CD79B

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

Basic information

Region (hg38): 17:63928738-63932336

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 (Moderate), 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 (164 variants)
not_specified (23 variants)
not_provided (6 variants)
CD79B-related_disorder (4 variants)
Malignant_lymphoma,_large_B-cell,_diffuse (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. These statistics are base on transcript: NM_000000626.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	55 clinvar	2 clinvar	59
missense	1 clinvar	1 clinvar	57 clinvar	4 clinvar		63
nonsense	1 clinvar					1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	2	1	59	59	2

Highest pathogenic variant AF is 0.0000020524412

Loading clinvar variants...

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

loftool
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