Case#: OO.II.1, subject 95. Male. Age of Onset: 18 y.o. Age of evaluation: 24 y.o. Origin in Germany, Caucasian.

DiseaseAssertion: CVID

FamilyInfo: Patient was included in group of families who had a documented mutation at Exon: 2 and AA Position: 75. Mutations were: p.R75W (c.223C>T) and p.R75Q (c.224G>A). Family groups were: Family E, Family X, Family JJ, Family UU; Family OO.

CasePresentingHPOs: ORPHA:1572 (CVID), HP:0004313 (Hypogammaglobulinemia), HP:0004315 (Low IgG), HP:0001744 (Splenomegaly), HP:0200117 (Recurrent upper and lower respiratory tract infections), HP:0002090 (Pneumonia), HP:0002110 (Bronchiectasis), HP:0002726 (Recurrent Staphylococcus aureus infections), OMIM:188030 (Immune thrombocytopenic purpura/ITP)

CaseHPOFreeText: Respiratory involvement, Low IgM, Low IgA, Lymphoproliferation, Respiratory tract involvement, GLILD, Cytopenia, Autoimmune cytopenia

Bacterial infection: Hemophilus influenzae

Lymphocytic or granulomatous organ infiltration - Lung.

CaseNotHPOs: large phenotype table with unreported symptoms in table S1

CaseNotHPOFreeText: Patient was checked for a number of additional phenotypes but none were identified. Please see Supplementary table S1 for details.

CasePreviousTesting: Genome-wide methods were not used (sequencing of CTLA4 was performed, but no reference made to other genes tested). Some families received whole-exome sequencing but we are unsure if this patient was included.

GenotypingMethod: The authors imply that they sequenced the four exons of CTLA4.

PreviouslyPublished: N/A

Variant: NM_005214.5:c.224G>A

ClinVarID: 943305

CAID: CA350138321

gnomAD: Not found

SupplementalData: extensive data in S1

Note: Functionally tested using transendocytosis

Case#: AAA.II.1, subject 130. Male. Age of Onset: 23y.o. Age of evaluation: 46 y.o. Origin in Switzerland, Caucasian.

DiseaseAssertion: Gastrointestinal involvement

FamilyInfo: None found

CasePresentingHPOs: HP:0008207 (Addison's disease), HP:0004313 (Hypogammaglobulinemia), HP:0002720 (Low IgA), HP:0002014 (Diarrhea), HP:0002242 (Enteropathy), HP:0012410 (PRCA/Pure red cell aplasia)

CaseHPOFreeText: Lymphoproliferation, Cytopenia, Autoimmune cytopenia, Endocrinological involvement, Kidney involvement

Lymphocytic or granulomatous organ infiltration of the gut

Thirty-five percent of affected mutation carriers (27/78) were under antibiotic prophylaxis. In one affected mutation carrier (the patient) treatment with vedolizumab (blocking α4β7 integrin) improved colitis, and in the same individual PRCA responded well to cyclosporine A.

IgG levels: no values were available before IVIG or Rituximab

CaseNotHPOs: large phenotype table with unreported symptoms in table S1

CaseNotHPOFreeText: Patient was checked for a number of additional phenotypes but none were identified. Please see Supplementary table S1 for details.

CasePreviousTesting: Genome-wide methods were not used (sequencing of CTLA4 was performed, but no reference made to other genes tested). Some families received whole-exome sequencing but we are unsure if this patient was included.

GenotypingMethod: The authors imply that they sequenced the four exons of CTLA4.

PreviouslyPublished: Yes, Navarini et al. PMID: 27908448

Variant: NM_005214.5:c.257C>T

ClinVarID: 661941

CAID: CA2067080

gnomAD: 2:204735456 C / T

SupplementalData: extensive data in S1

Note: Functionally tested using transendocytosis

Case#: N/A. Patient was the only one included in this paper. Male. Age of Onset: 9 y.o. Age of evaluation: 42 y.o onwards. Age of Death: ~49 y.o. Origin in Portugal, ethnicity not specified.

DiseaseAssertion: Evans Syndrome

FamilyInfo: No familial segregation analysis could be performed as the patient′s first‐degree relatives (reportedly healthy) refused genetic testing, and the patient had no progeny. Additionally, when the patient was diagnosed and treated for other health conditions, it was noted that "There was no relevant family history".

CasePresentingHPOs: ORPHA:1959 (Evan's syndrome), HP:0002014 (Diarrhea), HP:4000055 (Intestinal Inflammation), HP:0002719 (Severe/Recurrent Infections), HP:0000403 (Recurrent Otitis), HP:0002254 (Intermittent Diarrhea), HP:0001873 (Severe Thrombocytopenia), HP:0002090 (Pneumonia), HP:0004315 (low IgG), HP:0002720 (low IgA), HP:0001082 (Cholecystitis), HP:0001433 (Hepatosplenomegaly), HP:0008711 (Benign prostatic hypertrophy), HP:0012227 (urethral stricture), HP:0003508 (Proportionate Short Stature), HP:0001888 (Lymphopenia), HP:0410385 (Low levels of CD8+ T cells), HP:0410378 (Low levels of CD4+ T cells),

CaseHPOFreeText: Lymphoproliferation, mild ileal inflammatory infiltrate on histology and hemolysis, lower limb cellulitis, IgE and IgD levels were undetectable, but IgM levels were normal, Bilateral osteonecrosis of femoral head and condyles at age 43, Facial vitiligo, Hemoglobin 12.5 g/L; leukocytes: 8700/μL; platelets 28000/μL, trabeculated bladder.

Duodenal, ileal and bladder biopsy: inflammatory infiltrate (not characterized) Negative: direct Coombs, ANA, EBV DNA, CMV DNA, hepatitis B, C, HIV, proteinuria, urinary Ig loss Antiplatelet Ab positive.

Normal total leukocyte count but patient had lymphopenia.

Antidiphtheria Ab: 0.44 UI/mL (protection titer >1.0 UI/mL); peripheral blood mononuclear cell proliferation to PHA, PPD, and Candida were slightly reduced.

Normal levels of CD3+ and CD4+ but low levels of CD8+ (T cells), Low levels of B cells, NK cells and CD4+ (CD45RA+ and CD45RO+) cells. Normal levels of CD45RA+ but high levels of CD45RO+ (CD8 + T cells).

Born to nonconsanguineous parents.

CaseNotHPOs: N/A

CaseNotHPOFreeText: In 2013, the 45‐year‐old patient was admitted for sepsis. An elective total right hip replacement 6 months before had been followed by recurrent urosepsis. Postoperative diagnosis: recurrent urosepsis caused by Enteroccocus faecalis, Klebsiella pneumoniae and Pseudomonas aeruginosa.

For the next 3 years, the patient remained free of infection on IVIG replacement (0.6–0.8 g/kg) every 3–4 weeks, with a median IgG concentration of approximately 6 g/L. In October 2016, he underwent a transurethral resection of the prostate and soon afterward developed diarrhea and significant weight loss. He was again admitted to our hospital, but after extensive investigation, no infectious or immune‐mediated cause could be found. There was an excellent response to a short course of a higher dose of oral prednisolone (30 mg/day, tapered over the next 2 months to 5 mg/day). In February 2017, he was admitted to his local hospital with left‐sided epididymo‐orchitis and rapidly died from hospital‐acquired pneumonia.

CasePreviousTesting: Broad genetic screening using a custom panel of many immune‐related genes using an ion proton next‐generation sequencer, followed by Sanger sequencing, was performed at the Laboratory of Clinical and Infectious Diseases of the National Institute of Allergy and Infectious Diseases, Bethesda, Maryland. See Table 1.

GenotypingMethod: CTLA‐4 sequencing was performed after amplification of the four exons. See Table 1.

PreviouslyPublished: N/A

Variant: NM_005214.5:c.380A>G

ClinVarID: 949358

CAID: CA350138668

gnomAD: Not found

SupplementalData: N/A

Note: Not functionally tested using transendocytosis

Case#: N/A. This patient is the only one studied in this paper. Female. Age of Onset: 11 y.o. Age of evaluation: 13 y.o. Origin not specified but looking at the author information, I believe it can be safely inferred that the patient is originally from Japan.

DiseaseAssertion: Autoimmune enteropathy with CTLA4 haploinsufficiency

FamilyInfo: Patient had no family history of autoimmune diseases, except for hypothyroidism in her mother and hyperthyroidism in her sister. The patient’s mother and sister were found to have the same heterozygous mutation, but they showed only thyroid gland dysfunction that was manageable with medication, which suggests incomplete penetrance.

CasePresentingHPOs: HP:0002720 (low IgA), OMIM:188030 (immune thrombocytopenic purpura (ITP)), sometimes accompanied by HP:0001890 (autoimmune hemolytic anemia), HP:0001882 (leukopenia), and ORPHA:56425 (cold agglutinin disease).

CaseHPOFreeText: Persistent watery diarrhea, immunoglobulin A (IgA) deficiency with low IgG2 and IgG4 subclass, recurrent immune thrombocytopenic purpura (ITP).

The patient had CTLA4 haploinsufficiency and was positive for anti-AIE-75 autoantibody but was successfully treated with 6-mercaptopurine (6-MP)

Patient was suspected of having interstitial nephritis

The patient responded well to prednisolone (PSL; 2 mg/kg/day) that was used to treat ITP at every onset, and the treatment was successfully tapered off. However, watery diarrhea appeared during the tapering of PSL while the treatment for the fifth episode of ITP was ongoing.

Her height was 155 cm (third to fifth percentile) and weight was 48 kg (fifth percentile)

In our patient, clinical remission was achieved with 40 mg/day of PSL. Clinical remission was maintained on 6-MP even after cessation of PSL for 4 years.

CaseNotHPOs: N/A.

CaseNotHPOFreeText: After analyzing the patient’s past laboratory data, we found that following cessation of PSL, ITP relapsed in association with the normalization of IgG levels (861–1,747 mg/dL). In addition, we found that serum levels of sIL-2R were extremely elevated at the onset of AIE. There was no manifestation of AIE, ITP, or other autoimmune diseases for 4 years, while the dose of 6-MP was adjusted to keep the levels of IgG and sIL-2R below 700 mg/dL and 1,500 U/mL, respectively (Fig. 3).

Flow cytometry analysis showed reduced frequency of CD4+ CD25+ FOXP3+ Tregs (Fig. 4) [10]. Consistent with clinical remission of AIE, an endoscopy and histological study 3 years after the achievement of remission demonstrated recovery from villous atrophy (Fig. 5). After 4 years of 6-MP administration, we tried to reduce the amount of 6-MP because we were concerning about the risk of secondary malignancies such as malignant lymphoma caused by 6-MP. Unfortunately, it led to the relapse of diarrhea and ITP along with soar up of serum level of rIL-2 receptor (Fig. 3).

CasePreviousTesting: The patient underwent many different types of testing:

None of the viruses, namely, adenovirus, enterovirus, cytomegalovirus, Epstein-Barr virus, norovirus, and rotavirus, were detected in the patient’s stool sample using polymerase chain reaction. In addition, no pathogenic bacteria were cultured from the stool. Besides, a toxin detection test for Clostridium difficile also yielded negative results. A computed tomography scan of her abdomen revealed a small volume of ascites.

An esophagogastroduodenoscopy and a colonoscopy demonstrated prominent atrophy of the villus in the duodenum (Fig. 1A) and terminal ileum. Colon was intact endoscopically (Fig. 1B). Histopathological examinations of the duodenum and ileum showed severe villous atrophy. Crypt apoptosis, and infiltration of lymphoplasmacytes into the lamina propria were seen in the biopsies of duodenum, ileum, and colon (Fig. 1C-​-E).E). Immunostaining of the normal small intestine tissue with the patient’s serum showed positive staining of the brush borders of the intestinal epithelium, indicating the presence of anti-enterocyte autoantibodies in the serum of the patient (Fig. 2A and ​andB).B). Furthermore, autoantibodies against AIE-75 were detected by Western blotting, using a recombinant protein as an antigen (Fig. 2C). The patient was diagnosed with AIE and was administered an increased dose of PSL (40 mg/day) as induction therapy.

Whole-exome sequencing demonstrated a heterozygous missense mutation in the CTLA4 gene. Flow cytometry analysis showed reduced frequency of CD4+ CD25+ FOXP3+ Tregs

GenotypingMethod: Whole-exome sequencing demonstrated a heterozygous missense mutation in the CTLA4 gene

PreviouslyPublished: Yes, PMID: 29729943. Schwab et al.

Variant: NM_001037631.2:c.119T>C

ClinVarID: None found

CAID: CA350138103

gnomAD: None found

SupplementalData: N/A

Note: Not functionally tested using transendocytosis