CD207
protein-codingCD207 molecule, the group of C-type lectin domain containing|CD molecules|Scavenger receptors
Gene summary
The protein encoded by this gene is expressed only in Langerhans cells which are immature dendritic cells of the epidermis and mucosa. It is localized in the Birbeck granules, organelles present in the cytoplasm of Langerhans cells and consisting of superimposed and zippered membranes. It is a C-type lectin with mannose binding specificity, and it has been proposed that mannose binding by this protein leads to internalization of antigen into Birbeck granules and providing access to a nonclassical antigen-processing pathway. Mutations in this gene result in Birbeck granules deficiency or loss of sugar binding activity. [provided by RefSeq, Aug 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~5.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0013251
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
Manifestation: General
Intervention: General
Rationale: The clinical relevance of the condition is unclear
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CD207 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015717.5. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 3 | 4 | |||
| missense | 50 | 4 | 1 | 55 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | 2 | |||
| Total | 0 | 0 | 52 | 7 | 2 | 61 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056532.4 | 6 | MANE Select | |
| Ensembl | ENSP00000386378.3 | 6 | MANE Select | |
| Ensembl | ENSP00000812387.1 | 6 | Standard | |
| RefSeq | XP_011531177.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Immune System
- Adaptive Immune System
- Antigen processing-Cross presentation
- Class I MHC mediated antigen processing & presentation
- Cross-presentation of soluble exogenous antigens (endosomes)
Biological Process
- antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent
- receptor-mediated endocytosis
- defense response to virus
Molecular Function
- protein binding
- mannose binding
- carbohydrate binding
Cellular Component
- plasma membrane
- integral component of membrane
- endocytic vesicle
- clathrin-coated endocytic vesicle membrane
- early endosome membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000410009
- Coding exons
- 6
- Length
- 5606
- Individuals with no LoFs
- 650
- Homozygous LoFs
- 123989
- Heterozygous LoFs
- 2
- Defined
- 124641
- p
- 0.928
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0171 | 177 | 178 | 0.996 | 0.00000973 | 2130 |
| Missense (PolyPhen) | 45 | 43.317 | 1.0389 | 592 | ||
| Synonymous | -0.280 | 74 | 71.0 | 1.04 | 0.00000414 | 624 |
| Loss of Function | 0.797 | 10 | 13.1 | 0.762 | 6.43e-7 | 160 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 1.0 | 0.90 | notable |
| Latino/Admixed American | 1.0 | 0.93 | notable |
| Ashkenazi Jewish | 1.0 | 0.94 | notable |
| East Asian | 1.0 | 0.93 | notable |
| Finnish | 1.0 | 0.93 | notable |
| European (Non-Finnish) | 1.0 | 0.93 | notable |
| South Asian | 1.0 | 0.93 | notable |
| Other | 1.0 | 0.92 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Calcium-dependent lectin displaying mannose-binding specificity. Induces the formation of Birbeck granules (BGs); is a potent regulator of membrane superimposition and zippering. Binds to sulfated as well as mannosylated glycans, keratan sulfate (KS) and beta-glucans. Facilitates uptake of antigens and is involved in the routing and/or processing of antigen for presentation to T cells. Major receptor on primary Langerhans cells for Candida species, Saccharomyces species, and Malassezia furfur. Protects against human immunodeficiency virus-1 (HIV-1) infection. Binds to high-mannose structures present on the envelope glycoprotein which is followed by subsequent targeting of the virus to the Birbeck granules leading to its rapid degradation. {ECO:0000269|PubMed:10661407, ECO:0000269|PubMed:17334373, ECO:0000269|PubMed:20026605, ECO:0000269|PubMed:20097424}.;
- Disease
- DISEASE: Birbeck granule deficiency (BIRGD) [MIM:613393]: A condition characterized by the absence of Birbeck granules in epidermal Langerhans cells. Despite the lack of Birbeck granules, Langerhans cells are present in normal numbers and have normal morphologic characteristics and antigen-presenting capacity. {ECO:0000269|PubMed:15816828, ECO:0000269|PubMed:16567809}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.160
Essentials
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.125
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | High | Medium | High |