CD207

CD207 molecule, the group of C-type lectin domain containing|CD molecules|Scavenger receptors

Basic information

Region (hg38): 2:70830210-70835816

Links

ENSG00000116031 ∙ NCBI:50489 ∙ OMIM:604862 ∙ HGNC:17935 ∙ Uniprot:Q9UJ71 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Birbeck granule deficiency (No Known Disease Relationship), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Birbeck granule deficiency	AD	General	The condition may not involve clinical relevance	General	The clinical relevance of the condition is unclear

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CD207 gene.

• Inborn genetic diseases (17 variants)
• not specified (1 variants)
• not provided (1 variants)
• Birbeck granule deficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD207 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			1			1
missense			13	4	1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding						0
Total	0	0	14	4	2

Variants in CD207

This is a list of pathogenic ClinVar variants found in the CD207 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-70831053-C-T		CD207-related disorder	Benign (Oct 21, 2019)
2-70831057-T-G		not specified	Uncertain significance (Dec 09, 2023)
2-70831070-A-G		not specified	Uncertain significance (May 25, 2022)
2-70831075-C-A		not specified	Uncertain significance (Aug 17, 2021)
2-70831075-C-T		not specified	Uncertain significance (Mar 13, 2023)
2-70831095-C-T		CD207-related disorder	Benign (Oct 18, 2019)
2-70831156-T-G		not specified	Uncertain significance (Feb 05, 2024)
2-70831177-T-C		not specified	Uncertain significance (Jan 23, 2024)
2-70831189-G-A		not specified	Uncertain significance (Oct 14, 2023)
2-70831704-A-G		CD207-related disorder	Benign (Oct 17, 2019)
2-70831728-G-A		not specified	Uncertain significance (Dec 27, 2023)
2-70831747-A-G		Birbeck granule deficiency	Uncertain significance (Apr 04, 2024)
2-70831794-C-A		not specified	Uncertain significance (Jun 30, 2023)
2-70831800-G-A		not specified	Uncertain significance (Aug 16, 2021)
2-70832906-A-G		CD207-related disorder	Benign (Nov 06, 2019)
2-70832986-G-C		not specified	Uncertain significance (Dec 26, 2023)
2-70833033-A-G		not specified	Uncertain significance (Nov 28, 2023)
2-70833044-A-C		not specified	Uncertain significance (May 31, 2023)
2-70833651-C-T		not specified	Likely benign (Jun 02, 2023)
2-70833685-C-T		not specified	Likely benign (May 04, 2022)
2-70833699-A-G		not specified	Uncertain significance (May 10, 2023)
2-70833805-G-C		CD207-related disorder	Benign (Oct 21, 2019)
2-70833809-G-A		Birbeck granule deficiency	Uncertain significance (Mar 30, 2021)
2-70833822-A-C		not specified	Uncertain significance (Jun 21, 2023)
2-70833856-C-T		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD207	protein_coding	protein_coding	ENST00000410009	6	5606

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000282	0.541	650	123989	2	124641	0.928

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0171	177	178	0.996	0.00000973	2130
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	2.01	1.90
Ashkenazi Jewish	1.00	0.939
East Asian	1.01	0.933
Finnish	1.00	0.933
European (Non-Finnish)	1.00	0.931
Middle Eastern	1.01	0.933
South Asian	1.00	0.928
Other	1.00	0.921

dbNSFP

Source: dbNSFP

• 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.
• Pathway: Immune System;Adaptive Immune System;Antigen processing-Cross presentation;Class I MHC mediated antigen processing & presentation;Cross-presentation of soluble exogenous antigens (endosomes) (Consensus)

Recessive Scores

• pRec: 0.160

Haploinsufficiency Scores

• pHI: 0.0381
• hipred: N
• hipred_score: 0.112
• ghis: 0.470

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.125

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	High	Medium	High

Mouse Genome Informatics

• Gene name: Cd207
• Phenotype: immune system phenotype; hematopoietic system phenotype; respiratory system phenotype; liver/biliary system phenotype

Gene ontology

• Biological process: antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent;receptor-mediated endocytosis;defense response to virus
• Cellular component: plasma membrane;integral component of membrane;endocytic vesicle;clathrin-coated endocytic vesicle membrane;early endosome membrane
• Molecular function: protein binding;mannose binding;carbohydrate binding