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A severe autosomal recessive developmental disorder characterized by multiple intestinal atresia apparent soon after birth. Affected infants have a distended abdomen and do not pass meconium. There is some evidence of inflammatory bowel disease. Death occurs in the first weeks of life. Some patients may also have immunodeficiency.
Data assembled from 6 of 12 sources · Last updated Sep 19, 2026, 4:33 PM UTC
Online Mendelian Inheritance in Man
Features include always present findings: Delayed fine motor development, Intellectual disability, Difficulty swallowing (dysphagia), and Delayed speech and language development and others; and very common findings: Inflammation of the large intestine. 40 total HPO annotations.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Brain and nerves | 11 | Dystonia, Seizure, Ataxia |
Muscles | 4 | Shrinkage of the cerebellum (cerebellar atrophy), Delayed gross motor development, Knee flexion contracture |
Lungs and breathing | 3 | Pulmonary hypoplasia, Bronchiectasis, Interstitial emphysema |
Digestive system | 3 | Intestinal atresia, Inflammation of the large intestine, Difficulty swallowing (dysphagia) |
Eyes | 2 | Nystagmus, Damage to the optic nerve (optic atrophy) |
Kidneys and urinary system | 1 | Dilatation of the renal pelvis |
Arms and legs | 1 | Overlapping fingers |
Bones and joints | 1 | Excessive outward curvature of the upper spine (kyphosis) |
Blood and immune system | 1 | Immunodeficiency |
PI4KA-related disorder is a clinically variable disorder characterized by neurologic dysfunction, gastrointestinal manifestations (intestinal atresia, inflammatory bowel disease), and immunodeficiency. Onset is typically antenatal or in early childhood. Four overlapping clinical phenotypes have been described: • Hypomyelinating leukodystrophy with pyramidal features including lower limb spasticity, developmental delay, and intellectual disability, with or without inflammatory bowel disease. The most common presentation; neurologic features typically present in infancy or early childhood. • Severe antenatal-onset neurologic disorder with arthrogryposis and structural brain anomalies (e.g., perisylvian polymicrogyria, cerebellar hypoplasia) • Multiple intestinal atresia presenting shortly after birth, with or without immunodeficiency • Rarely, later-onset pure hereditary spastic paraplegia To date, 24 individuals have been identified with PI4KA pathogenic variants . The following description of the phenotypic features associated with this condition is based on these reports. Table 2. PI4KA-Related Disorder: Frequency of Select Features
Feature | Proportion ofPersons w/Feature1 | Comment |
|---|---|---|
manifestations |
PI4KA function has not been fully characterized.
Gastrointestinal defects and immunodeficiency syndrome 2 is associated with mutations in the PI4KA gene on chromosome 22.
To date, the limited number of individuals described with PI4KA-related disorder prevents identification of conclusive phenotype-genotype correlations. However, some patterns have emerged:
Source: GeneReviews — "PI4KA-Related Disorder"
PI4KA-related disorder is a clinically variable disorder characterized by neurologic dysfunction, gastrointestinal manifestations (bowel atresia, inflammatory bowel disease), and immunodeficiency. PI4KA-related disorder should be suspected in individuals with the following clinical, laboratory, and imaging features.
Clinical features
• Neurologic
Peripheral spasticity, often more marked in lower than upper limbs
Truncal hypotonia
Global developmental delay
Intellectual disability (mild to severe)
Seizures
Ataxia
Nystagmus
Intention tremor
Dysmetria
Dystonia
Arthrogryposis/contractures
Kyphosis or scoliosis
• Gastrointestinal
Source: GeneReviews — "PI4KA-Related Disorder"
The differential diagnosis of PI4KA-related disorder includes hypomyelinating leukodystrophies with early childhood onset (see for a nonexhaustive list of hypomyelinating leukodystrophies) and TTC7A-related gastrointestinal defects and immunodeficiency syndrome. Table 3. Genes of Interest in the Differential Diagnosis of PI4KA-Related Disorder
Gene | DiffDx Disorder | MOI | Key Features of DiffDx Disorder |
|---|---|---|---|
Hypomyelination congenital cataract | AR | Hypomyelinating leukodystrophy. Cerebellar signs are variably present. | Congenital cataracts variably present psychomotor regression; peripheral neuropathy present in majority of affected persons. Polymicrogyria, IBD, immunodeficiency have not been described. |
Genetic testing for PI4KA is available. Testing is considered confirmatory for diagnosis.
Biomarker and diagnostic research for gastrointestinal defects and immunodeficiency syndrome 2 has been reported in the published literature.
No approved treatments are currently available for gastrointestinal defects and immunodeficiency syndrome 2. The disease remains an area of unmet medical need.
No clinical practice guidelines for PI4KA-related disorder have been published. Evaluations Following Initial Diagnosis To establish the extent of disease and needs in an individual diagnosed with PI4KA-related disorder, the evaluations summarized (if not performed as part of the evaluation that led to the diagnosis) are recommended. Table 4. Recommended Evaluations Following Initial Diagnosis in Individuals with PI4KA-Related Disorder
System/Concern | Evaluation | Comment |
|---|---|---|
anomalies | Consider renal ( pelvic) imaging. | Assess for structural anomalies. |
Hearing | Audiologic assessment | Assess for hearing loss. |
Vision | Ophthalmologic assessment | Assess for nystagmus, visual acuity, optic nerve atrophy, strabismus, ocular motor dyspraxia. Genetic |
counseling | By genetics professionals1 | To inform affected persons their families re nature, MOI, implications of PI4KA-related disorder to facilitate medical personal decision making Family support resources |
Treatment of Manifestations in Individuals with PI4KA-Related Disorder Manifestation/Concern | Treatment | Considerations/Other Limb spasticity motor delays |
Source: GeneReviews — "PI4KA-Related Disorder"
Recent investigation of anti-apoptotic medications in laboratory and animal models of TTC7A-related gastrointestinal defects and immunodeficiency syndrome (OMIM 243150) suggest that leflunomide may be a potential treatment for bowel inflammation and stenosis in this condition . Due to the phenotypic and mechanistic overlap between TTC7A- and PI4KA-related bowel disease, this treatment may be applicable to PI4KA-related disorder. To date, however, no data exist to support the efficacy of leflunomide in treating PI4KA-related bowel disease. 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. Note: There may not be clinical trials for this disorder.
Source: GeneReviews — "PI4KA-Related Disorder"
View trials for gastrointestinal defects and immunodeficiency syndrome 2
To date, no general surveillance guidelines have been developed; monitoring should be individualized. Table 6. Recommended Surveillance for Individuals with PI4KA-Related Disorder
System/Concern | Evaluation | Frequency |
|---|---|---|
Neurologic | Neurologic assessment to monitor for progression of limb spasticity, dysphagia, cerebellar signs, dystonia, seizures | Annually as indicated by symptomatology Developmental delay/ |
Intellectual disability | Assessment of developmental milestones by pediatrician | As indicated by clinical presentation Inflammatory bowel disease |
Hearing | Audiology eval | Annually throughout childhood Vision |
Source: GeneReviews — "PI4KA-Related Disorder"
Phenotype severity distribution: 6 always present features, 1 very common feature, 9 common features.
No clinical trials have been registered for gastrointestinal defects and immunodeficiency syndrome 2.
127 publications have been identified in PubMed for gastrointestinal defects and immunodeficiency syndrome 2. Kisho has analyzed 70 by research type. Research spans Review / Meta-Analysis (26%), Clinical Trial Publication (19%), and Basic Science / Preclinical (19%).
Research Type | Count | % of Total |
|---|---|---|
Research summaries | 18 | 26% |
Clinical study results | 13 | 19% |
Laboratory research | 13 | 19% |
Disease patterns and progression | 13 | 19% |
Patient case studies | 10 | 14% |
Other research | 2 | 3% |
Testing and diagnosis research | 1 | 1% |
Davita TR (2026). [PMID: 41862227](https://pubmed.ncbi.nlm.nih.gov/41862227/). *Immunobiology*. [Case Report / Case Series]
Lin S (2026). [PMID: 41517791](https://pubmed.ncbi.nlm.nih.gov/41517791/). *Medicine (Baltimore)*. [Case Report / Case Series]
Thawabteh FA (2026). [PMID: 41958672](https://pubmed.ncbi.nlm.nih.gov/41958672/). *Front Immunol*. [Review / Meta-Analysis]
Metzger O (2026). [PMID: 41604639](https://pubmed.ncbi.nlm.nih.gov/41604639/). *N Engl J Med*. [Clinical Trial Publication]
Chamarthi VS (2026). [PMID: 31747205](https://pubmed.ncbi.nlm.nih.gov/31747205/). *Unknown Journal*. [Other]
Wingard JR (2026). [PMID: 41406403](https://pubmed.ncbi.nlm.nih.gov/41406403/). *J Clin Oncol*. [Clinical Trial Publication]
Cascorbi I (2026). [PMID: 41289068](https://pubmed.ncbi.nlm.nih.gov/41289068/). *Dtsch Arztebl Int*. [Review / Meta-Analysis]
Blair HA (2026). [PMID: 41882319](https://pubmed.ncbi.nlm.nih.gov/41882319/). *Mol Diagn Ther*. [Review / Meta-Analysis]
Muniraju T (2026). [PMID: 42055761](https://pubmed.ncbi.nlm.nih.gov/42055761/). *BMJ Case Rep*. [Case Report / Case Series]
Chin AT (2025). [PMID: 40571245](https://pubmed.ncbi.nlm.nih.gov/40571245/). *J Allergy Clin Immunol Pract*. [Basic Science / Preclinical]
Limb spasticity |
16/16 |
Developmental delay | 14/16 | — |
Intellectual disability | 15/16 | — |
Seizures | 10/16 | — |
Ataxia | 10/16 | — |
Nystagmus | 8/16 | Brain MRI |
findings | Hypomyelinating leukodystrophy/delayed myelination | 12/16 |
Cerebellar hypoplasia/ atrophy | 12/19 | — |
Dysplastic/thin corpus callosum | 11/19 | — |
Perisylvian polymicrogyria | 4/19 | — |
Multiple intestinal atresia | 5/24 | — |
Inflammatory bowel disease | 4/24 | — |
Immunodeficiency | 6/21 | 1. Affected persons who died before a specific clinical sign would become apparent are not included in the table. Limb spasticity. All individuals with molecularly confirmed PI4KA-related disorder reported to date who survived beyond age one month developed or presented with limb spasticity. |
Source: GeneReviews — "PI4KA-Related Disorder"
PLP1 |
PLP1 disorders incl Pelizaeus-Merzbacher disease spastic paraplegia 2 (SPG2) |
XL |
Hypomyelinating leukodystrophy. Prominent cerebellar features. Variable age of onset w/spastic paraparesis described as SPG2 in those w/later onset. |
RARS1 | RARS1-related hypomyelinating leukodystrophy (OMIM 616140) | AR | Hypomyelinating leukodystrophy. Severe refractory epilepsy/ epileptic encephalopathy has been described. |
TTC7A | Gastrointestinal defects immunodeficiency syndrome (OMIM 243150) | AR | Heterogeneous intestinal immunologic disease manifestations incl but not limited to multiple intestinal atresia, very early-onset IBD, combined immunodeficiency |
Source: GeneReviews — "PI4KA-Related Disorder"
Speech impairment | Speech-language therapy; use of communication aids (e.g., talker) | — |
Intellectual disability | Educational support | — |
Seizures | Use of standard anti-seizure medications; dependent on specific seizure type | Dysphagia |