CD209

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

Basic information

Region (hg38): 19:7739992-7747564

Links

ENSG00000090659 ∙ NCBI:30835 ∙ OMIM:604672 ∙ HGNC:1641 ∙ Uniprot:Q9NNX6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CD209 gene.

• not provided (11 variants)
• Inborn genetic diseases (6 variants)
• Susceptibility to HIV infection;Dengue virus, susceptibility to;Mycobacterium tuberculosis, susceptibility to (1 variants)
• Mycobacterium tuberculosis, susceptibility to;Susceptibility to HIV infection;Dengue virus, susceptibility to (1 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	2	6
missense			8	4	1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	8	3

Variants in CD209

This is a list of pathogenic ClinVar variants found in the CD209 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-7743058-G-C		not specified	Uncertain significance (Dec 01, 2023)
19-7743069-G-A			Benign (Jun 21, 2018)
19-7743119-T-C		not specified	Uncertain significance (Aug 10, 2021)
19-7743183-C-T			Benign (Jun 21, 2018)
19-7743197-C-T		not specified	Uncertain significance (Jan 04, 2022)
19-7744127-G-A			Benign (Nov 01, 2023)
19-7744191-C-A			Likely benign (Sep 01, 2023)
19-7744193-T-C		CD209-related disorder	Benign (Oct 29, 2019)
19-7744959-G-T			Likely benign (May 25, 2018)
19-7744999-A-G		not specified	Uncertain significance (Feb 12, 2024)
19-7745535-T-C			Likely benign (Sep 01, 2023)
19-7745597-C-T			Likely benign (Jan 01, 2023)
19-7745604-C-T		CD209-related disorder	Benign (Oct 31, 2019)
19-7745624-C-G		Mycobacterium tuberculosis, susceptibility to;Dengue virus, susceptibility to;Susceptibility to HIV infection • CD209-related disorder	Conflicting classifications of pathogenicity (Mar 30, 2021)
19-7745625-T-C		not specified	Uncertain significance (Feb 12, 2024)
19-7745631-T-A		not specified	Uncertain significance (Oct 26, 2021)
19-7745666-C-T			Likely benign (Jan 01, 2023)
19-7745673-C-T			Likely benign (Mar 01, 2023)
19-7745700-T-A		Dengue virus, susceptibility to;Mycobacterium tuberculosis, susceptibility to;Susceptibility to HIV infection	Uncertain significance (Mar 30, 2021)
19-7745744-A-G			Likely benign (Mar 01, 2023)
19-7745844-G-T		not specified	Uncertain significance (Sep 25, 2023)
19-7745872-C-A		not specified	Uncertain significance (Oct 26, 2022)
19-7745880-C-T			Likely benign (Sep 01, 2023)
19-7746042-T-C		not specified	Uncertain significance (Jul 12, 2023)
19-7746466-C-A		not specified	Uncertain significance (Oct 06, 2023)

GnomAD

Source: gnomAD

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: 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}.
• 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

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