26150177	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	38028841	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	28403883, 31766099		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant tumor of colon	Colonic Neoplasms	BEFREE	28109307, 31766099		★★★★★ ★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	31772670		★★★★★ ★☆☆☆☆ Found in Text Mining only
Severe Acute Respiratory Syndrome	Severe Acute Respiratory Syndrome	BEFREE	15950449, 16369534, 18697825		★★★★★ ★☆☆☆☆ Found in Text Mining only
Severe Acute Respiratory Syndrome	Severe Acute Respiratory Syndrome	LHGDN	17715238		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	28403883, 31766099		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	31766099	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Thyroid Neoplasms	Thyroid cancer	Pubtator	32970391	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
von Willebrand Disease	von Willebrand disorder	BEFREE	25832887		★★★★★ ★☆☆☆☆ Found in Text Mining only
von Willebrand Disease Type 1	Von willebrand disorder	Pubtator	25832887, 29389944	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
von Willebrand Disease, Type 1	von Willebrand disorder	BEFREE	23529928, 25832887, 29389944		★★★★★ ★☆☆☆☆ Found in Text Mining only
von Willebrand Disease, Type 2	von Willebrand disorder	BEFREE	25832887		★★★★★ ★☆☆☆☆ Found in Text Mining only

CLEC4M (C-type lectin domain family 4 member M)