CD79B

CD79b molecule, the group of V-set domain containing|CD molecules

Basic information

Region (hg38): 17:63928737-63932336

Previous symbols: [ "IGB" ]

Links

ENSG00000007312 ∙ NCBI:974 ∙ OMIM:147245 ∙ HGNC:1699 ∙ Uniprot:P40259 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal agammaglobulinemia (Supportive), mode of inheritance: AD
• agammaglobulinemia 6, autosomal recessive (Definitive), mode of inheritance: AR
• agammaglobulinemia 6, autosomal recessive (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Agammaglobulinemia 6	AR	Allergy/Immunology/Infectious	Antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial	Allergy/Immunology/Infectious	17675462; 17709424

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CD79B gene.

• Agammaglobulinemia 6, autosomal recessive (133 variants)
• not provided (11 variants)
• not specified (6 variants)
• Inborn genetic diseases (6 variants)
• CD79B-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD79B 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	41	3	45
missense			48			48
nonsense						0
start loss						0
frameshift						0
inframe indel			2			2
splice donor/acceptor (+/-2bp)						0
splice region			4	9	1	14
non coding				24	11	35
Total	0	0	51	65	14

Variants in CD79B

This is a list of pathogenic ClinVar variants found in the CD79B region.

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

Position	Type	Phenotype	Significance	ClinVar
17-63929072-G-A			Benign (Nov 10, 2018)
17-63929073-G-C			Benign (Nov 10, 2018)
17-63929137-A-G		not specified	Benign (Jan 24, 2024)
17-63929237-C-T		Agammaglobulinemia 6, autosomal recessive	Uncertain significance (Jul 24, 2021)
17-63929238-T-G		Agammaglobulinemia 6, autosomal recessive	Likely benign (Oct 11, 2019)
17-63929244-C-T		Agammaglobulinemia 6, autosomal recessive	Likely benign (Dec 07, 2021)
17-63929247-A-G		Agammaglobulinemia 6, autosomal recessive	Likely benign (Oct 12, 2022)
17-63929252-C-G		not specified	Uncertain significance (Jun 14, 2022)
17-63929252-C-T		Agammaglobulinemia 6, autosomal recessive	Uncertain significance (Jan 21, 2021)
17-63929268-C-T		Agammaglobulinemia 6, autosomal recessive	Likely benign (Oct 23, 2023)
17-63929270-C-G		Agammaglobulinemia 6, autosomal recessive • not specified	Uncertain significance (Dec 16, 2022)
17-63929271-T-C		Agammaglobulinemia 6, autosomal recessive	Likely benign (Jan 10, 2024)
17-63929275-C-T		Agammaglobulinemia 6, autosomal recessive	Uncertain significance (May 03, 2022)
17-63929280-C-T		Agammaglobulinemia 6, autosomal recessive	Likely benign (Oct 07, 2022)
17-63929281-G-A		Agammaglobulinemia 6, autosomal recessive	Uncertain significance (Jan 24, 2020)
17-63929295-A-G		Agammaglobulinemia 6, autosomal recessive	Likely benign (Jun 03, 2023)
17-63929330-G-C		Agammaglobulinemia 6, autosomal recessive	Likely benign (Aug 17, 2023)
17-63929418-C-T		Agammaglobulinemia 6, autosomal recessive	Likely benign (Jun 19, 2022)
17-63929421-C-T		Agammaglobulinemia 6, autosomal recessive	Likely benign (May 12, 2021)
17-63929430-T-A		Agammaglobulinemia 6, autosomal recessive	Uncertain significance (Feb 10, 2022)
17-63929434-C-T		Agammaglobulinemia 6, autosomal recessive	Uncertain significance (Aug 23, 2021)
17-63929436-C-G		not specified	Uncertain significance (Dec 08, 2023)
17-63929439-A-G		Malignant lymphoma, large B-cell, diffuse	Likely pathogenic (Jul 25, 2023)
17-63929440-G-C		Agammaglobulinemia 6, autosomal recessive	Likely benign (Dec 07, 2023)
17-63929441-G-C		Agammaglobulinemia 6, autosomal recessive	Uncertain significance (Jun 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD79B	protein_coding	protein_coding	ENST00000392795	6	3615

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.916	0.0836	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	93	136	0.683	0.00000880	1508
Missense in Polyphen		28	56.117	0.49896		668
Synonymous	-0.111	58	56.9	1.02	0.00000400	438
Loss of Function	2.99	1	12.4	0.0809	6.28e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
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: Required in cooperation with CD79A for initiation of the signal transduction cascade activated by the B-cell antigen receptor complex (BCR) which leads to internalization of the complex, trafficking to late endosomes and antigen presentation. Enhances phosphorylation of CD79A, possibly by recruiting kinases which phosphorylate CD79A or by recruiting proteins which bind to CD79A and protect it from dephosphorylation. {ECO:0000269|PubMed:12097390, ECO:0000269|PubMed:8617796, ECO:0000269|PubMed:9057631}.
• Disease: DISEASE: Agammaglobulinemia 6, autosomal recessive (AGM6) [MIM:612692]: A primary immunodeficiency characterized by profoundly low or absent serum antibodies and low or absent circulating B-cells due to an early block of B-cell development. Affected individuals develop severe infections in the first years of life. {ECO:0000269|PubMed:17675462}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: B cell receptor signaling pathway - Homo sapiens (human);B Cell Receptor Signaling Pathway;Antigen activates B Cell Receptor (BCR) leading to generation of second messengers;bcr signaling pathway;ctcf: first multivalent nuclear factor;B cell receptor signaling;Signaling by the B Cell Receptor (BCR);Immune System;Adaptive Immune System;CD22 mediated BCR regulation;BCR;BCR signaling pathway (Consensus)

Recessive Scores

• pRec: 0.322

Intolerance Scores

• rvis_EVS: -0.45
• rvis_percentile_EVS: 24

Haploinsufficiency Scores

• pHI: 0.241
• hipred: Y
• hipred_score: 0.597
• ghis: 0.658

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.769

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd79b
• Phenotype: hematopoietic system phenotype; normal phenotype; immune system phenotype

Gene ontology

• Biological process: adaptive immune response;immune response;signal transduction;response to bacterium;B cell differentiation;B cell receptor signaling pathway;protein homooligomerization
• Cellular component: nucleoplasm;Golgi apparatus;cytosol;plasma membrane;integral component of plasma membrane;external side of plasma membrane;B cell receptor complex;extracellular exosome
• Molecular function: transmembrane signaling receptor activity;protein binding;protein homodimerization activity