rs4804803

Associated with modified resistance to several infectious diseases

Orientation

plus

Stabilized

plus

Geno	Mag	Summary
(A;A)
(A;G)
(G;G)

Reference

GRCh38 38.1/141

Chromosome

19

Position

7747847

Gene

CD209

is a	snp
is	mentioned by
dbSNP	rs4804803
dbSNP (classic)	rs4804803
ClinGen	rs4804803
ebi	rs4804803
HLI	rs4804803
Exac	rs4804803
Gnomad	rs4804803
Varsome	rs4804803
LitVar	rs4804803
Map	rs4804803
PheGenI	rs4804803
Biobank	rs4804803
1000 genomes	rs4804803
hgdp	rs4804803
ensembl	rs4804803
geneview	rs4804803
scholar	rs4804803
google	rs4804803
pharmgkb	rs4804803
gwascentral	rs4804803
openSNP	rs4804803
23andMe	rs4804803
SNPshot	rs4804803
SNPdbe	rs4804803
MSV3d	rs4804803
GWAS Ctlg	rs4804803

GMAF

0.2117

Max Magnitude

0

The SNP rs4804803 is a variant (-336A>G) in the promoter region for the CD209 gene that results in altered CD209 transcription. It is associated with modified resistance to several infectious diseases, including viruses (Hepatitis C, HIV, dengue, SARS), and bacteria (Mycobacterium tuberculosis), as well as other disorders of varying etiology (ulcerative colitis). The CD209 gene encodes a transmembrane receptor found on the surface of dendritic cells and macrophages. The protein product of CD209, DC-SIGN, plays an important role within both the innate and adaptive immune systems.

DC-SIGN's role differs depending on which cell type it resides. On macrophages, DC-SIGN is responsible for recognizing and binding to mannose-type carbohydrates, which are found in almost all pathogenic organisms (viruses, bacteria, fungi, etc.) but not human cells; this binding induces phagocytosis of the offending pathogen by the macrophage [PMID 15653305]. On dendritic cells, DC-SIGN binds the ICAM-3 molecule on naive T-cells with high affinity, mediating the initial interaction of T-cells with dendritic cells that is responsible for initiating the adaptive immune response [PMID 10721994]. However, pathogens can also exploit this T-cell adhesion for their own purposes (see sections on HIV and Hepatitis C virus).

Mechanism of Action

The rs4804803 SNP is located in the promoter region of CD209, 212 base pairs from the major transcription start site toward the 5' end of the gene [PMID 12957386]. Variants at this location affect transcription factor binding sites for Sp1/GATA1/CACCC and Sp1/GATA1/CACAC-binding transcription factors of the type GGGTGGG; the G allele at position 5 (GGGTGGG) is associated with transcription factor binding, and the A allele (GGGTAGG) with its absence [PMID 15838506]. The rs4804803 SNP is empirically known to affect the binding of nuclear extract proteins to the promoter region of CD209 [PMID 15838506]. Both electrophoretic mobility shift assays (EMSA) and promoter activity assays have revealed that the presence of the A allele results in higher rates of CD209 transcription and the production of more DC-SIGN gene product.

Associations with Disease

Hepatitis C Virus

In one study of 131 Irish women who had received HCV-contaminated anti-D-immunoglobulin (resulting in chronic HCV infection) and 79 healthy controls, Ryan et al found no association between rs4804803 genotype and the risk of HCV chronicity [PMID 20470843]. However, of those women with chronic HCV infection, presence of at least one G-allele at position 366 was associated with more advanced liver disease. Specifically, patients with the AG or GG genotype had significantly worse liver fibrosis scores (p<0.05, Mann-Whitney U-test) and higher alanine aminotransferase (biomarker for hepatocellular injury) levels (p<0.01, Mann-Whitney U-test) than those with the AA genotype. This study tested only the rs4804803 SNP, so p<0.05 was considered significant.

The exact mechanism behind the HCV/DC-SIGN association is still unknown. However, DC-SIGN binds proteins on the surface of Hepatitis C virions (HCV), specifically the E1 and E2 viral glycoproteins [PMID 15166245]. Capture of circulating Hepatitis C viral particles by DC-SIGN on cells within the liver may facilitate viral infection of nearby hepatocytes and lymphocyte subpopulations, which can lead to the establishment of chronic HCV infection and hepatocellular damage [PMID 15371595].

Human T-cell Lymphotropic Virus Type 1

A study of HTLV-1 occurrence in four different Brazilian ethnic groups revealed that the -336A variant was more frequently-observed in HTLV-1-infected patients than in controls (OR = 2.511, p = 0.0197) [PMID 19264667]. The study tested four CD209 variants (336A/G, 332A/G, 201T/G and 139A/G; significance threshold approximately p<0.0125); the protective effect of the rs4804803 G-allele for HTLV-1 infection (the reverse of what is observed for HCV) should therefore be considered weak. These authors also observed that the -336G allele occurred with higher frequency among Afro-Brazilians (42.0%) and Caucasians (26.7%) than in Asians (5.4%), and was not observed at all in the Amerindian group.

Dengue Fever Virus

The G allele of the rs4804803 SNP was associated with strong protection against dengue fever in three independent Thai cohorts [PMID 15838506]. This study investigated the effects of 40 separate CD209 polymorphisms on dengue susceptibility (significance threshold approximately p=0.00125), and rs4804803 was the only polymorphism that displayed a significant association. The carrier frequency of the G allele among individuals with dengue fever was 4.7%, compared to 22.4% in individuals with dengue hemorrhagic fever, and 19.5% in controls. This seems to indicate that the presence of the G allele at rs4804803 provides dominant protection against dengue fever (OR for protection = 4.90, p = 2e-6), but not against dengue hemorrhagic fever. Among individuals with dengue, genotypes GG and GA increased the risk of contracting dengue hemorrhagic fever instead of dengue fever (OR = 5.84, p = 1.4e-7).

In another study that investigated only the rs4804803 SNP (significance threshold p=0.05), investigators found that GG/AG genotypes at SNP rs4804803 occurred at a significantly higher rate in dengue patients than in patients with non-dengue febrile illnesses (OR = 3.23, p = 0.002), and population controls (OR = 2.36, p = 0.020) [PMID 21245921]. A strong association between GG/AG genotypes of rs4804803 and the risk of dengue hemorrhagic fever was found when compared to dengue fever, non-dengue febrile illness, and control patients (p = 0.004, 3e-5, 0.001 respectively). The AA genotype was associated with protection against dengue infection compared with non-dengue febrile illnesses and controls (p = 0.002 and 0.020 respectively). In addition, dendritic cells from individuals from individuals with the AG genotype displayed higher levels of DC-SIGN expression and significantly higher expression of several important cytokines compared to those from AA individuals in response to dengue infection, but the viral replication in dendritic cells with the AG genotype was lower than those with the AA genotype [PMID 21245921]. This study seemed to contradict the result from [PMID 15838506] that the G allele was protective against dengue; however, the authors mentioned that the definitions of dengue fever and dengue hemorrhagic fever used in the two studies were different; in addition, the latter study was conducted in Taiwan while the former was conducted in Thailand, and the frequency of the G allele differed significantly between the two study populations (3.8% in populations of Chinese descent; 9.5-10.4% in Thailand).

Mycobacterium Tuberculosis

One study that investigated the role of the rs4804803 SNP (significance threshold p=0.05) on tuberculosis in a large cohort of individuals from sub-Saharan Africa found that the -336G allele provided significant overall protection against pulmonary tuberculosis (OR = 0.86, p = 0.006), and patients homozygous for the G allele had a decreased risk of tuberculosis-induced lung cavitation, a more severe form of TB (OR = 0.42, p = 0.00003) [PMID 18167547].

In a previous study of a South African cohort (8 SNPs investigated; significance threshold approximately p=0.00625), Barreiro and colleagues found that rs4804803 genotypes GG and GA were more frequently observed in tuberculosis cases (70.6%) than controls (61.9%, p = 0.01). The presence of the G allele was therefore associated with an increased risk of developing TB [PMID 16379498]. Because the A allele was mainly confined to Eurasian populations, the authors speculated that this variant may have increased in frequency in non-African populations as a result of host genetic adaptation to a longer history of exposure to tuberculosis.

Human Immunodeficiency Virus (HIV)

Using samples obtained from 1,611 European-American participants at risk for parenteral or mucosal HIV infection (5 SNPs investigated; significance threshold approximately p=0.01), Martin et al found that individuals at risk for parenterally-acquired infection who had the -336G polymorphism were more susceptible to infection than individuals with the -336A allele (odds ratio = 1.87, p = 0.001) [PMID 15564514].

The mechanism by which this variant may lead to differential HIV infection risk is unknown; however, it is known that the HIV virus attaches to dendritic cells via the binding of viral protein gp120 to DC-SIGN [PMID 10721995]. By binding to DC-SIGN, the virus is engulfed into a mildly-acidic endosomal compartment within the cell, which protects it as the dendritic cell makes its way to lymphoid tissue and promotes trans-infection of T-cells [PMID 10721995].

SARS Coronavirus

DC-SIGN shares 77% amino acid similarity with CLEC4M, the usual binding receptor for the SARS coronavirus (SARS-CoV) [PMID 10975799]. It was found to interact with the spike protein of the virus, facilitating viral transmission to susceptible cells [PMID 15140961].

SARS patients with a -336G-positive genotype (either AG or GG) have a 2.5-fold greater chance of having lower lactate dehydrogenase (LDH) levels compared with -336AA patients (one SNP tested; significance threshold = 0.05; p = 0.014) [PMID 20359516]. High LDH levels are known to be an independent predictor for poor SARS clinical outcome, possibly because of the increased tissue destruction that is the result of immune hyperactivity [PMID 20359516]. Thus, SARS patients with the AA genotype have a 60% greater chance of a poor prognosis than GG or AG patients [PMID 20359516].

Inflammatory Bowel Diseases

The CD209 gene is located in a region previously linked to inflammatory bowel diseases (IBD), including ulcerative colitis and Crohn's disease [PMID 16865785]. One group found no initial association between the rs4804803 SNP and IBD, but upon stratification of ulcerative colitis patients by HLA-DR3 status (a strong protective allele), showed that carriage of the -366G allele increased susceptibility in the HLA-DR3-positive individuals (one SNP tested; significance threshold = 0.05; OR = 1.77, p = 0.03) relative to controls [PMID 18070336].

Summary of Effects

Overall, the empirically-observed effects between the rs4804803 SNP and risk for various diseases have been contradictory, even among studies of the same disease. For HCV, the presence of the G allele appears to cause a worse clinical outcome than the A allele [PMID 2047083], while for HTLV-1, the G allele is protective [PMID 19264667]. For dengue, two separate studies yielded two different results: in a Thai cohort, the G allele was strongly protective [PMID 15838506], while for a Taiwanese cohort the A allele was protective [PMID 21245921]. A similar contradiction was observed for tuberculosis, where one study observed that the G allele was protective [PMID 18167547] and another observed that it was destructive [PMID 16379498]. So far, the G allele appears protective for SARS [PMID 20359516], but the A allele is protective for both HIV and inflammatory bowel diseases [PMID 15564514] [PMID 16865785].

Perhaps these contradictory results are due to the conflicting effects of DC-SIGN expression when an organism is confronted with different infectious organisms. The A allele at position 336 in CD209 is correlated with increased DC-SIGN expression in vitro, but it is unclear how this would manifest itself clinically. For example, increased DC-SIGN expression on dendritic cells could lead to a faster and stronger immune response to certain infections, but it could cause others (for example, viruses that can use DC-SIGN as an entry portal to host cells) to increase in severity. It is clear, however, that differences in expression of the CD209 gene product do lead to differential host response to infection; much of the variability among studies could be due to geographic/ethnic differences in study population, or different mechanisms of pathogenesis for the organisms involved. Clearly, further work is needed to firmly establish the clinical effects of this important SNP.

[PMID 22629172] DC-SIGN (CD209) Promoter -336 A/G (rs4804803) Polymorphism Associated with Susceptibility of Kawasaki Disease

[PMID 22061615] Single nucleotide polymorphism in the promoter region of the CD209 gene is associated with human predisposition to severe forms of tick-borne encephalitis

[PMID 22027159] 'Lethal' combination of Mycobacterium tuberculosis Beijing genotype and human CD209 -336G allele in Russian male population.

Tuberculosis Susceptibility

[PMID 24023637] Gender-Specific Effects of Genetic Variants within Th1 and Th17 Cell-Mediated Immune Response Genes on the Risk of Developing Rheumatoid Arthritis

[PMID 23624202] Association of promoter region polymorphisms of CD209 gene with clinical outcomes of dengue virus infection in Western India.

[PMID 23751770] CD209 promoter -336 A/G (rs4804803) polymorphism is associated with susceptibility to pulmonary tuberculosis in Zahedan, southeast Iran.

[PMID 25883525] Association of Dectin-1 and DC-SIGN gene single nucleotide polymorphisms with fungal keratitis in the northern Han Chinese population

[PMID 27401010] Association of BAK1 single nucleotide polymorphism with a risk for dengue hemorrhagic fever.

[PMID 29130827] Association of Single-Nucleotide Polymorphisms in Immune-Related Genes with Development of Dengue Hemorrhagic Fever in a Mexican Population.

[PMID 31979279] CD209 and Not CD28 or STAT6 Polymorphism Mediates Clinical Malaria and Parasitemia among Children from Nigeria.