CD209
CD209 molecule, the group of CD molecules|Scavenger receptors|C-type lectin domain containing
Basic information
Region (hg38): 19:7739993-7747564
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (25 variants)
- not_provided (13 variants)
- CD209-related_disorder (3 variants)
- Mycobacterium_tuberculosis,_susceptibility_to (2 variants)
- Dengue_virus,_susceptibility_to (2 variants)
- Susceptibility_to_HIV_infection (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD209 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021155.4. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 8 | |||||
| missense | 27 | 32 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 27 | 8 | 5 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CD209 | protein_coding | protein_coding | ENST00000315599 | 7 | 7586 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 2.74e-13 | 0.0381 | 125692 | 0 | 56 | 125748 | 0.000223 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.104 | 215 | 211 | 1.02 | 0.0000119 | 2588 |
| Missense in Polyphen | 44 | 54.041 | 0.81419 | 752 | ||
| Synonymous | 1.44 | 71 | 88.2 | 0.805 | 0.00000502 | 782 |
| Loss of Function | 0.229 | 20 | 21.1 | 0.946 | 0.00000107 | 222 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000148 | 0.000148 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00141 | 0.00141 |
| Finnish | 0.0000929 | 0.0000924 |
| European (Non-Finnish) | 0.000142 | 0.000141 |
| Middle Eastern | 0.00141 | 0.00141 |
| South Asian | 0.000196 | 0.000196 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- 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}.;
- Pathway
- 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;Ebola Virus Pathway on Host;CD209 (DC-SIGN) signaling;C-type lectin receptors (CLRs);Butyrophilin (BTN) family interactions;Innate Immune System;Immune System;Adaptive Immune System
(Consensus)
Recessive Scores
- pRec
- 0.268
Intolerance Scores
- loftool
- 0.979
- rvis_EVS
- 0.31
- rvis_percentile_EVS
- 72.6
Haploinsufficiency Scores
- pHI
- 0.114
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.606
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.581
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cd209e
- Phenotype
Gene ontology
- 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;cell-cell recognition;modulation by virus of host morphology or physiology;virion attachment to host cell;viral genome replication;antigen processing and presentation;intracellular signal transduction;positive regulation of T cell proliferation;regulation of T cell proliferation;innate immune response;viral entry into host cell;peptide antigen transport;intracellular transport of virus;B cell adhesion
- Cellular component
- extracellular region;cytoplasm;plasma membrane;external side of plasma membrane;cell surface;membrane;integral component of membrane;host cell
- Molecular function
- virus receptor activity;protein binding;mannose binding;carbohydrate binding;peptide antigen binding;virion binding;metal ion binding