CD79A

Summary

CD79A (CD79a molecule, HGNC:1698) is a protein-coding gene on chromosome 19q13.2, encoding B-cell antigen receptor complex-associated protein alpha chain (P11912). 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.

The B lymphocyte antigen receptor is a multimeric complex that includes the antigen-specific component, surface immunoglobulin (Ig). Surface Ig non-covalently associates with two other proteins, Ig-alpha and Ig-beta, which are necessary for expression and function of the B-cell antigen receptor. This gene encodes the Ig-alpha protein of the B-cell antigen component. Alternatively spliced transcript variants encoding different isoforms have been described.

Source: NCBI Gene 973 — RefSeq curated summary.

At a glance

• Gene–disease (curated): agammaglobulinemia 3, autosomal recessive (Definitive, ClinGen) — +1 more curated relationship
• GWAS associations: 1
• Clinical variants (ClinVar): 186 total — 6 pathogenic, 2 likely-pathogenic
• Phenotypes (HPO): 39
• MANE Select transcript: NM_001783

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1698
Approved symbol	CD79A
Name	CD79a molecule
Location	19q13.2
Locus type	gene with protein product
Status	Approved
Aliases	MB-1, Ig-alpha, MB1, IGAlpha
Ensembl gene	ENSG00000105369
Ensembl biotype	protein_coding
OMIM	112205
Entrez	973

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000221972, ENST00000444740, ENST00000597454

RefSeq mRNA: 2 — MANE Select: NM_001783 NM_001783, NM_021601

CCDS: CCDS12589, CCDS46088

Canonical transcript exons

ENST00000221972 — 5 exons

Exon	Start	End
ENSE00000708638	41880670	41880738
ENSE00000708639	41879535	41879653
ENSE00000708640	41878990	41879289
ENSE00000842534	41877279	41877383
ENSE00001053091	41880867	41881372

Expression profiles

Bgee: expression breadth ubiquitous, 182 present calls, max score 98.63.

FANTOM5 (CAGE): breadth broad, TPM avg 29.0192 / max 4366.2704, expressed in 328 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
176079	27.7256	271
176078	0.9620	200
176085	0.1269	34
176084	0.0595	25
176083	0.0546	23
176081	0.0463	12
176082	0.0444	19

Top tissues by expression

280 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
spleen	UBERON:0002106	98.63	gold quality
granulocyte	CL:0000094	97.91	gold quality
lymph node	UBERON:0000029	97.73	gold quality
vermiform appendix	UBERON:0001154	97.37	gold quality
caecum	UBERON:0001153	93.83	gold quality
bone marrow cell	CL:0002092	92.53	gold quality
blood	UBERON:0000178	91.47	gold quality
ileal mucosa	UBERON:0000331	90.27	gold quality
mucosa of transverse colon	UBERON:0004991	90.21	gold quality
bone marrow	UBERON:0002371	89.76	gold quality
rectum	UBERON:0001052	89.13	gold quality
small intestine Peyer’s patch	UBERON:0003454	88.61	gold quality
colonic epithelium	UBERON:0000397	88.18	gold quality
parotid gland	UBERON:0001831	87.84	silver quality
tonsil	UBERON:0002372	86.63	gold quality
superficial temporal artery	UBERON:0001614	86.53	gold quality
small intestine	UBERON:0002108	85.63	gold quality
thymus	UBERON:0002370	83.88	gold quality
leukocyte	CL:0000738	81.99	gold quality
gall bladder	UBERON:0002110	81.28	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	80.99	gold quality
mononuclear cell	CL:0000842	80.43	gold quality
trachea	UBERON:0003126	80.39	gold quality
pylorus	UBERON:0001166	80.31	gold quality
monocyte	CL:0000576	80.23	gold quality
transverse colon	UBERON:0001157	78.97	gold quality
duodenum	UBERON:0002114	78.89	gold quality
saliva-secreting gland	UBERON:0001044	77.72	gold quality
minor salivary gland	UBERON:0001830	76.03	gold quality
colonic mucosa	UBERON:0000317	75.64	gold quality

Single-cell (SCXA)

Detected in 55 experiment(s), a significant marker in 52.

Experiment	Marker?	Max mean expression
E-MTAB-8207	yes	2912.61
E-GEOD-139324	yes	2677.53
E-GEOD-149689	yes	2215.74
E-MTAB-6505	yes	2162.11
E-CURD-88	yes	1975.94
E-HCAD-4	yes	1921.72
E-CURD-55	yes	1907.25
E-CURD-112	yes	1864.19
E-CURD-122	yes	1823.92
E-MTAB-7407	yes	1718.67
E-CURD-120	yes	1597.49
E-MTAB-8911	yes	1581.43
E-MTAB-8410	yes	1501.10
E-HCAD-24	yes	1454.00
E-HCAD-32	yes	1444.38

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
BCL2L1	Repression

Upstream regulators (CollecTRI, top): BCL6, CHD4, EBF1, EGR1, ELF1, ELF2, ELF4, ETS1, ETS2, FLI1, FOXN1, GABPA, GLI3, ID1, ID2, IRF6, MYC, MYEF2, NEUROD1, PAX5, PHF5A, PURA, RORA, RUNX1, RUNX3, SMAD3, SMAD4, SMAD7, STAT1, TBX21, TCF3, TFCP2

miRNA regulators (miRDB)

26 targeting CD79A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-5010-5P	99.94	64.11	705
HSA-MIR-4525	99.94	64.38	675
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-4434	99.10	67.01	1984
HSA-MIR-5703	99.10	67.09	2053
HSA-MIR-661	99.09	65.94	2062
HSA-MIR-625-5P	99.02	68.64	2031
HSA-MIR-4656	98.79	66.22	1306
HSA-MIR-9500	98.62	66.54	1845
HSA-MIR-4266	98.53	67.29	1035
HSA-MIR-6873-5P	98.45	66.14	1417
HSA-MIR-5088-5P	97.97	64.28	487
HSA-MIR-4446-3P	97.91	64.29	991
HSA-MIR-637	97.91	64.05	1517
HSA-MIR-663B	97.40	62.91	664
HSA-MIR-6866-5P	96.64	68.06	624
HSA-MIR-1291	96.28	65.89	1224
HSA-MIR-6775-3P	95.76	65.91	982
HSA-MIR-885-3P	95.14	63.08	448

Literature-anchored findings (GeneRIF, showing 26)

• Unlike the B29 octamer motif, the mb-1 octamer motif does not have the essential sequence required for OBF-1/Bob1 interaction, therefore its promoter is not transactivated by OBF-1/Bob1. (PMID:11907094)
• B cell-restricted mb-1 gene: expression, function, and lineage infidelity. Review. (PMID:12403343)
• There is a somatic hypermutation of this gene in B-cell lymphoma and multiple myeloma. (PMID:12651942)
• Results indicate that PAX5 is a more specific marker than CD79a for B-cell ALL diagnosis. (PMID:15492262)
• lower levels of B-cell receptor surface expression observed in chronic lymphocytic leukemia are accounted for by an impaired glycosylation and folding of the mu and CD79a chains. (PMID:15591116)
• FISH findings indicate that CD79a, despite its specificity for B-cell differentiation, represented the aberrant presence of a B-cell antigen in leukemias of distinct myeloid linage. (PMID:16271957)
• Acute leukemia with t(8;21) coexpresses CytCD79a represent biphenotypic acute leukemia. (PMID:17350472)
• Anti-CD79b antibodies downregulated surface B-cell receptor and were trafficked to the lysosomal-like major histocompatibility complex class II-positive compartment of a mouse xenograft model of non-Hodgkin lymphoma. (PMID:17374736)
• Ig-alpha was phosphorylated in all myeloma IgG BCR isolates, the 31-kD variant being phosphorylated most frequently. It was not phosphorylated in normal control B cells. (PMID:17701175)
• Median survival time of cytoplasmic CD79 alpha positive group was shorter than that of cytCD79a negative group in acute myeloid leukemia. (PMID:18160827)
• we determined the significance of loss or downregulation of CD79a, overexpression of cyclinD1, and c-maf expression in bone marrow specimens with plasma cell myeloma (PMID:19883431)
• CD79a may be helpful marker in the differential diagnosis of classical Hodgkin’s lymphoma and primary mediastinal B-cell lymphoma (PMID:20102401)
• STN produced significant antitumor effects in a mouse xenograft model of CD79A/B-mutated DLBCL. (PMID:21324920)
• CD79a plays a functional role in the tumor promoting effects of myeloid cells, and may represent a novel target for cancer therapy. (PMID:24146823)
• Phosphorylation of CD79a causes a decrease in helical propensity in the C-terminal region, for CD79b, the opposite was observed and phosphorylation resulted in an increase of helical propensity in the C-terminal part. (PMID:24769851)
• High intensity of caries is associated with increased levels of some salivary components - sIgA, histatin-5 and lactoperoxidase. (PMID:24974109)
• Data show that Bruton tyrosine kinase (BTK)inhibitor Ibrutinib augments MALT lymphoma associated translocation protein (MALT1) inhibition by S-Mepazine in CD79 antigen mutant activated B cell-subtype (ABC) of diffuse large B cell lymphoma (DLBCL). (PMID:26540570)
• The incidence of MYD88 and CD79B mutations in patients with CD5(+) DLBCL is lower than that in patients with DLBCL-SS, suggesting that CD5(+) DLBCL is not the same disease as DLBCL-SS in terms of gene mutation status. (PMID:27915469)
• Aberrant CD79a and/or PAX5 expression can be found in Acute Myelogenous Leukemia cases with RUNX1 mutations even without the translocation t(8; 21). (PMID:30396184)
• Clinicopathological significance of CD79a expression in classic Hodgkin lymphoma. (PMID:32641598)
• CD79a promotes CNS-infiltration and leukemia engraftment in pediatric B-cell precursor acute lymphoblastic leukemia. (PMID:33452446)
• Selective IgA Deficiency May Be an Underrecognized Risk Factor for Severe COVID-19. (PMID:36241155)
• Galactose-deficient IgA1 Is Involved in IgA Deposition in Renal Grafts Biopsied One Hour after Kidney Transplantation. (PMID:36288981)
• Mechanism of CD79A and CD79B Support for IgM+ B Cell Fitness through B Cell Receptor Surface Expression. (PMID:36426942)
• Compromised antigen binding and signaling interfere with bispecific CD19 and CD79a chimeric antigen receptor function. (PMID:36469024)
• Immunoglobulin A levels and its correlation with neutrophil-to-lymphocyte ratio as inflammatory biomarkers for dry eye disease in type 2 diabetes: a retrospective study. (PMID:37520541)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cd79a	ENSDARG00000037473
mus_musculus	Cd79a	ENSMUSG00000003379
rattus_norvegicus	Cd79a	ENSRNOG00000020125

Paralogs (1): CD79B (ENSG00000007312)

Protein

Protein identifiers

B-cell antigen receptor complex-associated protein alpha chain — P11912 (reviewed: P11912)

Alternative names: Ig-alpha, MB-1 membrane glycoprotein, Membrane-bound immunoglobulin-associated protein, Surface IgM-associated protein

All UniProt accessions (2): P11912, M0QX61

UniProt curated annotations — full annotation on UniProt →

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.

Subunit / interactions. Heterodimer of alpha and beta chains; disulfide-linked. Part of the B-cell antigen receptor complex where the alpha/beta chain heterodimer is non-covalently associated with an antigen-specific membrane-bound surface immunoglobulin of two heavy chains and two light chains. Interacts through its phosphorylated ITAM domain with the SH2 domains of SYK which stimulates SYK autophosphorylation and activation. Also interacts, when phosphorylated on Tyr-210, with the SH2 domain of BLNK/SLP65, bringing BLNK into proximity with SYK and allowing SYK to phosphorylate BLNK which is necessary for trafficking of the BCR to late endosomes. Interacts with Src-family tyrosine kinases including FYN and LYN, increasing their activity.

Subcellular location. Cell membrane.

Tissue specificity. B-cells.

Post-translational modifications. Phosphorylated on tyrosine, serine and threonine residues upon B-cell activation. Phosphorylation of tyrosine residues by Src-family kinases is an early and essential feature of the BCR signaling cascade. The phosphorylated tyrosines serve as docking sites for SH2-domain containing kinases, leading to their activation which in turn leads to phosphorylation of downstream targets. Phosphorylated by LYN. Phosphorylation of serine and threonine residues may prevent subsequent tyrosine phosphorylation. Arginine methylation in the ITAM domain may interfere with the binding of SYK. It promotes signals leading to B-cell differentiation.

Disease relevance. 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. The disease is caused by variants 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.

Domain organisation. The transmembrane helices of CD79A and CD79B chains and two IgM heavy chains assembly in a four-helix bundle structure that appears to be conserved among different BCR isotypes.

Isoforms (2)

UniProt ID	Names	Canonical?
P11912-1	1, Long	yes
P11912-2	2, Short

RefSeq proteins (2): NP_001774, NP_067612 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003110	Phos_immunorcpt_sig_ITAM	Repeat
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR007110	Ig-like_dom	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily

Pfam: PF02189, PF13927

UniProt features (43 total): strand 10, glycosylation site 6, mutagenesis site 5, modified residue 4, helix 4, sequence conflict 3, disulfide bond 2, topological domain 2, domain 2, signal peptide 1, chain 1, splice variant 1, transmembrane region 1, site 1

Structure

Experimental structures (PDB)

5 structures.

PDB	Method	Resolution (Å)
7WSO	ELECTRON MICROSCOPY	3.03
7XQ8	ELECTRON MICROSCOPY	3.3
7XT6	ELECTRON MICROSCOPY	3.63
7WSP	ELECTRON MICROSCOPY	4.09
1CV9	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P11912-F1	77.56	0.39

Antibody-complex structures (SAbDab): 1 — 7XQ8

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 210 (required for binding to blnk)

Post-translational modifications (4): 204, 210, 188, 199

Disulfide bonds (2): 54–106, 119

Glycosylation sites (6): 57, 63, 73, 88, 97, 112

Mutagenesis-validated functional residues (5):

Position	Phenotype
152	blocks igm bcr assembly.
156	blocks igm bcr assembly.
197	increased phosphorylation of y-188; when associated with a-203 and v-209.
203	increased phosphorylation of y-188; when associated with a-197 and v-209.
209	increased phosphorylation of y-188; when associated with a-197 and a-203.

Function

Pathways and Gene Ontology

Reactome pathways

10 pathways

ID	Pathway
R-HSA-5690714	CD22 mediated BCR regulation
R-HSA-9679191	Potential therapeutics for SARS
R-HSA-983695	Antigen activates B Cell Receptor (BCR) leading to generation of second messengers
R-HSA-1280218	Adaptive Immune System
R-HSA-1643685	Disease
R-HSA-168256	Immune System
R-HSA-5663205	Infectious disease
R-HSA-9679506	SARS-CoV Infections
R-HSA-9824446	Viral Infection Pathways
R-HSA-983705	Signaling by the B Cell Receptor (BCR)

MSigDB gene sets: 340 (showing top): PID_BCR_5PATHWAY, MCLACHLAN_DENTAL_CARIES_UP, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, GOBP_B_CELL_ACTIVATION, MODULE_45, MODULE_64, GOBP_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY, GOCC_CELL_SURFACE, GOBP_B_CELL_PROLIFERATION, BIOCARTA_CTCF_PATHWAY, MODULE_118, GOBP_REGULATION_OF_IMMUNE_RESPONSE, MODULE_75, GOBP_LEUKOCYTE_PROLIFERATION, MODULE_171

GO Biological Process (7): adaptive immune response (GO:0002250), B cell differentiation (GO:0030183), B cell proliferation (GO:0042100), B cell activation (GO:0042113), B cell receptor signaling pathway (GO:0050853), immune system process (GO:0002376), cell surface receptor signaling pathway (GO:0007166)

GO Molecular Function (3): transmembrane signaling receptor activity (GO:0004888), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (7): multivesicular body (GO:0005771), plasma membrane (GO:0005886), external side of plasma membrane (GO:0009897), B cell receptor complex (GO:0019815), membrane raft (GO:0045121), IgM B cell receptor complex (GO:0071755), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-7 pathways:

Category	Pathways
Signaling by the B Cell Receptor (BCR)	2
SARS-CoV Infections	1
Immune System	1
Disease	1
Viral Infection Pathways	1
Infectious disease	1
Adaptive Immune System	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
B cell activation	2
immune response	1
lymphocyte differentiation	1
lymphocyte proliferation	1
lymphocyte activation	1
antigen receptor-mediated signaling pathway	1
biological_process	1
signal transduction	1
signaling receptor activity	1
protein binding	1
binding	1
late endosome	1
membrane	1
cell periphery	1
plasma membrane	1
cell surface	1
side of membrane	1
immunoglobulin complex	1
plasma membrane signaling receptor complex	1
membrane microdomain	1
B cell receptor complex	1
IgM immunoglobulin complex	1
cellular anatomical structure	1

Protein interactions and networks

STRING

2386 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CD79A	VPREB1	P12018	994
CD79A	CD79B	P40259	993
CD79A	LYN	P07948	992
CD79A	IGLL1	P15814	992
CD79A	SYK	P43405	992
CD79A	BLNK	Q8WV28	991
CD79A	CXCL9	Q07325	988
CD79A	CD19	P15391	971
CD79A	CD22	P20273	945
CD79A	IGHV4-38-2	P0DP08	926
CD79A	IGLL5	B9A064	909
CD79A	PAX5	Q02548	907
CD79A	BTK	Q06187	907
CD79A	FYN	P06241	890
CD79A	BCL6	P41182	874

IntAct

514 interactions, top by confidence:

A	B	Type	Score
CD79A	FATE1	psi-mi:“MI:0915”(physical association)	0.720
SEC22B	CD79A	psi-mi:“MI:0915”(physical association)	0.560
TMBIM6	CD79A	psi-mi:“MI:0915”(physical association)	0.560
TMEM86B	CD79A	psi-mi:“MI:0915”(physical association)	0.560
STX8	CD79A	psi-mi:“MI:0915”(physical association)	0.560
CD79A	MMD2	psi-mi:“MI:0915”(physical association)	0.560
COL4A5	CD79A	psi-mi:“MI:0915”(physical association)	0.560
DEFB127	CD79A	psi-mi:“MI:0915”(physical association)	0.560
RTP2	CD79A	psi-mi:“MI:0915”(physical association)	0.560
SLC41A1	CD79A	psi-mi:“MI:0915”(physical association)	0.560
SMCO4	CD79A	psi-mi:“MI:0915”(physical association)	0.560
LPAR3	CD79A	psi-mi:“MI:0915”(physical association)	0.560
LHFPL5	CD79A	psi-mi:“MI:0915”(physical association)	0.560
DOLK	CD79A	psi-mi:“MI:0915”(physical association)	0.560
FDFT1	CD79A	psi-mi:“MI:0915”(physical association)	0.560
GIMAP1	CD79A	psi-mi:“MI:0915”(physical association)	0.560
MMD2	CD79A	psi-mi:“MI:0915”(physical association)	0.560
CD79A	METTL15	psi-mi:“MI:0914”(association)	0.530
CD79A	FATE1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (277): FATE1 (Two-hybrid), XRCC6BP1 (Affinity Capture-MS), NME4 (Affinity Capture-MS), TTC28 (Affinity Capture-MS), SLC10A7 (Affinity Capture-MS), MTG2 (Affinity Capture-MS), CDYL (Affinity Capture-MS), METTL15 (Affinity Capture-MS), HARS2 (Affinity Capture-MS), TYK2 (Affinity Capture-MS), MICU1 (Affinity Capture-MS), NSUN3 (Affinity Capture-MS), GTPBP6 (Affinity Capture-MS), PEX16 (Affinity Capture-MS), PEX6 (Affinity Capture-MS)

ESM2 similar proteins: A0A5F4BST2, A5PJC7, A8MWV9, D3ZZP4, O14836, P0CAN6, P11911, P11912, P14753, Q01114, Q07303, Q13113, Q2KI80, Q2KL21, Q3TS39, Q3URD2, Q4V9L6, Q5F267, Q5FVJ4, Q5FVQ7, Q5RA41, Q5T1S8, Q6P9G4, Q6UWJ8, Q6UX34, Q80VJ8, Q810F0, Q86XR5, Q8BRJ3, Q8BX43, Q8K064, Q8K5A9, Q8N112, Q8N4K4, Q8N6L0, Q8NBR0, Q8NC24, Q8QZT4, Q8R138, Q923S2

Diamond homologs: P0CAN6, P11911, P11912, P40293, P01693, P15530, P40259

SIGNOR signaling

9 interactions.

A	Effect	B	Mechanism
CD79A	“form complex”	BCR-Mk	binding
CD79A	“form complex”	BCR-Ml	binding
CD79A	“form complex”	BCR-Dk	binding
CD79A	“form complex”	BCR-Dl	binding
SH2B1	“down-regulates activity”	CD79A	dephosphorylation
CD79A	“down-regulates quantity by repression”	BCL2L1	“transcriptional regulation”
CHD4	“down-regulates quantity by repression”	CD79A	“transcriptional regulation”
FYN	“up-regulates activity”	CD79A	phosphorylation
LYN	“up-regulates activity”	CD79A	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 131 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
R-HSA-425366	6	17.0×	1e-04
SLC-mediated transmembrane transport	9	8.3×	1e-04
Transport of small molecules	11	4.3×	3e-03

GO biological processes:

GO term	Partners	Fold	FDR
vesicle fusion	5	26.9×	6e-04
endoplasmic reticulum to Golgi vesicle-mediated transport	7	8.5×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

186 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	6
Likely pathogenic	2
Uncertain significance	75
Likely benign	85
Benign	7

Top pathogenic / likely-pathogenic (8)

Variant ID	HGVS	Classification
17706	NM_001783.4(CD79A):c.380-2A>G	Pathogenic
2128215	NC_000019.10:g.41878996_41879009del	Pathogenic
4702574	NM_001783.4(CD79A):c.465C>A (p.Cys155Ter)	Pathogenic
4781785	NM_001783.4(CD79A):c.67_73del (p.Ala23fs)	Pathogenic
570771	NM_001783.4(CD79A):c.198G>A (p.Trp66Ter)	Pathogenic
827697	NM_001783.4(CD79A):c.323T>G (p.Val108Gly)	Pathogenic
17707	NM_001783.4(CD79A):c.379+1G>A	Likely pathogenic
2105348	NM_001783.4(CD79A):c.499-1G>A	Likely pathogenic

SpliceAI

730 predictions. Top by Δscore:

Variant	Effect	Δscore
19:41878985:CACA:C	acceptor_loss	1.0000
19:41878987:CA:C	acceptor_loss	1.0000
19:41878988:A:AG	acceptor_gain	1.0000
19:41878988:A:T	acceptor_loss	1.0000
19:41878988:AG:A	acceptor_gain	1.0000
19:41878989:G:GG	acceptor_gain	1.0000
19:41878989:GG:G	acceptor_gain	1.0000
19:41878989:GGC:G	acceptor_gain	1.0000
19:41878989:GGCC:G	acceptor_gain	1.0000
19:41878989:GGCCC:G	acceptor_gain	1.0000
19:41879285:GCGCC:G	donor_gain	1.0000
19:41879286:CGCCG:C	donor_loss	1.0000
19:41879287:GCC:G	donor_gain	1.0000
19:41879287:GCCGT:G	donor_loss	1.0000
19:41879288:CC:C	donor_gain	1.0000
19:41879288:CCG:C	donor_loss	1.0000
19:41879289:CGT:C	donor_loss	1.0000
19:41879290:G:GG	donor_gain	1.0000
19:41879291:T:A	donor_loss	1.0000
19:41879531:GCAG:G	acceptor_loss	1.0000
19:41879532:CA:C	acceptor_loss	1.0000
19:41879533:A:AG	acceptor_gain	1.0000
19:41879533:AG:A	acceptor_loss	1.0000
19:41879534:G:GG	acceptor_gain	1.0000
19:41879534:GA:G	acceptor_gain	1.0000
19:41879534:GAGC:G	acceptor_gain	1.0000
19:41879534:GAGCC:G	acceptor_gain	1.0000
19:41879652:GG:G	donor_gain	1.0000
19:41879653:GG:G	donor_gain	1.0000
19:41880665:TACA:T	acceptor_loss	1.0000

AlphaMissense

1474 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:41879578:G:C	K141N	0.999
19:41879578:G:T	K141N	0.999
19:41879108:G:C	W66C	0.998
19:41879108:G:T	W66C	0.998
19:41879600:G:A	G149R	0.998
19:41879600:G:C	G149R	0.998
19:41879610:T:A	L152H	0.998
19:41879618:T:C	C155R	0.998
19:41880871:T:C	L191P	0.998
19:41880894:T:C	Y199H	0.998
19:41880895:A:G	Y199C	0.998
19:41879226:T:A	C106S	0.997
19:41879227:G:C	C106S	0.997
19:41879594:G:C	A147P	0.997
19:41879595:C:A	A147D	0.997
19:41879599:G:C	E148D	0.997
19:41879599:G:T	E148D	0.997
19:41879610:T:C	L152P	0.997
19:41879610:T:G	L152R	0.997
19:41879622:C:A	A156E	0.997
19:41880867:G:C	G190R	0.997
19:41880904:T:C	I202T	0.997
19:41879220:T:G	Y104D	0.996
19:41879226:T:C	C106R	0.996
19:41879601:G:A	G149E	0.996
19:41879633:G:A	G160R	0.996
19:41879633:G:C	G160R	0.996
19:41879634:G:A	G160E	0.996
19:41879227:G:A	C106Y	0.995
19:41879228:C:G	C106W	0.995

dbSNP variants (sampled 300 via entrez): RS1000324207 (19:41878824 C>T), RS1000345480 (19:41878583 G>C), RS1000678454 (19:41877079 A>G), RS1001296119 (19:41879886 C>T), RS1003308151 (19:41876673 A>G), RS1003667355 (19:41881496 G>A,C), RS1004496801 (19:41881212 C>T), RS1006220888 (19:41876390 T>C), RS1006251985 (19:41876143 A>G), RS1006898670 (19:41879240 G>A), RS1007229095 (19:41877840 C>G,T), RS1007260094 (19:41877528 C>A,T), RS1007863919 (19:41880292 G>A), RS1007897900 (19:41880541 A>G), RS1011018162 (19:41881653 T>C)

Disease associations

OMIM: gene MIM:112205 | disease phenotypes: MIM:613501, MIM:601495

GenCC curated gene-disease

Disease	Classification	Inheritance
agammaglobulinemia 3, autosomal recessive	Definitive	Autosomal recessive
autosomal agammaglobulinemia	Supportive	Autosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
agammaglobulinemia 3, autosomal recessive	Definitive	AR

Mondo (3): agammaglobulinemia 3, autosomal recessive (MONDO:0013288), autosomal recessive agammaglobulinemia 1 (MONDO:0020729), autosomal agammaglobulinemia (MONDO:0011096)

Orphanet (0):

HPO phenotypes

39 total (30 of 39 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000218	High palate
HP:0000246	Sinusitis
HP:0000286	Epicanthus
HP:0000316	Hypertelorism
HP:0000377	Abnormal pinna morphology
HP:0000389	Chronic otitis media
HP:0000403	Recurrent otitis media
HP:0000509	Conjunctivitis
HP:0000988	Skin rash
HP:0001287	Meningitis
HP:0001369	Arthritis
HP:0001508	Failure to thrive
HP:0001581	Recurrent skin infections
HP:0001875	Decreased total neutrophil count
HP:0001944	Dehydration
HP:0001945	Fever
HP:0002014	Diarrhea
HP:0002024	Malabsorption
HP:0002110	Bronchiectasis
HP:0002205	Recurrent respiratory infections
HP:0002718	Recurrent bacterial infections
HP:0002719	Recurrent infections
HP:0002721	Immunodeficiency
HP:0002754	Osteomyelitis
HP:0002783	Recurrent lower respiratory tract infections
HP:0002837	Recurrent bronchitis
HP:0002843	Abnormal T cell morphology
HP:0003593	Infantile onset
HP:0003623	Neonatal onset

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST010703_14	Brain morphology (MOSTest)	1.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C538056	Agammaglobulinemia, non-Bruton type (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
(+)-JQ1 compound	decreases expression	2
aristolochic acid I	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
tamibarotene	increases expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	increases expression	1
licochalcone B	increases expression	1
bisphenol S	increases expression	1
gardiquimod	decreases expression, decreases reaction	1
Bortezomib	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	increases expression, increases abundance	1
Benzo(a)pyrene	affects methylation	1
Carmustine	decreases expression	1
Ethyl Methanesulfonate	decreases expression	1
Flavonoids	decreases expression	1
Formaldehyde	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Plant Extracts	decreases expression	1
Tetrachlorodibenzodioxin	affects expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	increases expression	1
Valproic Acid	increases methylation	1
Protein Kinase Inhibitors	decreases expression, decreases reaction	1
Particulate Matter	increases abundance, increases expression	1
Polyphenols	decreases expression	1

Cellosaurus cell lines

5 cell lines: 5 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_8795	OCI-Ly10	Cancer cell line	Female
CVCL_B8AM	Abcam Raji CD79A KO	Cancer cell line	Male
CVCL_B8D8	Abcam HCT 116 CD79A KO	Cancer cell line	Male
CVCL_B8TR	Abcam MCF-7 CD79A KO	Cancer cell line	Female
CVCL_B9FF	Abcam A-549 CD79A KO	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.