Case#: Grammatikos_2021_Case 1, female, 35 y.o. (onset) 51 y.o. (report), origin not reported

DiseaseAssertion: CTLA4 haploinsufficiency

FamilyInfo: affected younger daughter (case 2), affected son (case 3). 2 brothers of case 1 were affected by Evans syndrome. Another brother was affected by unexplained lymphadenopathy. Deceased brother passed due to eft ventricular fibrosis at age 40. Case 1 also had a niece with recurrent cutaneous ulceration and was a LRBA mutation carrier. The eldest daughter of case 1 developed AML (age 14).

CasePresentingHPOs: HP:0001903, HP:0002716, HP:0001945,HP:0003326, HP:0002829, HP:0031457, HP:0033608, HP:0002110, HP:0001744, HP:0033805, HP:0040312, HP:0002840, HP:0002113, HP:0005479, HP:0010976, HP:0025379, HP:0002922, HP:0001974, HP:0032289, HP:0002321, HP:0002013, HP:0001250, HP:0012534, HP:0001260, HP:0001310 (anaemia, lymphadenopathy, fevers, myalgia, arthralgia, scattered opacification, nodules in lung, bronchiectasis, splenomegaly, non-necrotising granulomas, arthritis of left temporomandibular joint, granulomatous lymphadenitis, migratory infiltrates, decreased IgE, low b-cell count, increased TPO antibodies, increased protein CSF, increased WBC, IgG oligoclonoal pattern, vertigo, vomiting, seizures, right-facial dysesthesia, dysarthria, right-sided dysmetria)

CaseHPOFreeText: mass of 1.4 cm resolving spontaneously behind tibialis posterior tendon. MRI revealed mass in the right middle cerebellar peduncle with surrounding edema. Cellular infiltration by CD4:CD* T cells, plasma cells, microglia (2:1 ratio). Neutrophilic infiltrate of the lymphatic system, EBV-related lymphoprliferation, bile salt malabsorption

CaseNotHPOs: HP:0031693, HP:0005344, HP:0003116 (serum EBV, abnormal carotid ultrasound, abnormal echocardiogram)

CaseNotHPOFreeText: presence of inflammatory markers

CasePreviousTesting: 194 genes associated with immune deficiency, next-gen sequencing. Heterozygous VUS found in LRBA.

GenotypingMethod: confirmation of CTLA4 c.81dup by Sanger sequencing

PreviouslyPublished: not reported

Variant: Heterozygous NM_005214.4(CTLA4):c.81_82insT (p.Leu28fs), Heterozygous NM_006726.4(LRBA):c.6424T>C (p.Phe2142Leu)

ClinVarID: 644629, 1038663

CAID: CA645516071, CA358607456

gnomAD: not found, not found

SupplementalData: Figure S1 shows extensive family history

Table S1 lists two additional INSR variants identified in the proband during whole exome sequencing:

1. NM_000208.3:c.*104A>G – a 3′ UTR variant, homozygous, annotated as benign in ClinVar (rs1051690).
2. NM_000208.3:c.2666G>A (p.Arg889Gln) – a heterozygous missense variant, classified as a variant of uncertain significance in ClinVar (rs187282966).

Case#: 20-year-old Spanish man

DiseaseAssertion: Immune dysregulation with autoimmunity, immunodeficiency, and lymphoproliferation

FamilyInfo: Maternally inherited CTLA4 variant and paternally inherited CLEC7A variant. Patient's mother had been diagnosed with mild sarcoidosis, dysphagia with eosinophilic infiltrates of esophagus, low IgM, and decreased percentages of memory B cells.

CasePresentingHPOs: HP:0100651 (Type I diabetes mellitus) HP:0001045 (Vitiligo) HP:0001047 (Atopic dermatitis) HP:0002205 (Recurrent respiratory infections) HP:0001541 (Ascites) HP:0002014 (Diarrhea) HP:0410151 (Eosinophilic infiltration of the esophagus) HP:0410147 (Eosinophilic infiltration in the stomach mucosa) HP:0033351 (Candida esophagitis) HP:0100806 (Sepsis) HP:0032061 (Hypereosinophilia) HP:0032064 (Gastrointestinal eosinophilia)

CaseHPOFreeText: Type 1 diabetes was diagnosed at 15 months old. Patient has a history of severe enteritis. Investigations, which were undertaken due to hypereosinophilia and eosinophilic infiltration, revealed a clonal γδ T cell band, characterized as reactive, with subsequent exclusion of FIP1L1-FDGFRA and PDGFRB rearrangements, as well as any abnormal karyotype. Sepsis was due to Salmonella typhi and Clostridium difficile infection.

Article provides functional evidence of CLEC7A variant affecting phenotype of this patient. Their data suggest that partial loss of DECTIN-1 in a patient with CTLA-4h may enhance IDAIL penetrance and confer additional unique phenotypes, with persistent marked hypereosinophilia as the most remarkable uncommon clinical manifestation.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Whole-genome sequencing was performed on the patient's whole blood sample. The variants were confirmed with Sanger sequencing. Presence of a somatic CTLA4 variant was ruled out with high-coverage WGS of sorted peripheral T cells.

GenotypingMethod: Whole-genome sequencing was performed on the patient's whole blood sample. The variants were confirmed with Sanger sequencing. Presence of a somatic CTLA4 variant was ruled out with high-coverage WGS of sorted peripheral T cells.

PreviouslyPublished: No

Variant: NM_005214.5:c.208C>T p.Arg70Trp

ClinVar: 161114

CAID: CA173999

gnomAD: 0.000001313 https://gnomad.broadinstitute.org/variant/2-203870684-C-T?dataset=gnomad_r4

Variant: NM_197947.3:c.547C>T p.Leu183Phe

ClinVar: 717363

CAID: CA6443934

gnomAD: 0.01719 https://gnomad.broadinstitute.org/variant/12-10123309-G-A?dataset=gnomad_r4

SupplementalData: Detailed clinical info and and immunological test results can be found in Supplementary Materials.f

Case: Patient, Male, 4 months old <br /> DiseaseAssertion: SCID <br /> FamilyInfo: third child of non-consanguineous parents; has twin brother that is asymptomatic with no immune defects; no family history of primary immunodeficiencies <br /> CasePresentingHPOs: HP:0002014, HP:0020099, HP:0030148 <br /> CaseHPOFreeText: diarrhea, norovirus infection, heart murmur <br /> CaseNotHPOs: increased CRP <br /> CasePreviousTesting: N/A <br /> Gene: IL2RG <br /> Variant: NM_000206(IL2RG): <br /> ClinVar: <br /> CAID: <br /> gnomAD: <br /> SupplementalData:

Case#: 55-year-old man

DiseaseAssertion: single coronary artery (SCA) and presented with dilated cardiomyopathy (DCM)

FamilyInfo: Unremarkable

ParentalTesting: NR

CasePresentingHPOs: HP:0002094, HP:0031352, HP:0001638, HP:0001644, HP:0010741

CaseHPOFreeText: chest tightness and dyspnoea after activity lasting for 2 months. CTCA showed congenital absence of the right coronary artery. TTE revealed enlargement of the left heart and cardiomyopathy. CMR revealed DCM. oedema of both lower limbs. Laboratory data in Table 1.

CaseNotHPOs: NR

CaseNotHPOFreeText: Stenosis

CasePreviousTesting: See NGS results in Supplementary Table 1

Genotyping Method: Genetic screening (NGS results in Supplementary Table 1) with confirmation by Sanger

FunctionalAnalysis: NR

Variant: c.1858C>T (p.Arg620Cys)

ClinVar: 67694

CAID: CA015449

gnomAD: v4.1.0 GrpMax FAF: 0.00002033 (European non-Finnish)

AdditionalInfo: The patient also has APOA5:c.990_993delAACA (p. Asp332Valfs*5) (P/LP in ClinVar with 2 stars)

Gene: DICER1 PMCID: PMC8451242 PMID: 34552563 Pathogenic Inheritance Pattern: Autosomal Dominant MultipleDiseaseEntities Disease Entity: DICER1 syndrome, multinodular goitre, cystic nephroma, anaplastic renal sarcoma, Wilms tumour, differentiated thyroid carcinoma, gynandroblastoma, ciliary body medulloepithelioma, embryonal rhabdomyosarcoma, pineoblastoma, pituitary blastoma, kidney cyst, pulmonary cyst, Sertoli-Leydig Cell Tumor. Mutation: Germline MultipleGeneVariants Variant & Clinvar IDs: c.3452_3453del (485534), c.316del (no ClinVar ID), c.171_172insAC (no ClinVar ID), c.3434del (no ClinVar ID), c.988C>T (933007), c.5388dup (no ClinVar ID) Zygosity: None provided. Case: At time of operation, the goitre patients living in Denmark were ages 21, 12, 21, 8, 14, and 16. Four underwent total thyroidectomies, and two underwent partial thyroidectomies. The patient originally aged 21 previously had a kidney cyst at age 14 and a pulmonary cyst at an unknown age. The patient aged 14 at time of partial thyroidectomy later manifested a Sertoli-Leydig Cell Tumor at age 15. All six patients were female. CasePresentingHPO: None provided. CasePreviousTesting: thyroidectomy gnomAD: ENSG00000100697.10, https://gnomad.broadinstitute.org/gene/ENSG00000100697 Mutation Type: Frameshift, Nonsense

• Gene Name: DICER1 Syndrome (OMIM 606241, 601200)
• PMID: 34599283
• Hugo Gene Nomenclature Committee (HGNCID): N/A
• Inheritance Pattern: Autosomal Dominant
• Disease Entity: pleuropulmonary blastoma (PPB), Sertoli-Leydig cell tumor, gynandroblastoma, embryonal rhabdomyosarcomas of the cervix and other sites, multinodular goiter, differentiated and poorly differentiated thyroid carcinoma, cervical-thyroid teratoma, cystic nephroma-anaplastic sarcoma of kidney, nasal chondromesenchymal hamartoma, intestinal juvenile-like hamartomatous polyp, ciliary body medulloepithelioma, pituitary blastoma, pineoblastoma, primary central nervous system sarcoma, embryonal tumor with multilayered rosettes-like cerebellar tumor, PPB-like peritoneal sarcoma, DICER1-associated presacral malignant teratoid neoplasm and other non-neoplastic associations.
• Mutation: Germline
• Zygosity: Heterozygous
• Variant: has multiple variants associated with it
• Family Information: Germ cell tumors have been reported in family members
• Case: identified affected families w/ pleuropulmonary blastoma (PPB): germline and somatic DICER1 mutations also identified in other familial associated tumors
• CasePreviousTesting: numerous studies confirmed relationship b/t DICER1 variants in carriers and development of range neoplasms and non-neoplastic conditions

GeneName: DICER1 PMID: 30715996 HGNCID: N/A Inherritence pattern: autosomal dominant Disease Entity: multiple gene variants mutation: germline Zygosity: N/A Variant: Not found Family Info: N/A

Gene: DICER1 PMID: 30672147 HGNCID: n/a Inheritance Pattern: autosomal dominant Disease Entity: Pleuropulmonary Blastoma, Cystic Nephroma, Sertoli-Leydig tumors, Multinodular goiter, thyroid cancer, rhabdomysarcoma, pineoblastoma Mutation: Germline Zygosity: n/a MultipleGeneVariants Variant: p.Gly1824Val, p.Ser1160Tyr, p.Ala1578Thr, p.Leu1469Pro, p.Ser1160Tyr, p.Ile528Thr, p.Pro1836Leu, p.Glu904*, p.Tyr1835Ser, p.Ile528Thr, p.Arg1342His, p.Phe1650Cys, p.Trp1481Arg, p.Arg201His, p.Asp1390His, p.Trp1397Arg, p.Ala1578Thr <br /> Family Info: n/a gnomAD: n/a

Gene Name: OMIN PMID: 34599283 Autosomal Dominant Gynandroblastoma cERMS Pediatric Paratesticular Sarcomas nephrolithiasis or nephrocalcinonsis Cystic Nephroma Anaplastic Sarcoma of Kidney Wilms tumor Cystic Hepatic Neoplasm Hamartomatous polyps

Germline mutation heterozygosity Multiple Gene Variants There is usually a family history or a carrier for the mutation it rarely occurs out of nowhere.