Agammaglobulinemia

disease
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Also known as antibody DeficiencyGammaglobulin DeficiencyImmunoglobulin Deficiency

Summary

Agammaglobulinemia (MONDO:0015977) is a disease (an umbrella term covering 10 Mondo subtypes) with 6 cohort genes and 14 clinical trials. Top therapeutic interventions include dextrose and human immunoglobulin g.

At a glance

  • Prevalence: 1-9 / 1 000 000 (France) [Orphanet-validated]
  • Umbrella term: 10 Mondo subtypes
  • Cohort genes: 6
  • ClinVar variants: 133
  • Clinical trials: 14

Clinical features

Epidemiology

Prevalence records

9 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Point prevalence1-9 / 1 000 0000.287FranceValidated
Point prevalence1-9 / 1 000 0000.134SpainValidated
Point prevalence1-9 / 1 000 0000.192NetherlandsValidated
Point prevalence<1 / 1 000 0000.045TurkeyValidated
Point prevalence<1 / 1 000 0000.094United KingdomValidated
Point prevalence1-9 / 1 000 0000.205ItalyValidated
Point prevalence<1 / 1 000 0000.077GermanyValidated
Point prevalence<1 / 1 000 0000.071PolandValidated
Point prevalence1-9 / 1 000 0000.13EuropeNot yet validated

Identifiers

Disease identifiers

FieldValue
Canonical nameagammaglobulinemia
Mondo IDMONDO:0015977
MeSHD000361
OMIM601495
Orphanet183669
DOIDDOID:2583
UMLSC0001768
MedGen168
GARD0020320
MedDRA10001471
Is cancer (heuristic)no

Also known as: agammaglobulinemia · antibody Deficiency · Gammaglobulin Deficiency · Immunoglobulin Deficiency

Data availability: 133 ClinVar variants · 3 GenCC gene-disease records.

Disease family

An umbrella term covering 10 Mondo subtypes.

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

Related subtypes (4): immunoglobulin beta deficiency, hyperimmunoglobulin syndrome, selective immunoglobulin deficiency disease, PAX5-related B lymphopenia and autism spectrum disorder

Subtypes (10): congenital agammaglobulinemia, immunodeficiency 61, Good syndrome, isolated agammaglobulinemia, syndromic agammaglobulinemia, activated PI3K-delta syndrome, agammaglobulinemia 9, autosomal recessive, agammaglobulinemia 10, autosomal dominant, agammaglobulinemia, autosomal recessive, due to BOB1 deficiency, agammaglobulinemia 8b, autosomal recessive

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

ClinVar germline variants

133 retrieved; paginated sample, class counts are floors:

99 benign, 21 pathogenic, 10 uncertain significance, 2 likely pathogenic, 1 conflicting classifications of pathogenicity

ClinVarVariant (HGVS)GeneClassificationReview
3392518NM_003120.3(SPI1):c.[147_155del;157T>G159C>G]Pathogenicno assertion criteria provided
3392517Single alleleAGBL2Pathogenicno assertion criteria provided
1335903NM_003120.3(SPI1):c.363C>A (p.Tyr121Ter)SPI1Pathogeniccriteria provided, single submitter
3341167NM_003120.3(SPI1):c.100G>T (p.Glu34Ter)SPI1Pathogenicno assertion criteria provided
3341168NM_003120.3(SPI1):c.471del (p.Leu159fs)SPI1Pathogenicno assertion criteria provided
3341179NM_003120.3(SPI1):c.525C>A (p.Phe175Leu)SPI1Pathogenicno assertion criteria provided
3341190NM_003120.3(SPI1):c.538C>T (p.Leu180Phe)SPI1Pathogenicno assertion criteria provided
3341200NM_003120.3(SPI1):c.571T>C (p.Trp191Arg)SPI1Pathogenicno assertion criteria provided
3341201NM_003120.3(SPI1):c.639G>A (p.Trp213Ter)SPI1Pathogenicno assertion criteria provided
3341202NM_003120.3(SPI1):c.676C>T (p.Gln226Ter)SPI1Pathogenicno assertion criteria provided
3341203NM_003120.3(SPI1):c.701del (p.Asn234fs)SPI1Pathogenicno assertion criteria provided
3341204NM_003120.3(SPI1):c.112del (p.Tyr38fs)SPI1Pathogenicno assertion criteria provided
3341205NM_003120.3(SPI1):c.733AAG[2] (p.Lys247del)SPI1Pathogenicno assertion criteria provided
3341235NM_003120.3(SPI1):c.346C>T (p.Arg116Trp)SPI1Pathogenicno assertion criteria provided
3341255NM_003120.3(SPI1):c.407del (p.Gly136fs)SPI1Pathogenicno assertion criteria provided
3341265NM_003120.3(SPI1):c.438dup (p.Asp147Ter)SPI1Pathogenicno assertion criteria provided
3341276NM_003120.3(SPI1):c.441del (p.Asp147fs)SPI1Pathogenicno assertion criteria provided
3392519NM_003120.3(SPI1):c.536T>C (p.Leu179Pro)SPI1Pathogenicno assertion criteria provided
585156NM_001080547.2(SPI1):c.325_327delinsAG (p.Gly109fs)SPI1Pathogenicno assertion criteria provided
989449NM_003120.3(SPI1):c.693_694del (p.Leu232fs)SPI1Pathogenicno assertion criteria provided
989450NM_003120.3(SPI1):c.328C>T (p.Gln110Ter)SPI1Pathogeniccriteria provided, single submitter
801321NM_003120.3(SPI1):c.722T>G (p.Val241Gly)SPI1Likely pathogeniccriteria provided, single submitter
801322NM_003120.3(SPI1):c.632A>C (p.His211Pro)SPI1Likely pathogeniccriteria provided, single submitter
2870679NM_001330360.2(POLA1):c.3944G>A (p.Arg1315His)POLA1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
2319048NM_003120.3(SPI1):c.283G>A (p.Val95Ile)SPI1Uncertain significancecriteria provided, single submitter
2403927NM_003120.3(SPI1):c.442G>A (p.Gly148Ser)SPI1Uncertain significancecriteria provided, single submitter
2553801NM_003120.3(SPI1):c.409G>A (p.Glu137Lys)SPI1Uncertain significancecriteria provided, single submitter
3169075NM_003120.3(SPI1):c.293C>T (p.Thr98Ile)SPI1Uncertain significancecriteria provided, single submitter
3169079NM_003120.3(SPI1):c.760G>A (p.Gly254Ser)SPI1Uncertain significancecriteria provided, single submitter
3341207NM_003120.3(SPI1):c.37G>A (p.Val13Ile)SPI1Uncertain significancecriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 6 · Orphanet: 5 · 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
SLC39A7StrongAutosomal recessiveagammaglobulinemia 9, autosomal recessive3
POU2AF1ModerateAutosomal recessiveagammaglobulinemia
TNFSF13LimitedAutosomal recessiveagammaglobulinemia2

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
SLC39A7Orphanet:693627Agammaglobulinemia-skin involvement-failure to thrive syndrome
POU2AF1Orphanet:186Primary biliary cholangitis
SPI1Orphanet:33110Autosomal non-syndromic agammaglobulinemia
POLA1Orphanet:163976X-linked intellectual disability, Van Esch type
POLA1Orphanet:85453X-linked reticulate pigmentary disorder

Cohort genes → proteins

6 cohort genes, 6 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence6

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
TNFSF13HGNC:11928ENSG00000161955O75888Tumor necrosis factor ligand superfamily member 13gencc
SLC39A7HGNC:4927ENSG00000112473Q92504Zinc transporter SLC39A7gencc
POU2AF1HGNC:9211ENSG00000110777Q16633POU domain class 2-associating factor 1gencc
SPI1HGNC:11241ENSG00000066336P17947Transcription factor PU.1clinvar
AGBL2HGNC:26296ENSG00000165923Q5U5Z8Cytosolic carboxypeptidase 2clinvar
POLA1HGNC:9173ENSG00000101868P09884DNA polymerase alpha catalytic subunitclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
TNFSF13Tumor necrosis factor ligand superfamily member 13Cytokine that binds to TNFRSF13B/TACI and to TNFRSF17/BCMA.
SLC39A7Zinc transporter SLC39A7Transports Zn(2+) from the endoplasmic reticulum (ER)/Golgi apparatus to the cytosol, playing an essential role in the regulation of cytosolic zinc levels.
POU2AF1POU domain class 2-associating factor 1Transcriptional coactivator that specifically associates with either POU2F1/OCT1 or POU2F2/OCT2.
SPI1Transcription factor PU.1Pioneer transcription factor, which controls hematopoietic cell fate by decompacting stem cell heterochromatin and allowing other transcription factors to enter otherwise inaccessible genomic sites.
AGBL2Cytosolic carboxypeptidase 2Metallocarboxypeptidase that mediates deglutamylation of tubulin and non-tubulin target proteins.
POLA1DNA polymerase alpha catalytic subunitCatalytic subunit of the DNA polymerase alpha complex (also known as the alpha DNA polymerase-primase complex) which plays an essential role in the initiation of DNA synthesis.

Protein-family classification

Druggable: 1 · Difficult: 1 · Unknown: 4 · Druggable fraction: 0.17

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
Protease16.1×0.459
Transcription factor11.4×0.539
Other/Unknown41.2×0.539

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
TNFSF13Other/UnknownnoTNF_dom, Tumour_necrosis_fac-like_dom, TNF_CS
SLC39A7Other/UnknownnoZIP
POU2AF1Other/UnknownnoPD-C2-AF1, OCA
SPI1Other/UnknownnoEts_dom, WH-like_DNA-bd_sf, WH_DNA-bd_sf
AGBL2ProteaseyesPeptidase_M14, Pepdidase_M14_N, Cytosolic_carboxypeptidase
POLA1Transcription factorno2.7.7.102DNA-dir_DNA_pol_B_exonuc, DNA-dir_DNA_pol_B_multi_dom, DNA-dir_DNA_pol_B

Expression context

Cohort genes with no expression data: 0.

6 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)6
unknown0

Top tissues across cohort

TissueCohort genes
granulocyte2
leukocyte2
monocyte2
body of pancreas1
islet of Langerhans1
stromal cell of endometrium1
cardia of stomach1
epithelium of nasopharynx1
pylorus1
left testis1
right testis1
right uterine tube1
calcaneal tendon1
sural nerve1
ventricular zone1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
TNFSF13134ubiquitousmarkermonocyte, leukocyte, granulocyte
SLC39A7133ubiquitousmarkerstromal cell of endometrium, islet of Langerhans, body of pancreas
POU2AF1222broadmarkerepithelium of nasopharynx, pylorus, cardia of stomach
SPI1170broadmarkergranulocyte, monocyte, leukocyte
AGBL2133ubiquitousmarkerright uterine tube, left testis, right testis
POLA1231ubiquitousmarkerventricular zone, sural nerve, calcaneal tendon

Protein interactions among cohort

Intra-cohort edges: 1.

Hub genes (top 10 by interactor count)

SymbolInteractor count
SPI13,823
POLA13,189
SLC39A71,679
POU2AF11,344
TNFSF131,067
AGBL2513

Intra-cohort edges

ABSources
POU2AF1SPI1string_interaction

Structural data

PDB: 5 · AlphaFold-only: 1 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
SPI1P1794735
POLA1P0988421
TNFSF13O758881
SLC39A7Q925041
POU2AF1Q166331

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
AGBL2Q5U5Z872.22

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 28. Enrichment computed across 6 evidence-associated genes (5 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 5 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
DNA replication initiation1285.5×0.019POLA1
HuR (ELAVL1) binds and stabilizes mRNA1253.8×0.019TNFSF13
Zinc transporters1228.4×0.019SLC39A7
Zinc influx into cells by the SLC39 gene family1228.4×0.019SLC39A7
Processive synthesis on the lagging strand1228.4×0.019POLA1
Inhibition of replication initiation of damaged DNA by RB1/E2F11163.1×0.019POLA1
Telomere C-strand synthesis initiation1163.1×0.019POLA1
Polymerase switching1163.1×0.019POLA1
Removal of the Flap Intermediate1163.1×0.019POLA1
Metal ion SLC transporters1120.2×0.023SLC39A7
Polymerase switching on the C-strand of the telomere184.6×0.029POLA1
TNFs bind their physiological receptors178.8×0.029TNFSF13
G1/S-Specific Transcription171.4×0.030POLA1
Activation of the pre-replicative complex165.3×0.030POLA1
Carboxyterminal post-translational modifications of tubulin147.6×0.039AGBL2
R-HSA-425366136.2×0.048SLC39A7
Defective pyroptosis131.3×0.052POLA1
Transcriptional regulation by RUNX1129.3×0.052SPI1
Transcriptional regulation of granulopoiesis125.1×0.058SPI1
RUNX1 regulates transcription of genes involved in differentiation of HSCs119.0×0.072SPI1
SLC-mediated transmembrane transport111.8×0.109SLC39A7
Transport of small molecules15.0×0.234SLC39A7
RNA Polymerase II Transcription14.5×0.247SPI1
Post-translational protein modification13.8×0.274AGBL2
Gene expression (Transcription)13.6×0.281SPI1
Generic Transcription Pathway13.0×0.312SPI1
Developmental Biology12.9×0.312SPI1
Metabolism of proteins12.5×0.344AGBL2

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 6 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
germinal center B cell differentiation2561.7×3e-04SPI1, POU2AF1
regulation of ferroptosis12808.7×0.007SLC39A7
pro-T cell differentiation11404.3×0.007SPI1
negative regulation of neutrophil degranulation11404.3×0.007SPI1
regulation of myeloid progenitor cell differentiation11404.3×0.007SPI1
positive regulation of myeloid dendritic cell chemotaxis11404.3×0.007SPI1
myeloid leukocyte differentiation1936.2×0.007SPI1
lagging strand elongation1936.2×0.007POLA1
endothelial to hematopoietic transition1936.2×0.007SPI1
positive regulation of antifungal innate immune response1936.2×0.007SPI1
follicular B cell differentiation1702.2×0.007SPI1
leading strand elongation1702.2×0.007POLA1
skin epidermis development1702.2×0.007SLC39A7
positive regulation of microglial cell mediated cytotoxicity1702.2×0.007SPI1
negative regulation of MHC class II biosynthetic process1561.7×0.007SPI1
anatomical structure regression1561.7×0.007SPI1
pericyte cell differentiation1561.7×0.007SPI1
DNA replication, synthesis of primer1468.1×0.007POLA1
protein side chain deglutamylation1468.1×0.007AGBL2
regulation of erythrocyte differentiation1468.1×0.007SPI1
positive regulation of isotype switching to IgA isotypes1468.1×0.007TNFSF13
apoptotic process involved in blood vessel morphogenesis1468.1×0.007SPI1
mitotic DNA replication initiation1468.1×0.007POLA1
immature B cell differentiation1401.2×0.007SPI1
oncogene-induced cell senescence1401.2×0.007SPI1
negative regulation of adipose tissue development1401.2×0.007SPI1
lymphocyte homeostasis1312.1×0.008TNFSF13
DNA strand elongation involved in DNA replication1312.1×0.008POLA1
TRAIL-activated apoptotic signaling pathway1312.1×0.008SPI1
regulation of type I interferon production1280.9×0.008POLA1

Therapeutics

Drugs indicated for this disease

0 approved, 1 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

DrugDevelopment status
Human Immunoglobulin GPhase 3 (in late-stage trials)

Drug target analysis

Approved (phase 4): 1 · Phase ≥3: 1 · Phased (≥1): 1 · Undrugged: 5

Druggability breadth: 4 of 6 evidence-associated genes (67%) 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
POLA1RUCAPARIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
POLA134
TNFSF1300
SLC39A700
POU2AF100
SPI100
AGBL200

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
RUCAPARIB4POLA1
ADEFOVIR DIPIVOXIL4POLA1
RESVERATROL3POLA1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

SymbolAssaysType breakdown
POLA173Binding:64, ADMET:5, Functional:4
AGBL23Binding:3
SLC39A72Binding:1, Functional:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
POLA12.7.7.102DNA primase AEP

Pharmacogenomics

Cohort genes with a PharmGKB record: 6; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

3 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)
RUCAPARIB4POLA1
ADEFOVIR DIPIVOXIL4POLA1
RESVERATROL3POLA1

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1POLA1
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug1AGBL2
EDifficult family or no structure, no drug4TNFSF13, SLC39A7, POU2AF1, SPI1

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
TNFSF130
SLC39A72
POU2AF10
SPI10
AGBL23

Clinical trials & evidence

Clinical trials

Clinical trials: 14.

Phase distribution (across all retrieved trials)

PhaseTrials
PHASE37
PHASE43
Not specified2
PHASE21
PHASE11

Top trials by phase / activity

NCTPhaseStatusTitle
NCT07135427PHASE4RECRUITINGGenetic Variation in IgG in Alpha 1 Antitrypsin Deficiency
NCT00520494PHASE4COMPLETEDEfficacy and Safety of Vivaglobin® in Previously Untreated Patients With Primary Immunodeficiency
NCT05612607PHASE4UNKNOWNSwitched Memory B-cells as a Marker for Humoral Immune System Recovery in Patients With Secondary Antibody Deficiency Due to Hematological Malignancies
NCT06954441PHASE3RECRUITINGV-IMMUNE: A Novel Immunoglobulin Therapy for Immunodeficiency
NCT00168012PHASE3COMPLETEDEfficacy and Safety of Intravenous Immunoglobulin IVIG-F10 in Patients With Primary Immunodeficiencies (PID)
NCT00168025PHASE3COMPLETEDEfficacy and Safety of Intravenous Immunoglobulin IgPro10 in Patients With Primary Immunodeficiencies (PID)
NCT00220766PHASE3COMPLETEDRapid Infusion of Immune Globulin Intravenous (Human) In Primary Immunodeficiency Patients
NCT00322556PHASE3COMPLETEDSafety and Efficacy of Intravenous Immunoglobulin IgPro10 in Patients With Primary Immunodeficiencies (PID)
NCT01581593PHASE3COMPLETEDEfficacy and Safety Study of Kedrion IVIG 10% to Treat Subjects With Primary Immunodeficiency (PID)
NCT03578341PHASE3UNKNOWNOral Colostrum and Its Effect on Immune System
NCT00161993PHASE2COMPLETEDSafety, Pharmacokinetic and Efficacy Study of a 10% Triple Virally Reduced Intravenous Immune Globulin Solution in Patients With Primary Immunodeficiency (Hypo- or Agammaglobulinemia)
NCT05584631PHASE1RECRUITINGIVIG vs SCIG in CIDP
NCT00661401Not specifiedCOMPLETEDSpecific IgG Antibody in Patients With Primary Antibody Deficiencies Treated With Subcutaneous Immunoglobulin
NCT02972281Not specifiedCOMPLETEDSystematic Search for Primary Immunodeficiency in Adults With Infections

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
DEXTROSE41
HUMAN IMMUNOGLOBULIN G41
CHEMBL42370701