CD81

CD81 molecule, the group of Tetraspanins|CD molecules

Basic information

Region (hg38): 11:2376177-2397802

Previous symbols: [ "TAPA1" ]

Links

ENSG00000110651 ∙ NCBI:975 ∙ OMIM:186845 ∙ HGNC:1701 ∙ Uniprot:P60033 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• common variable immunodeficiency (Supportive), mode of inheritance: AD
• immunodeficiency, common variable, 6 (Limited), mode of inheritance: Unknown
• immunodeficiency, common variable, 6 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency, common variable, 6	AR	Allergy/Immunology/Infectious	Antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial	Allergy/Immunology/Infectious; Renal	20237408

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CD81 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD81 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				51	6	57
missense			71			71
nonsense			1			1
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			11	14		25
non coding			2	52	20	74
Total	0	0	76	103	26

Variants in CD81

This is a list of pathogenic ClinVar variants found in the CD81 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-2377192-T-C			Benign (Nov 10, 2018)
11-2377547-G-A			Uncertain significance (Apr 01, 2018)
11-2377558-G-C		CD81-related disorder	Likely benign (Sep 08, 2023)
11-2377560-A-G			Uncertain significance (Oct 04, 2023)
11-2377572-A-G			Uncertain significance (Jan 19, 2023)
11-2377575-G-A			Uncertain significance (Mar 04, 2022)
11-2377576-C-T			Likely benign (Oct 17, 2022)
11-2377586-C-T			Likely benign (Mar 20, 2021)
11-2377597-C-G			Likely benign (Nov 27, 2023)
11-2377598-T-C			Uncertain significance (May 23, 2023)
11-2377609-C-T			Likely benign (Aug 30, 2023)
11-2377619-A-G			Uncertain significance (Jun 23, 2022)
11-2377626-C-G			Likely benign (Nov 23, 2021)
11-2377629-CG-C			Benign (Aug 24, 2023)
11-2390138-G-A			Benign (Jun 19, 2021)
11-2390306-C-T			Benign (Nov 10, 2018)
11-2390392-C-A			Likely benign (Mar 17, 2023)
11-2390393-T-A			Likely benign (Jul 16, 2023)
11-2390397-C-T			Benign (Jan 29, 2024)
11-2390399-C-T			Benign (Jan 19, 2024)
11-2390403-C-T			Likely benign (Nov 25, 2023)
11-2390414-G-A			Uncertain significance (Jun 05, 2022)
11-2390416-C-T			Uncertain significance (May 08, 2022)
11-2390423-C-A			Benign (Jan 12, 2024)
11-2390423-C-T			Likely benign (Nov 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD81	protein_coding	protein_coding	ENST00000263645	8	21243

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.918	0.0815	125029	0	1	125030	0.00000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.806	110	137	0.806	0.00000858	1545
Missense in Polyphen		39	67.17	0.58062		719
Synonymous	-2.04	79	59.0	1.34	0.00000437	445
Loss of Function	3.01	1	12.4	0.0804	5.42e-7	149

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play an important role in the regulation of lymphoma cell growth. Interacts with a 16-kDa Leu-13 protein to form a complex possibly involved in signal transduction. May act as the viral receptor for HCV.
• Disease: DISEASE: Immunodeficiency, common variable, 6 (CVID6) [MIM:613496]: A primary immunodeficiency characterized by antibody deficiency, hypogammaglobulinemia, recurrent bacterial infections and an inability to mount an antibody response to antigen. The defect results from a failure of B-cell differentiation and impaired secretion of immunoglobulins; the numbers of circulating B-cells is usually in the normal range, but can be low. {ECO:0000269|PubMed:20237408}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: B cell receptor signaling pathway - Homo sapiens (human);Malaria - Homo sapiens (human);Hepatitis C - Homo sapiens (human);B Cell Receptor Signaling Pathway;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;BCR;Regulation of Complement cascade;Complement cascade;Beta1 integrin cell surface interactions;Alpha4 beta1 integrin signaling events (Consensus)

Recessive Scores

• pRec: 0.392

Intolerance Scores

• loftool: 0.219
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.142
• hipred: Y
• hipred_score: 0.825
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.660

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd81
• Phenotype: hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; skeleton phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: activation of MAPK activity;cell surface receptor signaling pathway;protein localization;cell population proliferation;positive regulation of cell population proliferation;regulation of complement activation;positive regulation of B cell proliferation;receptor internalization;regulation of protein stability;positive regulation of 1-phosphatidylinositol 4-kinase activity;positive regulation of transcription by RNA polymerase II;viral entry into host cell;receptor-mediated virion attachment to host cell;positive regulation of peptidyl-tyrosine phosphorylation;regulation of immune response;protein localization to lysosome;cellular response to low-density lipoprotein particle stimulus;positive regulation of protein catabolic process in the vacuole;regulation of cell motility
• Cellular component: immunological synapse;plasma membrane;integral component of plasma membrane;focal adhesion;membrane;basolateral plasma membrane;vesicle;extracellular exosome
• Molecular function: virus receptor activity;integrin binding;protein binding;MHC class II protein complex binding;transferrin receptor binding