| Name of syndrome | Primary defect | Gene | Immune defect | Associated features |
| Acrodermatitis enteropathica | Specific organ dysfunction | SLC39A4 | T, B, Ph | Vesiculobullous dermatitis, alopecia, diarrhea; caused by zinc deficiency, may be associated with opportunistic infections |
| ARPC1B deficiency | Specific organ dysfunction | ARPC1B | B, Ph | Thrombocytopenia, vasculitis |
| Ataxia-telangiectasia | Chromosomal instability and/or defective DNA repair | ATM | T, B | Progressive cerebellar ataxia, telangiectasias (conjunctival), choreoathetosis |
| Ataxia-telangiectasia-like disorder | Chromosomal instability and/or defective DNA repair | MRE11A | T, B | Progressive cerebellar ataxia, choreoathetosis |
| B cell immunodeficiency, distal limb anomalies, and urogenital malformations (BILU) syndrome (Hoffman syndrome) | Specific organ dysfunction | ? | B | Limb defects, urogenital malformations |
| Bloom syndrome | Chromosomal instability and/or defective DNA repair | BLM | T, B, NK | Short stature, telangiectatic erythema of face, sensitivity to sunlight, pneumonia, otitis media, risk for leukemia/lymphoma |
| Branched chain amino acidemias | Inborn errors of metabolism | MUT, IVD, PCCA/PCCB | T, B, Ph | Methylmalonic propionic and isovaleric acidemias, acidosis, vomiting, ketosis |
| Cartilage-hair hypoplasia | Specific organ dysfunction | RMRP | T, B, Ph | Metaphyseal dysplasia, fine/sparse hair |
| CD4 lymphocytopenia | Immune dysregulation | ? | T (+/– B, NK) | Malignancy (particularly lymphomas), autoimmune disorders |
| CHARGE association | Growth deficiency | CHD7, SEMA3E | T, B | Coloboma, heart defect, atresia choanae, retarded growth and development, genital hypoplasia, ear anomalies/deafness |
| Congenital disorders of glycosylation, Types Ia, Ig, Ik | Inborn errors of metabolism | PMM2, ALG12, ALG1 | B, Ph | Decreased glycosylation hypotonia, poor growth, other organ systems may be involved depending on the type |
| Deletion of short arm of chromosome 4 (4p16) (Wolf-Hirschhorn syndrome) | Chromosomal abnormalities of number or structure | Chromosome 4p16 deletion | B | Growth and developmental deficiency, "Greek helmet"-like facies, microcephaly, coloboma, respiratory infections |
| DiGeorge syndrome | Chromosomal abnormalities of number or structure | Del22q11, del10p13, TBX1 | T | Aortic arch anomalies, hypocalcemia, thymic hypoplasia, cleft palate, facial dysmorphism |
| Dyskeratosis congenita (DKC) - Autosomal dominant | Specific organ dysfunction | TERC, TERT, TINF2 | T, B, Ph | Atrophy and pigmentation of skin, nail dystrophy, leukoplakia of oral mucosa |
| Dyskeratosis congenita (DKC) - Autosomal recessive | Specific organ dysfunction | NHP2, NOP10, RTEL1 | T, B, Ph | Atrophy and pigmentation of skin, nail dystrophy, leukoplakia of oral mucosa |
| Facial dysmorphism, immunodeficiency, livedo, and short stature (FILS) syndrome | Specific organ dysfunction | POLE1 | T, B | Facial dysmorphism, livedo, short stature |
| Familial intestinal polyatresia | Specific organ dysfunction | TTC7A | T, B | Multiple atresias from pylorus to rectum |
| Griscelli syndrome, type 2 | Specific organ dysfunction | RAB27A | T, B, NK, Ph | Partial albinism, frequent pyogenic infections, lymphohistiocytosis, episodic thrombocytopenia |
| Growth hormone pathway defects | Growth deficiency | BTK, STAT5B | T, B, NK | Defects in growth hormone synthesis or sensitivity deficiency, sinopulmonary infections |
| Hepatic veno-occlusive disease with immunodeficiency (VODI) | Specific organ dysfunction | SP110 | T, B | Hepatic veno-occlusive disease |
| Hereditary folate malabsorption | Specific organ dysfunction | SLC46A1 | T, B | Megaloblastic anemia, convulsions, movement disorder |
| Hoyeraal-Hreidarsson syndrome | Specific organ dysfunction | DKC1 | T, B, Ph | Cerebellar hypoplasia, absent corpus callosum, microcephaly, growth failure, pancytopenia, fungal sepsis |
| Hyper-IgE syndrome - Autosomal dominant (Type 1, Job syndrome) | Specific organ dysfunction | STAT3 | T, B | Eczema, scoliosis, bone fractures, joint hyperextensibility, coarse facies |
| Hyper-IgE syndrome - Autosomal recessive (Type 2) | Specific organ dysfunction | DOCK8 | T, B | Eczema, malignancy, CNS vasculitis/stroke |
| Hyper-IgE syndrome variant | Specific organ dysfunction | TYK2 | T, B | Eczema, mycobacterial infection |
| Hyper-IgE syndrome variant | Specific organ dysfunction | PGM3 | T, B, Ph | Eczema, developmental delay, myoclonus |
| Hypohidrotic/anhidrotic ectodermal dysplasia with immunodeficiency | Specific organ dysfunction | NEMO/NFKBIA | T, B | Alopecia, hypohidrosis/anhydrosis, tooth anomalies, hypogammaglobulinemia |
| ICF syndrome | Chromosomal instability and/or defective DNA repair | DNMT3B | T, B | Intellectual disability, chromosomal instability, facial dysmorphism; sinopulmonary, gastrointestinal, cutaneous infections |
| Ikaros deficiency | Specific organ dysfunction | IKZF1 | B, Ph, NK | Pancytopenia |
| Immunodeficiency with multiple intestinal atresia | Specific organ dysfunction | TTC7A | T, B | Multiple atresias from pylorus to rectum |
| Incontinentia pigmenti | Specific organ dysfunction | NEMO | T, B, Ph | Erythematous vesiculobullous eruptions, CNS involvement, swirling of macules or hyperpigmentation |
| Kabuki syndrome | Growth deficiency | KMT2D, KDM6A | B | Long palpebral fissures, prominent eyelashes, skeletal anomalies, congenital heart disease, increased risk of autoimmune diseases |
| Loeys-Dietz syndrome | Specific organ dysfunction | TGFBR1 | B | Aortic aneurysm, cleft palate, hypertelorism, eczema |
| Lysinuric protein intolerance | Inborn errors of metabolism | SLC7A7 | T, B, NK, Ph | Dibasic aminoaciduria, hepatomegaly, failure to thrive, severe varicella infection |
| Minichromosome maintenance complex component 4 (MCM4) deficiency | Specific organ dysfunction | MCM4 | NK | Growth failure, microcephaly, glucocorticoid deficiency |
| Missing or abnormal X chromosome (Turner syndrome; XO, isoX, ring X) | Chromosomal abnormalities of number or structure | X chromosome abnormality | T, B | Short stature, webbed neck, broad chest, ovarian dysgenesis, congenital lymphedema, pulmonary/ear infections, autoimmune disease (eg, thyroid disease, celiac disease, arthritis), gonadoblastoma (if Y chromosome material present) |
| MTHFD1 deficiency | Specific organ dysfunction | MTHFD1 | T, B | Megaloblastic anemia, neurologic abnormalities, hemolytic uremic syndrome |
| Myotonic dystrophy | Specific organ dysfunction | DMPK, ZNF9 | B | Myotonia, muscle wasting, cataract, hypogonadism, cardiac arrhythmia; caused by triplet repeat expansion |
| Netherton syndrome | Specific organ dysfunction | SPINK5 | T, B, Ph | Trichorrhexis invaginata (bamboo hair), ichthyosiform dermatitis, atopic diathesis, skin infections |
| Nijmegen breakage syndrome | Chromosomal instability and/or defective DNA repair | NBS1 | T, B | Microcephaly, intellectual disability, prenatal-onset short stature, bird-like facies, malignancy (lymphoma), sinopulmonary and urinary tract infections |
| OLEDAID syndrome | Specific organ dysfunction | NEMO | B | Anhidrotic ectodermal dysplasia, osteopetrosis, lymphedema |
| Omenn syndrome | Specific organ dysfunction | RAG1/RAG2/ARTEMIS | T, B | Erythematous dermatitis, eosinophilia, lymphadenopathy, hemophagocytosis, severe combined immunodeficiency |
| Postmeiotic segregation increased 2 deficiency | Specific organ dysfunction | PMS2 | B | Cancer, brain anomalies, café au lait macules |
| Radiosensitivity, immunodeficiency, dysmorphic features and learning difficulties (RIDDLE) syndrome | Chromosomal instability and/or defective DNA repair | RNF168 | B | Characteristic facies, learning difficulties, radiosensitivity |
| Roifman syndrome | Growth deficiency | RNU4ATAC | B | Short stature, spondyloepiphyseal dysplasia, developmental delay |
| Rubinstein-Taybi syndrome | Growth deficiency | EP300 | T, B | Broad thumbs and halluces, prominent nasal septum below ala nasi, cryptorchidism, intellectual disability |
| Schimke immunoosseous dysplasia | Growth deficiency | SMARCAL1 | T, B | Spondyloepiphyseal dysplasia, progressive neuropathy, episodic lymphopenia, pigmentary skin changes |
| Severe dermatitis, allergy, metabolic wasting (SAM) syndrome | Specific organ dysfunction | DSG1 | B | Eczema, palmoplantar keratoderma, hypotrichosis |
| Short-limb skeletal dysplasia with immunodeficiency | Growth deficiency | ADA, others | T, B | Short-limb skeletal dysplasia, metaphyseal dysplasia; may be associated with adenosine deaminase deficiency or Omenn syndrome; heterogeneous |
| Sideroblastic anemia with immunodeficiency, fevers, and developmental delay (SIFD) | Specific organ dysfunction | TRNT1 | B | Sideroblastic microcytic anemia, periodic fever, developmental delay |
| SPENCD1 syndrome | Growth deficiency | SPENCD1 | T, B | Spondyloenchodrodysplasia, autoimmune conditions |
| Transcobalamin II deficiency | Specific organ dysfunction | TCN2 | B | Transport protein for B12; severe megaloblastic anemia, leukopenia, thrombocytopenia |
| Trichohepatoenteric syndrome | Specific organ dysfunction | TTC37 | B, Ph | Severe infantile diarrhea, hepatic cirrhosis, Trichorrhexis nodosa, characteristic facies |
| Trisomy 21 (Down syndrome) | Chromosomal abnormalities of number or structure | Chromosome 21 | T, B, Ph, NK | Hypotonia, flat facies, upslanting palpebral fissures, intellectual disability, sinopulmonary infections, risk of leukemia, autoimmune thyroiditis |
| WHIM syndrome | Specific organ dysfunction | CXCR4 | T, B, Ph | Warts, hypogammaglobulinemia, infection, myelokathexis |
| Wiskott-Aldrich syndrome | Specific organ dysfunction | WAS | T, B | Severe eczema, thrombocytopenia, bloody diarrhea, recurrent infection |
| Wiskott-Aldrich syndrome protein-interacting protein (WIP) deficiency | Specific organ dysfunction | WIPF1 | T, B | Severe eczema, thrombocytopenia, recurrent infection |
