A 12-year-old Saudi Arabian boy of consanguineous parents first presented in 2009 at the age of 7 months with chronic diarrhea, poor weight gain, malnutrition, and an eczematous skin rash. Anti-tissue transglutaminase IgA was slightly elevated [39.3 units, upper limit of normal (ULN) = 0-20] and mucosal biopsy of the duodenum showed mild villous atrophy and nonspecific inflammation [Figure 1(c)]. The patient failed to gain weight normally following a trial of a gluten-free diet, despite partial improvement of diarrhea on lactose-free and amino acid formulas. Skin manifestations were progressive, involving the whole skin surface with areas of localized dermatitis and scaling [Figure 1(a) and (b)]. Skin biopsy revealed mild hyperkeratosis with foci of lymphocytic exocytosis and interstitial chronic inflammatory infiltrate, mainly consisting of lymphocytes, with perivascular and peri-appendiceal aggregation seen mainly in the superficial and deep layers of the dermis [Figure 1(d)]. There was one episode of urinary tract infection with Klebsiella pneumoniae organism, which was treated with antibiotics. Renal ultrasonography showed bilateral miniscule renal stones that were detected on serial imaging studies.
At the age of 2 years, hepatomegaly with a moderate increase in liver enzymes was found (gamma-glutamyl transferase = 211 U/l, aspartate amino transferase = 132 U/l, alanine amino transferase = 226 U/l, alkaline phosphatase = 382 U/l, bilirubin = 9 umol/l). Percutaneous liver biopsy was performed, which showed expansion of the portal tracts and distension with chronic inflammatory cells, mainly lymphocytes and occasionally eosinophils, along with an ill-defined granuloma surrounded by dense inflammatory cells (Figure 2). Screening for autoimmune markers, including anti-smooth muscle antibody (SMA), anti-nuclear antibody (ANA), and anti-liver kidney microsomal antibody-1 (LKM-1), was negative as were the immunoglobulin (Ig) levels [IgG 19.5 g/l (5.4-16.1 g/l), IgA 3.87 g/l (0.8-2.8 g/l), IgM 1.35 g/l (0.5-1.9), and IgE 77 kU/l (0-195 kU/l)]. Liver enzymes declined with time, although liver enlargement continued.
At 4 years of age, following adenotonsillectomy, the boy developed mild splenomegaly and generalized lymphadenopathy of the cervical, axillary, and inguinal lymph nodes, accompanied by digital clubbing. Test results for tuberculosis (tuberculin skin test and chest X-ray), sarcoidosis, and parasitic infections were negative.
At 9 years of age, owing to persistent diarrhea, failure to grow, and a high fecal calprotectin level (6200 mg/kg), upper gastrointestinal endoscopy and colonoscopy were performed. Pancolitis was found during colonoscopy and normal upper gastrointestinal endoscopy. Chronic active inflammation was reported in the biopsy specimens, taken from the esophagus, stomach, duodenum, and colonic mucosa, with marked lymphocytic infiltration. In consideration of a possible diagnosis of IPEX (immune dysregulation, polyendocrinopathy, enteropathy, X-linked) syndrome, a screening for possible endocrinopathies was performed, but the thyroid function tests with thyroid antibodies were negative, and there were normal fasting blood sugar and hemoglobin A1c levels. There was no evidence of autoimmune neutropenia, anemia, or thrombocytopenia.
The patient continued to have alternating diarrhea and normal bowel motions. Anthropometric measures for his age were always under the third percentile for weight, height, and body mass index. Unfortunately, the patient passed away aged 10 years after developing septic shock.
Written informed consent was obtained from the parents for genetic testing and for reporting the case. Under HIPAA (Health Insurance Portability and Accountability Act), ethical approval is not needed for case reports.
Figure 3 shows the family pedigree of the patient being studied. The whole exome sequencing of the proband was performed on the Illumina, Hiseq2000 sequencing platform at 30x coverage. The full details of DNA purification, library preparation, sequencing, data filtration, and variation identification strategies we adopted are outlined in our recent publications. From the exome data of the proband, we observed a novel, homozygous, and likely pathogenic c.504 C>A variant located in the exon 4 region of the IL2RA gene, resulting in the substitution of a cysteine codon at amino acid position 168 with a termination codon in the IL2RA protein. Sanger sequencing of the proband and of both parents has confirmed the autosomal recessive mode of inheritance of this variant. This variant is absent from the GnomAD, 1000 Genomes Project, Saudi Human Genome Program, and DALIA databases. The functional characterization of the IL2RA variant was performed by various systems biology methods. First, the 3D model of IL2RA variant protein was constructed using the ab-initio method as described.   Then, RNAfold webserver was used to estimate the effect of the IL2RA, c.504 C>A variant on the corresponding RNA structure. Findings from mRNA secondary structure of IL2RA predictions have indicated no significant changes in the thermodynamic stability of the mRNA folding pattern due to c.504 C>A variant (Figure 4). Finally, the NCBI conserved domain database was used to map the IL2RA, c.504 C>A variant on the functional domains of the protein molecule.   From the results of functional domain analysis, we identified that the c.504 C>A variant falls into a canonical sushi-like functional domain (complement control protein, CCP), spanning between the 125th and 184th amino acids, and it most likely produces a premature protein (104 amino acids) that is shorter than the native IL2RA protein molecule (272 amino acids).