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Combined immunodeficiency with faciooculoskeletal anomalies is an extremely rare combined immunodeficiency disorder characterized by primary immunodeficiency manifesting with repeated bacterial, viral and fungal infections, in association with neurological manifestations (hypotonia, cerebellar ataxia, myoclonic seizures), developmental delay, optic atrophy, facial dysmorphism (high forehead, hypoplastic supraorbital ridges, palpebral edema, hypertelorism, flat nasal bridge, broad nasal root and tip, anteverted nares, thin lower lip overlapped by upper lip, square chin) and skeletal anomalies (short metacarpals/metatarsals with cone-shaped epiphyses, osteopenia).
Features include: Wide nasal bridge, Generalized myoclonic seizure, Ectopic kidney, and Global developmental delay and 17 more.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Brain and nerves | 5 | Generalized myoclonic seizure, Global developmental delay, Depressed nasal bridge |
Head and neck | 2 | Thin lower lip vermilion, Abnormal facial shape |
Bones and joints | 2 | Mild bone density loss (osteopenia), Joint inflammation (arthritis) |
Kidneys and urinary system | 1 | Ectopic kidney |
Lungs and breathing | 1 | Pneumonia |
Eyes | 1 | Damage to the optic nerve (optic atrophy) |
Muscles | 1 | Damage to the optic nerve (optic atrophy) |
Activated PI3K delta syndrome (APDS) is a rare inborn error of immunity characterized primarily by frequent infections, lymphoproliferation, and autoimmune manifestations. To date, at least 250 individuals have been identified with a pathogenic variant in PIK3CD (for APDS1) or PIK3R1 (for APDS2) [, , , , ]. The following description of the phenotypic features associated with this condition is based on these reports. It is important to note that the severity and presence of these clinical findings can vary widely among affected individuals. Some may present with mild symptoms, while others experience severe manifestations that significantly impact quality of life. The variability within the spectrum of APDS highlights the importance of individualized care and management strategies. Table 2. Activated PI3K Delta Syndrome: Frequency of Select Features
Feature | % of Persons w/Feature | Comment |
|---|---|---|
Sinopulmonary infections | 96%-100% | Severe /or recurrent |
KNSTRN encodes kinetochore localized astrin (SPAG5) binding protein (316 aa). Essential component of the mitotic spindle required for faithful chromosome segregation and progression into anaphase. Highest expression in Testis (94.2 TPM) and Thyroid (76.5 TPM).
Combined immunodeficiency with faciooculoskeletal anomalies is associated with mutations in the KNSTRN gene on chromosome 15.
KNSTRN is classified as a druggable target (Clinically Actionable category) with score 0.0.
PIK3CD function has not been fully characterized.
Combined immunodeficiency with faciooculoskeletal anomalies is associated with mutations in the PIK3CD gene on chromosome 1.
No clinically relevant genotype-phenotype correlations have been identified to date.
Source: GeneReviews — "Activated PI3K Delta Syndrome"
Penetrance in APDS is believed to approach 100%. However, there is considerable clinical variability, with presentations ranging from nearly asymptomatic with mild laboratory findings to severe manifestations of the disease .
Source: GeneReviews — "Activated PI3K Delta Syndrome"
No consensus clinical diagnostic criteria for activated PI3K delta syndrome (APDS) have been published.
APDS types 1 (APDS1) and 2 (APDS2) are characterized by a spectrum of clinical manifestations primarily involving the immune system, leading to increased susceptibility to infections, autoimmunity, and lymphoproliferation. APDS should be considered in probands with the following suggestive findings:
Clinical findings
Source: GeneReviews — "Activated PI3K Delta Syndrome"
Table 4. Genes of Interest in the Differential Diagnosis of Activated PI3K Delta Syndrome
Gene(s) | Disorder | MOI | Features of Disorder |
|---|---|---|---|
AICDA | Hyper IgM syndrome 2 (HIGM2) (OMIM 605258) | AR | Recurrent infections, hypogammaglobulinemia, IgM, lymphoid hyperplasia |
TNFRSF13C | Common variable immunodeficiency (CVID) (OMIM PS607594) | ARAD |
Genetic testing for KNSTRN, PIK3CD is available. Testing is considered confirmatory for diagnosis.
Biomarker and diagnostic research for combined immunodeficiency with faciooculoskeletal anomalies has been reported in the published literature.
No approved treatments are currently available for combined immunodeficiency with faciooculoskeletal anomalies. The disease remains an area of unmet medical need.
No clinical practice guidelines for activated PI3K delta syndrome (APDS) have been published. In the absence of published guidelines, the following recommendations are based on the authors' personal experience managing individuals with this disorder.
To establish the extent of disease and needs in an individual diagnosed with APDS, the evaluations summarized (if not performed as part of the evaluation that led to the diagnosis) are recommended.
Table 5.
Activated PI3K Delta Syndrome: Recommended Evaluations Following Initial Diagnosis
System/Concern | Evaluation | Comment
| Comprehensive physical exam | To assess for presence of lymphadenopathy, splenomegaly, hepatomegaly
| • Detailed review of infection history
EBV, CMV, HSV PCR in blood relevant serologic testing
JCV PCR if patient received rituximab1
| To identify patterns indicative of immunodeficiency
| • CBC w/differential
Immunoglobulin levels (IgG, IgA, IgM, IgE)
Lymphocyte subset analysis incl nave/memory T cells B-cell subsets
Vaccine-specific antibody titers
| To evaluate immune function identify immunodeficiency
| Imaging studies (e.g., ultrasound, CT, MRI) | To detect organomegaly lymphadenopathy
B-cell clonality studies by V-beta spectratyping
LDH, EBV/CMV PCR
| To evaluate for susceptibility to lymphoproliferative disorders
| • Spirometry
Consider chest CT
| To detect underlying respiratory issues
| • Endosc...
Source: GeneReviews — "Activated PI3K Delta Syndrome"
There are currently two clinical trials evaluating the safety and efficacy of leniolisib in individuals age one to six years (NCT05693129) and four to 11 years old (NCT05438407). Search ClinicalTrials.gov in the US and EU Clinical Trials Register in Europe for access to information on clinical studies for a wide range of diseases and conditions.
Source: GeneReviews — "Activated PI3K Delta Syndrome"
View trials for combined immunodeficiency with faciooculoskeletal anomalies
To monitor existing manifestations, the individual's response to supportive care, and the emergence of new manifestations, the evaluations summarized in are recommended. Table 8. Activated PI3K Delta Syndrome: Recommended Surveillance
System/Concern | Evaluation | Frequency |
|---|---|---|
Infections | Blood/sputum cultures | As needed for symptoms EBV/CMV/HSV PCR |
Lymphoproliferative disorders | CBC, B-cell counts, LDH | Every 6-12 months Abdominal US |
Autoimmune disorders | ANA testing, TSH, TPO | Annually |
Respiratory issues | Regular pulmonary function tests incl spirometry | Every 12 mos (to monitor lung health intervene early if issues are detected) Chest CT |
Gastrointestinal manifestations | Colonoscopy | Symptomatically as needed to identify manage gastrointestinal involvement Liver ultrasound studies |
Developmental | Psychiatric assessment | As needed ANA = antinuclear antibody; CMV = cytomegalovirus; EVB = Epstein-Barr virus; HSV= herpes simplex virus; LDH = lactate dehydrogenase; PCR = polymerase chain reaction; TSH = thyroid-stimulating hormone; TPO = thyroid peroxidase |
Source: GeneReviews — "Activated PI3K Delta Syndrome"
Estimated prevalence: <1 in 1,000,000 (VERY_RARE).
No clinical trials have been registered for combined immunodeficiency with faciooculoskeletal anomalies.
98 publications have been identified in PubMed for combined immunodeficiency with faciooculoskeletal anomalies. Research spans Case Report / Case Series (29%), Epidemiology / Natural History (22%), and Basic Science / Preclinical (16%).
Research Type | Count | % of Total |
|---|---|---|
Patient case studies | 28 | 29% |
Disease patterns and progression | 22 | 22% |
Laboratory research | 16 | 16% |
Research summaries | 12 | 12% |
Testing and diagnosis research | 10 | 10% |
Clinical study results | 8 | 8% |
Other research | 1 | 1% |
New treatment approaches | 1 | 1% |
Sonmez G (2026). [PMID: 42102262](https://pubmed.ncbi.nlm.nih.gov/42102262/). *Clin Exp Immunol*. [Case Report / Case Series]
Larson ME (2026). [PMID: 41129190](https://pubmed.ncbi.nlm.nih.gov/41129190/). *Journal of acquired immune deficiency syndromes (1999)*. [Epidemiology / Natural History]
Jeong PS (2026). [PMID: 40280544](https://pubmed.ncbi.nlm.nih.gov/40280544/). *Journal of advanced research*. [Basic Science / Preclinical]
Meric Z (2026). [PMID: 41275964](https://pubmed.ncbi.nlm.nih.gov/41275964/). *The journal of allergy and clinical immunology. In practice*. [Epidemiology / Natural History]
Zeng C (2026). [PMID: 41106466](https://pubmed.ncbi.nlm.nih.gov/41106466/). *International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases*. [Case Report / Case Series]
Masoch F (2026). [PMID: 41791989](https://pubmed.ncbi.nlm.nih.gov/41791989/). *La Revue de medecine interne*. [Review / Meta-Analysis]
Khanbabaee G (2026). [PMID: 41620725](https://pubmed.ncbi.nlm.nih.gov/41620725/). *BMC pulmonary medicine*. [Diagnostic / Biomarker]
Insalaco A (2026). [PMID: 41616907](https://pubmed.ncbi.nlm.nih.gov/41616907/). *European journal of medical genetics*. [Case Report / Case Series]
Li L (2026). [PMID: 41890715](https://pubmed.ncbi.nlm.nih.gov/41890715/). *Frontiers in immunology*. [Case Report / Case Series]
Haykır Solay A (2026). [PMID: 41896902](https://pubmed.ncbi.nlm.nih.gov/41896902/). *AIDS research and therapy*. [Epidemiology / Natural History]
Data assembled from 7 of 12 sources · Last updated Sep 20, 2026, 1:23 PM UTC
Online Mendelian Inheritance in Man
European rare disease database
Genetic and Rare Diseases Info Center
Common questions about combined immunodeficiency with faciooculoskeletal anomalies
Bronchiectasis |
18%-60% |
— |
Lymphoproliferation | 71%-89% | Incl splenomegaly, hepatomegaly, lymphadenopathy |
Growth delays | 45%-62% | — |
Herpes virus infections | 36%-49% | Persistent, severe, /or recurrent |
Enteropathy | 25%-51% | Lymphoid aggregates may be seen on histology. |
Lymphoma | 12%-28% | Particularly early onset |
Autoimmune cytopenias | 19%-30% | May be refractory to conventional therapy |
Autoimmune autoinflammatory disease | 17%-42% Neurodevelopmental delay | 19%-31% |
Source: GeneReviews — "Activated PI3K Delta Syndrome"
Recurrent infections, hypogammaglobulinemia, autoimmunity, lymphoproliferation
CD40 | Hyper IgM syndrome 3 (HIGM3) (OMIM 606843) | AR | Recurrent infections, hypogammaglobulinemia, IgM, lymphoid hyperplasia |
CD40LG | X-linked hyper IgM syndrome (HIGM1) | XL SH2D1A XIAP | — |
X-linked lymphoproliferative disease | XL | Immune dysregulation | More severe EBV infections |
UNG | Hyper IgM syndrome 5 (HIGM5) (OMIM 608106) | AR | Recurrent infections |
CTLA4 | CTLA4 haploinsufficiency (OMIM 616100) | AD | Recurrent infections, autoimmunity, lymphoproliferation |
LRBA | LRBA deficiency (OMIM 614700) | AR | — |
STAT3 | Autoimmune disease, multisystem, infantile-onset, 1 (OMIM 615952) | AD1 | T helper 17 cells phosphorylated STAT3 AD = autosomal dominant; APDS = activated PI3K delta syndrome; AR = autosomal recessive; CTLA-4 = cytotoxic T-lymphocyte protein 4; EBV = Epstein-Barr virus; MOI = mode of inheritance; STAT3 = signal transducer and activator of transcription 3; XL = X-linked 1. |
Source: GeneReviews — "Activated PI3K Delta Syndrome"