CD79A

CD79a molecule, the group of V-set domain containing|CD molecules

Basic information

Region (hg38): 19:41877279-41881372

Previous symbols: [ "IGA" ]

Links

ENSG00000105369 ∙ NCBI:973 ∙ OMIM:112205 ∙ HGNC:1698 ∙ Uniprot:P11912 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal agammaglobulinemia (Supportive), mode of inheritance: AD
• agammaglobulinemia 3, autosomal recessive (Strong), mode of inheritance: AR
• agammaglobulinemia 3, autosomal recessive (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Agammaglobulinemia 3, autosomal recessive	AR	Allergy/Immunology/Infectious	Antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial	Allergy/Immunology/Infectious	10525050; 11920841

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CD79A gene.

• Agammaglobulinemia 3, autosomal recessive (2 variants)
• Inherited Immunodeficiency Diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD79A 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				43		43
missense	1		66	1		68
nonsense	1		1			2
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)		2				2
splice region			4	5		9
non coding				18	6	24
Total	3	2	67	62	6

Variants in CD79A

This is a list of pathogenic ClinVar variants found in the CD79A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-41877312-G-C		Agammaglobulinemia 3, autosomal recessive	Uncertain significance (Nov 01, 2023)
19-41877316-T-G		Agammaglobulinemia 3, autosomal recessive	Likely benign (Jun 25, 2022)
19-41877317-C-T		not specified	Uncertain significance (Dec 19, 2022)
19-41877325-C-T		Agammaglobulinemia 3, autosomal recessive	Likely benign (Aug 16, 2022)
19-41877328-C-T		Agammaglobulinemia 3, autosomal recessive	Likely benign (Nov 13, 2021)
19-41877332-G-A		not specified • Agammaglobulinemia 3, autosomal recessive	Conflicting classifications of pathogenicity (Nov 25, 2023)
19-41877334-T-C		Agammaglobulinemia 3, autosomal recessive	Likely benign (Nov 16, 2019)
19-41877355-C-A		Agammaglobulinemia 3, autosomal recessive	Likely benign (Jan 12, 2022)
19-41877358-C-A		Agammaglobulinemia 3, autosomal recessive	Likely benign (Nov 01, 2022)
19-41877365-C-T		Agammaglobulinemia 3, autosomal recessive	Likely benign (Feb 18, 2023)
19-41877368-T-A		Agammaglobulinemia 3, autosomal recessive	Uncertain significance (Mar 06, 2020)
19-41877389-T-C		Agammaglobulinemia 3, autosomal recessive	Uncertain significance (Jun 04, 2022)
19-41877391-G-A		Agammaglobulinemia 3, autosomal recessive	Likely benign (Sep 06, 2022)
19-41877397-G-A		Agammaglobulinemia 3, autosomal recessive	Likely benign (Nov 08, 2023)
19-41878687-G-A			Benign (Jun 21, 2021)
19-41878978-G-A		Agammaglobulinemia 3, autosomal recessive	Likely benign (Aug 28, 2022)
19-41878986-ACAGGCCCTGGGTGC-A		Agammaglobulinemia 3, autosomal recessive	Pathogenic (Apr 20, 2022)
19-41878987-C-T		Agammaglobulinemia 3, autosomal recessive	Uncertain significance (Jun 02, 2020)
19-41878990-G-T		Agammaglobulinemia 3, autosomal recessive	Uncertain significance (Aug 26, 2020)
19-41878991-C-G		CD79A-related disorder	Likely benign (Mar 01, 2023)
19-41878997-G-C		CD79A-related disorder	Likely benign (Sep 01, 2023)
19-41879018-C-T		Agammaglobulinemia 3, autosomal recessive	Likely benign (Dec 02, 2022)
19-41879030-A-C		Agammaglobulinemia 3, autosomal recessive	Likely benign (Oct 14, 2023)
19-41879038-T-A		Agammaglobulinemia 3, autosomal recessive	Uncertain significance (Jul 16, 2020)
19-41879044-G-C		Agammaglobulinemia 3, autosomal recessive	Uncertain significance (Oct 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD79A	protein_coding	protein_coding	ENST00000221972	5	4250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.692	0.307	125720	0	8	125728	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	100	137	0.729	0.00000886	1457
Missense in Polyphen		28	50.383	0.55575		533
Synonymous	1.08	53	64.0	0.828	0.00000496	441
Loss of Function	2.76	2	12.5	0.159	7.84e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000166	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000364	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000333	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required in cooperation with CD79B for initiation of the signal transduction cascade activated by binding of antigen to the B-cell antigen receptor complex (BCR) which leads to internalization of the complex, trafficking to late endosomes and antigen presentation. Also required for BCR surface expression and for efficient differentiation of pro- and pre-B-cells. Stimulates SYK autophosphorylation and activation. Binds to BLNK, bringing BLNK into proximity with SYK and allowing SYK to phosphorylate BLNK. Also interacts with and increases activity of some Src- family tyrosine kinases. Represses BCR signaling during development of immature B-cells. {ECO:0000269|PubMed:8617796, ECO:0000269|PubMed:9057631}.
• Disease: DISEASE: Agammaglobulinemia 3, autosomal recessive (AGM3) [MIM:613501]: 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:10525050, ECO:0000269|PubMed:11920841}. Note=The disease is caused by mutations affecting the gene represented in this entry. Two different mutations, one at the splice donor site of intron 2 and the other at the splice acceptor site for exon 3, have been identified. Both mutations give rise to a truncated protein.
• Pathway: Primary immunodeficiency - Homo sapiens (human);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)

Intolerance Scores

• loftool: 0.258
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.455
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.874

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd79a
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; hematopoietic system phenotype; normal 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); renal/urinary system phenotype; immune system phenotype; liver/biliary system phenotype; neoplasm

Gene ontology

• Biological process: adaptive immune response;B cell differentiation;B cell proliferation;B cell activation;B cell receptor signaling pathway;protein homotetramerization
• Cellular component: multivesicular body;plasma membrane;external side of plasma membrane;integral component of membrane;B cell receptor complex;membrane raft
• Molecular function: transmembrane signaling receptor activity;protein binding;protein homodimerization activity