**Case#: ** P1, 19-years-old Saudi male

**DiseaseAssertion: ** P1 is asserted to have "Crohn disease" and "CMV gastritis"

CasePresentingHPOs: HP:0002028, HP:0005425, HP:0000964, HP:0011473, HP:0200120

CaseHPOFreeText: P1 is a 19 year old boy with history of chronic diarrhea, recurrent sinopulmonary infections and dermatitis since the age of 2 months. At age of 1 year full upper and lower endoscopy showed duodenal villous atrophy and mild duodenitis, and antrum biopsy was suggestive of CMV gastritis with no significant colon biopsy findings. At 13 years of age he was evaluated by immunology service to rule out IEI. His complete blood counts and differential, lymphocytes subsets, lymphocytes proliferation and oxidative burst assays were normal. His IgG level was subnormal for age (4.2 gm/L) with undetectable IgM levels (Table 1). He was started on intravenous immunoglobulins with good clinical response in regard to his recurrent sinopulmonary infections. He continued to have chronic diarrhea that on frequent occasions was bloody, but he had normal weight gain and growth. Upper and lower endoscopies were performed on several occasions and showed severe chronic active colitis with ulcerations, epithelial reactive changes with granulomatous tissue formation suggestive of Crohn disease. His diarrhea responded partially to sulfasalazine therapy and short courses of steroids.

Variant: NM_005026.4: c.433delinsGA: p.Q145Efs*51

GenotypingMethod: DNA from all individuals we had access to was submitted for whole-genome genotyping, to determine regions of autozygosity that are shared between all affecteds. This was done under the assumption of an autosomal recessive inheritance pattern, given the nature of the pedigree and the presence of parental consanguinity. Three such regions were highlighted by the software, of which the largest was a 12.3 Mb block on Chr 1 (Fig. 1B). Simultaneously we submitted the DNA from patient P1 for WES, and followed the NGS filtering scheme indicated in Fig. 1C. Once we had limited our search area to the regions of shared autozygosity which were exclusive to the three patients, no variants survived our filtering except for one

CAID: CA3252646241