GeneBe

CD209

protein-coding

CD209 molecule, the group of CD molecules|Scavenger receptors|C-type lectin domain containing

Gene 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 leprosy and tuberculosis mycobacteria, the Ebola, hepatitis C, HIV-1 and Dengue viruses, and the SARS-CoV acute respiratory syndrome coronavirus. The protein is organized into four distinct domains: a C-terminal carbohydrate recognition domain, a flexible tandem-repeat neck domain, a transmembrane region and an N-terminal cytoplasmic domain involved in internalization. This gene is closely related in terms of both sequence and function to a neighboring gene, CLEC4M (Gene ID: 10332), also known as L-SIGN. The two genes differ in viral recognition and expression patterns, with this gene showing high expression on the surface of dendritic cells. Polymorphisms in the neck region are associated with protection from HIV-1 infection, while single nucleotide polymorphisms in the promoter of this gene are associated with differing resistance and susceptibility to and severity of infectious disease, including rs4804803, which is associated with SARS severity. [provided by RefSeq, May 2020]

MANE transcript

NM_021155.4

Inheritance

—

ClinVar variants

U:33B:14

Top phenotype

CD209-related disorder

gnomAD constraint

pLI —, LoF o/e 0.95

Max pathogenic AF

—

Genomic locus

chr19:7,739,993-7,747,564

External References & Databases

Ensembl (ENSG00000090659)NCBI Gene (30835)OMIM (604672)HGNC:1641GenCCUniProt (Q9NNX6)AlphaFoldClinVar (CD209)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~7.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CD209 variants in ClinVar

6 Conditions Cataloged
not specifiedTotal: 30
not providedTotal: 14
CD209-related disorderTotal: 3
Mycobacterium tuberculosis, susceptibility toTotal: 2
Dengue virus, susceptibility toTotal: 2
Susceptibility to HIV infectionTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021155.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
5
clinvar
4
clinvar
 9
missense
33
clinvar
4
clinvar
1
clinvar
 38
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total00339547
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_021155.4RefSeqNP_066978.17MANE Select
ENST00000315599.12EnsemblENSP00000315477.67MANE Select
NM_001144893.2RefSeqNP_001138365.15Standard
NM_001144894.2RefSeqNP_001138366.15Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Phagosome - Homo sapiens (human)
  • C-type lectin receptor signaling pathway - Homo sapiens (human)
  • Tuberculosis - Homo sapiens (human)
  • Measles - Homo sapiens (human)
  • Ebola Virus Pathway on Host

Biological Process

  • stimulatory C-type lectin receptor signaling pathway
  • adaptive immune response
  • endocytosis
  • heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
  • leukocyte cell-cell adhesion

Molecular Function

  • virus receptor activity
  • protein binding
  • mannose binding
  • carbohydrate binding
  • peptide antigen binding

Cellular Component

  • extracellular region
  • cytoplasm
  • plasma membrane
  • external side of plasma membrane
  • cell surface

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000315599
Coding exons
7
Length
7586
Individuals with no LoFs
125692
Homozygous LoFs
0
Heterozygous LoFs
56
Defined
125748
p
0.000223
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.1042152111.020.00001192588
Missense (PolyPhen)4454.0410.81419752
Synonymous1.447188.20.8050.00000502782
Loss of Function0.2292021.10.9460.00000107222

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.0000870.000087rare
Ashkenazi Jewish00.0absent
East Asian0.00140.0014notable
Finnish0.0000930.000092rare
European (Non-Finnish)0.000140.00014rare
South Asian0.000200.00020rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Pathogen-recognition receptor expressed on the surface of immature dendritic cells (DCs) and involved in initiation of primary immune response. Thought to mediate the endocytosis of pathogens which are subsequently degraded in lysosomal compartments. The receptor returns to the cell membrane surface and the pathogen-derived antigens are presented to resting T-cells via MHC class II proteins to initiate the adaptive immune response. {ECO:0000269|PubMed:11859097}.; FUNCTION: (Microbial infection) Acts as an attachment receptor for HIV-1 and HIV-2. {ECO:0000269|PubMed:11799126, ECO:0000269|PubMed:12502850, ECO:0000269|PubMed:1518869}.; FUNCTION: (Microbial infection) Acts as an attachment receptor for Cytomegalovirus. {ECO:0000269|PubMed:12433371, ECO:0000269|PubMed:22496863}.; FUNCTION: (Microbial infection) Acts as an attachment receptor for Dengue virus. {ECO:0000269|PubMed:12682107}.; FUNCTION: (Microbial infection) Acts as an attachment receptor for Herpes simplex virus 1. {ECO:0000269|PubMed:18796707}.; FUNCTION: (Microbial infection) Acts as an attachment receptor for SARS coronavirus. {ECO:0000269|PubMed:15140961}.; FUNCTION: (Microbial infection) Acts as an attachment receptor for Lassa virus (PubMed:23966408). Acts as an attachment receptor for Marburg virusn. {ECO:0000269|PubMed:15479853}.; FUNCTION: (Microbial infection) Acts as an attachment receptor for Rift valley fever virus and uukuniemi virus. {ECO:0000269|PubMed:21767814}.; FUNCTION: (Microbial infection) Probably recognizes in a calcium- dependent manner high mannose N-linked oligosaccharides in a variety of bacterial pathogen antigens, including Leishmania pifanoi LPG, Lewis-x antigen in Helicobacter pylori LPS, mannose in Klebsiella pneumonae LPS, di-mannose and tri-mannose in Mycobacterium tuberculosis ManLAM and Lewis-x antigen in Schistosoma mansoni SEA (PubMed:16379498). Recognition of M.tuberculosis by dendritic cells occurs partially via this molecule (PubMed:16092920, PubMed:21203928). {ECO:0000269|PubMed:16092920, ECO:0000269|PubMed:16379498, ECO:0000269|PubMed:21203928}.;

Recessive Scores

pRec
0.268

Intolerance Scores

LoFtool
0.979
RVIS EVS
0.31
RVIS percentile EVS
72.6

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.581

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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