Autosomal agammaglobulinemia

disease
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Also known as agammaglobulinemia, non-Bruton typeAGM

Summary

Autosomal agammaglobulinemia (MONDO:0011096) is a disease (an umbrella term covering 8 Mondo subtypes) with 9 cohort genes. The dominant Reactome pathway is Antigen activates B Cell Receptor (BCR) leading to generation of second messengers (5 cohort genes).

At a glance

  • Prevalence: (Worldwide) [Orphanet-validated]
  • Umbrella term: 8 Mondo subtypes
  • Cohort genes: 9
  • Phenotypes (HPO): 29

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Cases/families100WorldwideValidated
Point prevalence<1 / 1 000 000EuropeNot yet validated

Signs & symptoms

Clinical features (HPO)

29 HPO clinical features (Orphanet curated; top 29 by frequency):

HPO IDTermFrequency
HP:0000246SinusitisVery frequent (80-99%)
HP:0000389Chronic otitis mediaVery frequent (80-99%)
HP:0000509ConjunctivitisVery frequent (80-99%)
HP:0000988Skin rashVery frequent (80-99%)
HP:0001581Recurrent skin infectionsVery frequent (80-99%)
HP:0001945FeverVery frequent (80-99%)
HP:0002014DiarrheaVery frequent (80-99%)
HP:0002205Recurrent respiratory infectionsVery frequent (80-99%)
HP:0002719Recurrent infectionsVery frequent (80-99%)
HP:0002721ImmunodeficiencyVery frequent (80-99%)
HP:0004432AgammaglobulinemiaVery frequent (80-99%)
HP:0012378FatigueVery frequent (80-99%)
HP:0012735CoughVery frequent (80-99%)
HP:0001369ArthritisFrequent (30-79%)
HP:0001508Failure to thriveFrequent (30-79%)
HP:0002754OsteomyelitisFrequent (30-79%)
HP:0000218High palateOccasional (5-29%)
HP:0000286EpicanthusOccasional (5-29%)
HP:0000316HypertelorismOccasional (5-29%)
HP:0001287MeningitisOccasional (5-29%)
HP:0001875Decreased total neutrophil countOccasional (5-29%)
HP:0001944DehydrationOccasional (5-29%)
HP:0002024MalabsorptionOccasional (5-29%)
HP:0002110BronchiectasisOccasional (5-29%)
HP:0012115HepatitisOccasional (5-29%)
HP:0100658CellulitisOccasional (5-29%)
HP:0100806SepsisOccasional (5-29%)
HP:0200043VerrucaeOccasional (5-29%)
HP:0000377Abnormal pinna morphologyOccasional (5-29%)

Identifiers

Disease identifiers

FieldValue
Canonical nameautosomal agammaglobulinemia
Mondo IDMONDO:0011096
MeSHC538056
Orphanet33110
UMLSC1832241
MedGen316941
GARD0009640
Is cancer (heuristic)no

Also known as: agammaglobulinemia, non-Bruton type · AGM

Data availability: 8 GenCC gene-disease records.

Disease family

An umbrella term covering 8 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › immune system disorderinborn error of immunityB cell deficiencyagammaglobulinemiaisolated agammaglobulinemiaautosomal agammaglobulinemia

Related subtypes (1): Bruton-type agammaglobulinemia

Subtypes (8): agammaglobulinemia 6, autosomal recessive, agammaglobulinemia 2, autosomal recessive, agammaglobulinemia 3, autosomal recessive, agammaglobulinemia 4, autosomal recessive, agammaglobulinemia 5, autosomal dominant, agammaglobulinemia 7, autosomal recessive, agammaglobulinemia 8, autosomal dominant, autosomal recessive agammaglobulinemia 1

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

No tiered GWAS variants or ClinVar records for this disease.

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 46 · Orphanet: 12 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
CD79ADefinitiveAutosomal recessiveagammaglobulinemia 3, autosomal recessive4
IGHMDefinitiveAutosomal recessiveautosomal recessive agammaglobulinemia 14
BLNKStrongAutosomal recessiveagammaglobulinemia 4, autosomal recessive4
CD79BStrongAutosomal recessiveagammaglobulinemia 6, autosomal recessive3
IGLL1StrongAutosomal recessiveagammaglobulinemia 2, autosomal recessive5
PIK3R1StrongAutosomal recessiveagammaglobulinemia 7, autosomal recessive13
TCF3StrongAutosomal dominantagammaglobulinemia 8, autosomal dominant5
TCF7L1StrongAutosomal dominantagammaglobulinemia 8, autosomal dominant6
LRRC8ASupportiveAutosomal dominantautosomal agammaglobulinemia2

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
TCF3Orphanet:33110Autosomal non-syndromic agammaglobulinemia
TCF3Orphanet:585956B-lymphoblastic leukemia/lymphoma with t(1;19)(q23;p13.3)
TCF3Orphanet:641375B-lymphoblastic leukemia/lymphoma with t(17;19)
BLNKOrphanet:33110Autosomal non-syndromic agammaglobulinemia
CD79AOrphanet:33110Autosomal non-syndromic agammaglobulinemia
CD79BOrphanet:33110Autosomal non-syndromic agammaglobulinemia
LRRC8AOrphanet:33110Autosomal non-syndromic agammaglobulinemia
IGHMOrphanet:33110Autosomal non-syndromic agammaglobulinemia
IGLL1Orphanet:33110Autosomal non-syndromic agammaglobulinemia
PIK3R1Orphanet:3163SHORT syndrome
PIK3R1Orphanet:33110Autosomal non-syndromic agammaglobulinemia
PIK3R1Orphanet:693681Activated PI3K-delta syndrome 2

Cohort genes → proteins

9 cohort genes, 9 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence9

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
TCF3HGNC:11633ENSG00000071564P15923Transcription factor E2-alphagencc
TCF7L1HGNC:11640ENSG00000152284Q9HCS4Transcription factor 7-like 1gencc
BLNKHGNC:14211ENSG00000095585Q8WV28B-cell linker proteingencc
CD79AHGNC:1698ENSG00000105369P11912B-cell antigen receptor complex-associated protein alpha chaingencc
CD79BHGNC:1699ENSG00000007312P40259B-cell antigen receptor complex-associated protein beta chaingencc
LRRC8AHGNC:19027ENSG00000136802Q8IWT6Volume-regulated anion channel subunit LRRC8Agencc
IGHMHGNC:5541ENSG00000211899P01871Immunoglobulin heavy constant mugencc
IGLL1HGNC:5870ENSG00000128322P15814Immunoglobulin lambda-like polypeptide 1gencc
PIK3R1HGNC:8979ENSG00000145675P27986Phosphatidylinositol 3-kinase regulatory subunit alphagencc

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
TCF3Transcription factor E2-alphaTranscriptional regulator involved in the initiation of neuronal differentiation and mesenchymal to epithelial transition.
TCF7L1Transcription factor 7-like 1Participates in the Wnt signaling pathway.
BLNKB-cell linker proteinFunctions as a central linker protein, downstream of the B-cell receptor (BCR), bridging the SYK kinase to a multitude of signaling pathways and regulating biological outcomes of B-cell function and development.
CD79AB-cell antigen receptor complex-associated protein alpha chainRequired 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…
CD79BB-cell antigen receptor complex-associated protein beta chainRequired 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 presentati…
LRRC8AVolume-regulated anion channel subunit LRRC8AEssential component of the volume-regulated anion channel (VRAC, also named VSOAC channel), an anion channel required to maintain a constant cell volume in response to extracellular or intracellular osmotic changes.
IGHMImmunoglobulin heavy constant muConstant region of immunoglobulin heavy chains.
IGLL1Immunoglobulin lambda-like polypeptide 1Critical for B-cell development.
PIK3R1Phosphatidylinositol 3-kinase regulatory subunit alphaBinds to activated (phosphorylated) protein-Tyr kinases, through its SH2 domain, and acts as an adapter, mediating the association of the p110 catalytic unit to the plasma membrane.

Protein-family classification

Druggable: 5 · Difficult: 2 · Unknown: 2 · Druggable fraction: 0.56

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Antibody/Immunoglobulin413.0×7e-04
Kinase13.1×0.692
Scaffold/PPI11.9×0.692
Transcription factor10.9×0.859
Other/Unknown20.4×0.992

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
TCF3Transcription factornobHLH_dom, HLH_DNA-bd_sf, NeuroDiff_E-box_TFs
TCF7L1Other/UnknownnoHMG_box_dom, CTNNB1-bd_N, TCF/LEF
BLNKScaffold/PPInoSH2, SH2_dom_sf, Immunoreceptor_sig_adapters
CD79AAntibody/ImmunoglobulinyesPhos_immunorcpt_sig_ITAM, Ig_sub2, Ig_sub
CD79BAntibody/ImmunoglobulinyesPhos_immunorcpt_sig_ITAM, Ig_sub, Ig-like_dom
LRRC8AOther/UnknownnoLeu-rich_rpt, Leu-rich_rpt_typical-subtyp, LRRC8_Pannexin-like
IGHMAntibody/ImmunoglobulinyesIg/MHC_CS, Ig_C1-set, Ig-like_dom
IGLL1Antibody/ImmunoglobulinyesIg/MHC_CS, Ig_C1-set, Ig-like_dom
PIK3R1Kinaseyes2.7.1.153RhoGAP_dom, SH2, SH3_domain

Expression context

Cohort genes with no expression data: 0.

9 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)9
unknown0

Top tissues across cohort

TissueCohort genes
granulocyte3
spleen3
corpus epididymis2
lymph node2
embryo1
ganglionic eminence1
ventricular zone1
aorta1
popliteal artery1
tibial artery1
oral cavity1
tongue squamous epithelium1
gingiva1
gingival epithelium1
nasal cavity epithelium1
vermiform appendix1
bone marrow1
bone marrow cell1
male germ line stem cell (sensu Vertebrata) in testis1
calcaneal tendon1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
TCF3294ubiquitousmarkerganglionic eminence, ventricular zone, embryo
TCF7L1230ubiquitousmarkerpopliteal artery, tibial artery, aorta
BLNK257broadmarkertongue squamous epithelium, oral cavity, corpus epididymis
CD79A182broadmarkerspleen, granulocyte, lymph node
CD79B210broadmarkergranulocyte, spleen, lymph node
LRRC8A262ubiquitousmarkergingival epithelium, nasal cavity epithelium, gingiva
IGHM180tissue_specificmarkerspleen, granulocyte, vermiform appendix
IGLL1112tissue_specificmarkerbone marrow, bone marrow cell, male germ line stem cell (sensu Vertebrata) in testis
PIK3R1294ubiquitousmarkercalcaneal tendon, caput epididymis, corpus epididymis

Protein interactions among cohort

Intra-cohort edges: 10.

Hub genes (top 10 by interactor count)

SymbolInteractor count
PIK3R15,168
CD79A3,177
CD79B2,382
TCF7L11,635
LRRC8A1,554
BLNK1,475
IGLL11,349
TCF3457
IGHM93

Intra-cohort edges

ABSources
BLNKCD79Abiogrid_interaction, string_interaction
BLNKCD79Bstring_interaction
BLNKIGLL1string_interaction
BLNKLRRC8Astring_interaction
CD79ACD79Bstring_interaction
CD79AIGLL1string_interaction
CD79ALRRC8Astring_interaction
CD79BIGLL1string_interaction
CD79BLRRC8Astring_interaction
IGLL1LRRC8Astring_interaction

Structural data

PDB: 8 · AlphaFold-only: 1 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
PIK3R1P27986105
IGHMP0187131
LRRC8AQ8IWT69
TCF3P159235
CD79AP119125
CD79BP402595
IGLL1P158143
BLNKQ8WV281

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
TCF7L1Q9HCS452.59

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 122. Enrichment computed across 9 evidence-associated genes (9 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 9 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Antigen activates B Cell Receptor (BCR) leading to generation of second messengers5198.3×2e-09BLNK, CD79A, CD79B, IGHM, PIK3R1
CD22 mediated BCR regulation3761.3×2e-07CD79A, CD79B, IGHM
Potential therapeutics for SARS450.8×3e-05BLNK, CD79A, CD79B, IGHM
Signaling by the B Cell Receptor (BCR)3115.3×6e-05BLNK, CD79A, CD79B
Regulation of signaling by CBL2110.3×0.003BLNK, PIK3R1
Interleukin-3, Interleukin-5 and GM-CSF signaling270.5×0.007BLNK, PIK3R1
SARS-CoV Infections318.5×0.008BLNK, CD79A, CD79B
Viral Infection Pathways310.3×0.037BLNK, CD79A, CD79B
Adaptive Immune System39.9×0.037BLNK, CD79A, CD79B
MET activates PI3K/AKT signaling1211.5×0.044PIK3R1
Activated NTRK3 signals through PI3K1211.5×0.044PIK3R1
Cell surface interactions at the vascular wall221.1×0.044IGHM, IGLL1
Infectious disease38.3×0.044BLNK, CD79A, CD79B
Activated NTRK2 signals through PI3K1181.3×0.044PIK3R1
Signaling by LTK in cancer1181.3×0.044PIK3R1
PI3K/AKT activation1141.0×0.044PIK3R1
Binding of TCF/LEF:CTNNB1 to target gene promoters1126.9×0.044TCF7L1
RUNX3 regulates WNT signaling1126.9×0.044TCF7L1
IRS-mediated signalling1115.3×0.044PIK3R1
PI3K events in ERBB4 signaling1115.3×0.044PIK3R1
Co-stimulation by ICOS1115.3×0.044PIK3R1
GP1b-IX-V activation signalling1105.7×0.044PIK3R1
Signaling by FGFR4 in disease1105.7×0.044PIK3R1
Erythropoietin activates Phosphoinositide-3-kinase (PI3K)1105.7×0.044PIK3R1
Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants197.6×0.044PIK3R1
Signaling by PDGFRA extracellular domain mutants197.6×0.044PIK3R1
Signaling by LTK197.6×0.044PIK3R1
Signaling by FLT3 ITD and TKD mutants184.6×0.044PIK3R1
Repression of WNT target genes179.3×0.044TCF7L1
Constitutive Signaling by EGFRvIII179.3×0.044PIK3R1

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 9 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
B cell differentiation5121.6×2e-08TCF3, BLNK, CD79A, CD79B, PIK3R1
B cell receptor signaling pathway4178.3×2e-07BLNK, CD79A, CD79B, IGHM
intracellular glucose homeostasis2129.1×0.003LRRC8A, PIK3R1
adaptive immune response328.1×0.003CD79A, CD79B, IGHM
pre-B cell differentiation11872.4×0.009LRRC8A
immune response315.7×0.010CD79B, IGLL1, PIK3R1
pre-B cell allelic exclusion1624.1×0.015IGHM
regulation of toll-like receptor 4 signaling pathway1624.1×0.015PIK3R1
positive regulation of endoplasmic reticulum unfolded protein response1624.1×0.015PIK3R1
myeloid leukocyte migration1468.1×0.018PIK3R1
B cell lineage commitment1374.5×0.018TCF3
taurine transmembrane transport1312.1×0.018LRRC8A
immunoglobulin V(D)J recombination1312.1×0.018TCF3
interleukin-18-mediated signaling pathway1312.1×0.018PIK3R1
monoatomic anion transmembrane transport1312.1×0.018LRRC8A
cyclic-GMP-AMP transmembrane import across plasma membrane1234.1×0.023LRRC8A
positive regulation of focal adhesion disassembly1208.1×0.024PIK3R1
response to osmotic stress1170.2×0.025LRRC8A
monoatomic anion transport1156.0×0.025LRRC8A
aspartate transmembrane transport1156.0×0.025LRRC8A
protein hexamerization1156.0×0.025LRRC8A
T follicular helper cell differentiation1156.0×0.025PIK3R1
growth hormone receptor signaling pathway1133.8×0.028PIK3R1
positive regulation of RNA splicing1117.0×0.031PIK3R1
positive regulation of leukocyte migration1110.1×0.031PIK3R1
negative regulation of cell-matrix adhesion198.5×0.032PIK3R1
regulation of Wnt signaling pathway198.5×0.032TCF7L1
immunoglobulin mediated immune response178.0×0.039IGLL1
cell volume homeostasis166.9×0.041LRRC8A
positive regulation of lamellipodium assembly166.9×0.041PIK3R1

Therapeutics

Drug target analysis

Approved (phase 4): 1 · Phase ≥3: 1 · Phased (≥1): 1 · Undrugged: 8

Druggability breadth: 2 of 9 evidence-associated genes (22%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

SymbolExample approved molecule
PIK3R1IDELALISIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
PIK3R1264
TCF300
TCF7L100
BLNK00
CD79A00
CD79B00
LRRC8A00
IGHM00
IGLL100

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
IDELALISIB4PIK3R1
ALPELISIB4PIK3R1
DUVELISIB4PIK3R1
COPANLISIB4PIK3R1
UMBRALISIB4PIK3R1
DACTOLISIB3PIK3R1
BUPARLISIB3PIK3R1
QUERCETIN3PIK3R1
OMIPALISIB2PIK3R1
VISTUSERTIB2PIK3R1
FIMEPINOSTAT2PIK3R1
EGANELISIB2PIK3R1
BERZOSERTIB2PIK3R1
BIMIRALISIB2PIK3R1
PICTILISIB2PIK3R1
ZSTK-4742PIK3R1
GSK-26367712PIK3R1
AMDIZALISIB2PIK3R1
RISOVALISIB2PIK3R1
DEZAPELISIB2PIK3R1
ROGINOLISIB2PIK3R1
AZD-80551PIK3R1
VS-55841PIK3R1
AZD-81861PIK3R1
GS-99011PIK3R1
AZD-76481PIK3R1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
PIK3R1493Binding:470, ADMET:23
CD79B1Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
PIK3R12.7.1.153phosphatidylinositol-4,5-bisphosphate 3-kinase

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

SymbolChEMBL assays
PIK3R1493

Pharmacogenomics

Cohort genes with a PharmGKB record: 9; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

26 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

CompoundMax phaseCohort target (bioactivity)
IDELALISIB4PIK3R1
ALPELISIB4PIK3R1
DUVELISIB4PIK3R1
COPANLISIB4PIK3R1
UMBRALISIB4PIK3R1
DACTOLISIB3PIK3R1
BUPARLISIB3PIK3R1
QUERCETIN3PIK3R1
OMIPALISIB2PIK3R1
VISTUSERTIB2PIK3R1
FIMEPINOSTAT2PIK3R1
EGANELISIB2PIK3R1
BERZOSERTIB2PIK3R1
BIMIRALISIB2PIK3R1
PICTILISIB2PIK3R1
ZSTK-4742PIK3R1
GSK-26367712PIK3R1
AMDIZALISIB2PIK3R1
RISOVALISIB2PIK3R1
DEZAPELISIB2PIK3R1
ROGINOLISIB2PIK3R1
AZD-80551PIK3R1
VS-55841PIK3R1
AZD-81861PIK3R1
GS-99011PIK3R1
AZD-76481PIK3R1

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1PIK3R1
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug4CD79A, CD79B, IGHM, IGLL1
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug4TCF3, TCF7L1, BLNK, LRRC8A

Undrugged target profiles

8 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
TCF30
TCF7L10
BLNK0
CD79A0
CD79B1
LRRC8A0
IGHM0
IGLL10

Clinical trials & evidence

Clinical trials

Clinical trials: 0.