Case#: P18, Female, German, 32.2 years old at the time of genetic diagnosis, alive at the time of publication

DiseaseAssertion: Mildly affected based on a CHAI score of 11.11%

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.416A>G (p.Tyr139Cys)

ClinVar ID: 623475

gnomAD: not found

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P17, Male, Belgian, 40 years at the time of genetic diagnosis, alive at the time of publication

DiseaseAssertion: n/a

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.407C>T (p.Pro136Leu)

ClinVar ID: 1711524

gnomAD: not found

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P16, male, german, age: n/a, alive at the time of publication

DiseaseAssertion: Severely affected based on a CHAI score of 45.83%

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.392T>C (p.Val131Ala)

ClinVar ID: 624171

gnomAD: Not found

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P02, Female, the age of clinical and genetic diagnosis: Unknown, Finnish, alive at the time of article's publication

DiseaseAssertion: N/A

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NC_000002.12:g.203868053T>A

ClinVar ID:

CAID: CA350138070

gnomAD: not found in any gnomAD version.

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P15, female, age: n/a, ethnicity: n/a, alive at the time of publication

DiseaseAssertion: n/a

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.384C>G (p.Ile128Met)

ClinVar ID: 662956

gnomAD: 0.000006814

https://gnomad.broadinstitute.org/variant/2-203870860-C-G?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P01, Female, clinical diagnosis at the age of 45, genetic diagnosis at the age of 56, German, alive at the time of article's publication

DiseaseAssertion: Patient is classified as "Mildly affected" based on a CHAI score of 10.42%.

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.109+1G>T

ClinVar ID: 161113

gnomAD: This variant was not found in any gnomAD version.

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P14, Female, Czech, 36 years old at the time of genetic diagnosis, daed at the time of publication

DiseaseAssertion: n/a

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: unregistered variant - without the bp change we can't confidently assert this variant at this time but it is possible it is CA2953901753

ClinVar ID: n/a

gnomAD: not found

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: 6-year-old female

DiseaseAssertion: Refractory AIHA

FamilyInfo: No family history of related disorders was documented, whole-exome sequencing of the familial trio revealed a novel heterozygous c.362_391del variant in CTLA-4

CasePresentingHPOs: HP:0001903, HP:0000952, HP:0040321, HP:0005505, HP:0001890, HP:0001298, HP:0001973

CaseHPOFreeText: Pale complexion, Hb: 48 g/L, a marked increase in reticulocytes, a positive DAT (IgG 3+, C3d 2+), total bilirubin 44.63 µmol/L, indirect bilirubin 25.32 µmol/L, positive DAT (IgG 3+, C3d 2+), normal glucose-6-phosphate dehydrogenase activity, normal levels of folic acid (6.07 ng/mL) and vitamin B12 (519.95 pg/mL), and bone marrow cytology indicative of hyperplastic anemia, hypertensive encephalopathy

CaseNotHPOFreeText: The ANA profile and antinuclear antibody test were negative, platelet counts remained within the normal range throughout the current disease course

CasePreviousTesting: NR

GenotypingMethod: Whole-exome sequencing

PreviouslyPublished: NR

Variant: NM_005214.5:c.362_391del

CAID: CA3273042436

gnomAD: N/A

SupplementalData: Table 1

Case#: II.1, 61-years-old male (deceased)

DiseaseAssertion: Hashimoto disease

Variant: c.379T >G variant in CTLA4

CasePresentingHPOs: HP:0034954

CaseHPOFreeText: Anti-AChR antibodies without myasthenia gravis, unilateral uveitis, Staphylococcus aureus pneumoniae, Candida kefyr pneumoniae, Erythroderma, autoimmune alopecia, diffuse interstitial lung disease

Case#: III.4, a 34-year-old female relative, unknown age of onset

DiseaseAssertion: Hashimoto disease

Variant: c.379T >G variant in CTLA4

GenotypingMethod: high-throughput sequencing

CAID: CA350138665

Case#: II.4, 56-year-old male relative, age of onset 44

DiseaseAssertion: Spondylarthritis

Variant: c.379T >G variant in CTLA4

Case#: Ye_2022_PL18, female, 1.5 yr (onset), Caucasian ancestry reported

DiseaseAssertion: APDS

FamilyInfo: family info unreported. Pedigree in Crank 2014 shows potential de novo occurance, but this is not confirmed or commented on.

CasePresentingHPOs: lymphoma (HP:0002665), elevated IgG (HP:0003237), elevated IgM (HP:0003496), decreased B-cell percentage (HP:0010976), recurrent otitis media (HP:0000403), recurrent sinopulmonary infection (HP:0005425), lymphadenopathy (HP:0002716), splenomegaly (HP:0001744), lymphoproliferation (HP:0005523), immune thrombocytopenia (HP:0001973),

CaseHPOFreeText: low CD3+ percentage, decreased CD4+ percentage, elevated NK percentage, decreased vaccine response,

CaseNotHPOs: abnormal IgA (HP:0410240), abnormal lymphocyte count (HP:0040088), abnormal B-cell count (HP:0010975),

CaseNotHPOFreeText: abnormal CD8+ percentage, EBV and CMV

CasePreviousTesting:

GenotypingMethod: Sanger sequencing in original article. These authors perform an additional WES from a blood sample. WES of tumor also performed to identify somatic variation.

PreviouslyPublished: Crank 2014 (PMID:24610295)

Variant: c.3061G>A, p.E1021K

ClinVarID: 88675

CAID:

gnomAD: NR

SupplementalData: S2 provides more information on the lymphoma.

Case#: Grammatikos_2021_ Case3, male, 17 y.o. (onset) 32 y.o. (report), origin not reported

DiseaseAssertion: CTLA4 Haploinsufficiency

FamilyInfo: Mother and sister affected. Extensive family autoimmune history and pedigree recorded in Figure S1.

CasePresentingHPOs: HP:0100651, HP:0000821, HP:0002315, HP:0002018, HP:0002354, HP:0000458, HP:0001973, HP:0001903, HP:0001744, HP:0025379, HP:0025329, HP:0002922, HP:0001882, HP:0032289, HP:0002275, HP:0033693, HP:0008765, HP:0100827 (type 1 diabetes, hypothyroidism, headaches, nausea, memory impairment, anosmia, autoimmune thrombocytopenia, anaemia, splenomegaly, increased TPO antibodies, increased GAD antibodies, increased protein CSF, increased WBC, IgG oligoclonal pattern, poor coordination, olfactory hallucination, auditory hallucination, lymphocytosis)

CaseHPOFreeText: "Electroencephalography confirmed complex partial seizures arising from the right hemisphere and occurring on a background of mild excess of nonspecific slow and theta activity."

CaseNotHPOs: HP:0002693 (abnormal skull base morphology)

CaseNotHPOFreeText: abnormal nasal endoscopy, abnormal upper endoscopy, abnormal venography

CasePreviousTesting: none

GenotypingMethod: not specified. It says, "Following her mother’s diagnosis of CTLA4 haploinsufficiency, she was confirmed to have the same genetic mutation." Mother was tested using NGS + Sanger

PreviouslyPublished: not reported

Variant: NM_005214.4:c.81_82insT (p.Leu28fs)

ClinVarID: 644629

CAID: CA645516071

gnomAD: not found

SupplementalData: Figure S1 shows extensive family history

Case#: Q.II.1, subject 44. Male. Age of Onset: 10 y.o. Age of evaluation/death: 15 y.o. Origin in UK, Caucasian.

DiseaseAssertion: Lymphoproliferation

FamilyInfo: Not found

CasePresentingHPOs: HP:0001744, HP:0002716, HP:0002783, HP:0000964, HP:0001873

CaseHPOFreeText: Three affected mutation carriers (including patient) died following alloHSCT due to GvHD. Patient received transplant due to having Thrombocytopenia and widespread lymphoid hyperplasia despite Rituximab. Patient died four months post transplant due to Acute GvHD Grade IV of the gut. See Table S2.

Lymphocytic or granulomatous organ infiltration - patient's brain was affected. Patient received a biopsy and was found to have B Cell and T Cell infiltration. Vaccination response - Tetanus, Pneumococcal vaccination. Respiratory tract involvement, GLILD, Cytopenia, Splenectomy, Autoimmune cytopenia, ITP, Neurological involvement, Dermatological involvement, Coombs.

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, Slatter, et al. PMID: 27102614

Variant: NM_005214.5:c.529T>G

ClinVarID: N/A

CAID: CA350139018

gnomAD: Not found

SupplementalData: extensive data in S1

Note: Not functionally tested using transendocytosis

Case#: Family_A_Patient_A.II.9, male, onset at or before the age of 17, death at age 37 years, ethnicity not specified

DiseaseAssertion: Patients are asserted to have "CTLA4 haploinsufficiency" or impaired ligand binding by CTLA4 resulting in "a complex syndrome with features of both autoimmunity and immunodeficiency".

FamilyInfo: The Family A pedigree is shown in Figure 1a and includes 39 members and 11 genotype-positive members, of whom 5 are affected.

CasePresentingHPOs: HP:0010444 (Pulmonary insufficiency), HP:0004313 (Decreased circulating antibody level), HP:0001744 (Splenomegaly), HP:0011108 (Recurrent sinusitis), HP:0002837 (Recurrent bronchitis), HP:0000787 (Nephrolithiasis), HP:0032262 (Pulmonary tuberculosis), HP:0032271 (Extrapulmonary tuberculosis), HP:0006532 (Recurrent pneumonia), HP:0025419 (Pulmonary pneumatocele), HP:0030875 (Abnormality of pulmonary circulation), HP:0010976 (B lymphocytopenia), HP:0004313 (Decreased circulating antibody level), HP:0002720 (Decreased circulating IgA level), HP:0002850 (Decreased circulating total IgM)

CaseHPOFreeText: Diagnosis at age 17 was accompanied by hypogammaglobulinemia and splenomegaly. Death at age 37 was due to pulmonary insufficiency. The patient had pulmonary hypertension and clubbing. Lobectomy and lung transplant were performed. Laboratory values included very low B cells and NK cells.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Genotyping was performed at the genome-wide level (whole exome sequencing), and additional linkage analysis was performed in this family.

GenotypingMethod: Genotyping was performed by whole exome sequencing as well as genetic linkage analysis with microsatellite markers, linking the disease locus to the D2S1384 marker on chromosome 2 (close to CTLA4).

PreviouslyPublished: No prior article is known to contain information on the same proband.

Variant: The patient harbors the NM_005214.5(CTLA4):c.105C>A (p.Cys35Ter) variant in the heterozygous state.

ClinVar: 161112

CAID: N/A (Not required, as there is already a ClinVar ID for this variant)

gnomAD: This variant was not found in gnomAD v.2.1.1.

SupplementalData: Yes, the description of the patient is located in the Supplementary Notes, while the clinical phenotypes and laboratory measurements are found in Tables S1 and S2.

Case#: III.3, a diseased 31-year-old male relative, age of onset 7

DiseaseAssertion: Evans syndrome (ITP and AIHA)

CaseHPOFreeText: Lymphadenopathy, colic and renal nonclonal proliferation, Extensive chicken pox, viral encephalitis, EBV chronic viremia including inside tissues, Ear, nose and throat infections, pneumoniae, multiple Clostridium difficile colitis infections, Interstitial pneumopathy, Epilepsy, transverse myelitis C2 and T12, ADEM, Transplantation for interstitial fibrosis, late rejection with nonmalignant lymphoproliferation and EBV replication, Portal hypertension with diffuse nodular hyperplasia

Variant: c.379T >G variant in CTLA4

GenotypingMethod: high-throughput sequencing

CAID: CA350138665

Case# III.6, 27-year-old male relative, unknown age of onset

CaseHPOFreeText: Infectious mononucleosis, severe CMV infectious (nonautoimmune thrombocytopenia, splenomegaly, lymphadenopathy and hepatitis), Toxoplasma gondii infection, Dermatitis

Variant: c.379T >G variant in CTLA4

GenotypingMethod: high-throughput sequencing

CAID: CA350138665

Case#: IV.2, a 15 year old male realtive, unknown age of onset

CaseHPOFreeText: Ear, nose and throat infections; Dermatitis

Variant: c.379T >G variant in CTLA4

GenotypingMethod: high-throughput sequencing

CAID: CA350138665

Case#: II.3, a 59 year old female, age of onset 58

DiseaseAssertion: Inflammatory polyarthritis

FamilyInfo: Table 1

CaseHPOFreeText: presented with lymphoid proliferation, central nervous system inflammation (transverse myelitis and extensive disseminated encephalomyelitis), epilepsy, chronic kidney disease with one transplantation (benign polyclonal B-cell infiltration, interstitial fibrosis), interstitial pneumopathy, splenomegaly, hepatic abnormality with diffuse nodular hyperplasia, rectocolitis, extensive varicella zoster virus infection (VZV), viral encephalitis without documentation, Epstein–Barr virus (EBV) chronic viremia, Clostridium difficile severe colitis

Variant: c.379T >G variant in CTLA4

GenotypingMethod: high-throughput sequencing

CAID: CA350138665

Case#: III.7, an 18-year-old female patient

DiseaseAssertion: immune thrombopenia, autoimmune hemolytic anemia, and Evans syndrome with infections early-onset herpes zoster and chronic Epstein-Barr virus

FamilyInfo: Table 1

CasePresentingHPOs: HP:0001433, HP:0002716

CaseHPOFreeText: severe necrotic dermohypodermitis of left leg caused by Pseudomonas aeruginosa, hypogammaglobulinemia

Variant: c.379T >G variant in CTLA4

GenotypingMethod: high-throughput sequencing

CAID: CA350138665

Case#: Garcia-Perez_2019_B.II.1, male

DiseaseAssertion: CTLA4 haploinsufficiency

FamilyInfo: mother is an asymptomatic carrier

CasePresentingHPOs: HP:0100651, HP:0000872, HP:0002242 (Type 1 diabetes, autoimmune thyroidosis, enteropathy)

CaseHPOFreeText: none

CaseNotHPOs: none

CaseNotHPOFreeText: none

CasePreviousTesting: none

GenotypingMethod: Sanger sequencing

PreviouslyPublished: not reported

Variant: NM_005214.5(CTLA4):c.457G>A

ClinVarID: 636389

CAID: CA350138843

gnomAD: not found

SupplementalData: n/a

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

Case#: Grammatikos_2021_Case2, female, 10 months (onset) 25 y.o. (report), origin not reported

DiseaseAssertion: CTLA4 haploinsufficiency

FamilyInfo: Mother and brother are also affected. Extensive family history of autoimmune phenotypes in Figure S1.

CasePresentingHPOs: HP:0002315, HP:000340, HP:0003394, HP:0004313, HP:0012115, HP:0001878, HP:0007565, HP:0001744, HP:0004315, HP:0006577, HP:0002090, HP:0002829, HP:0005263, HP:0006532, HP:0033542, HP:0032174, HP:0002110, HP:0011473 (headache, peripheral paresthesia, muscle cramps, hypogammaglobulinemia, autoimmune hepatitis, hemolytic anaemia, cafe au lait spots, splenomegaly, low IgG, macronodular cirrhosis, fungal pneumonia, arthralgia, antral gastritis, recurrent bacterial pneumonias, bronchial wall thickening, diffuse tree-in-bud infiltrates, bronchiectasis, focal total villous atrophy)

CaseHPOFreeText: Severe lesion in right cerebellar hemisphere and left superior frontal gyrus. Evan's syndrome, bronchial associated lymphoid hyperplasia, intestinal metaplasia, intraepithelial lymphocytes

CaseNotHPOs: HP:0001369, HP:0012538 (artritis, response to gluten)

CaseNotHPOFreeText: n/a

CasePreviousTesting: 2 benign polymorphisms found in perforin gene. Other genes tested: Fas, Fas ligand, Caspase 10, Caspase 8, NRAS. Heterozygous VUS found in LRBA gene.

GenotypingMethod: not specified. It says, "Following her mother’s diagnosis of CTLA4 haploinsufficiency, she was confirmed to have the same genetic mutation." Mother was tested using NGS + Sanger

PreviouslyPublished: not reported

Variant: NM_005214.4(CTLA4):c.81_82insT (p.Leu28fs) heterozygous

ClinVarID: 644629

CAID: CA645516071

gnomAD: not found

SupplementalData: Figure S1 shows extensive family history

Case#: P05, Male, age: n/a, ethnicity:n/a, alive at the time of publication

DiseaseAssertion: N/A

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: <br /> NM_005214.5(CTLA4):c.208C>T (p.Arg70Trp)

ClinVar ID: 161114

gnomAD: 6.195e-7 https://gnomad.broadinstitute.org/variant/2-203870684-C-T?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P13, Male, German, 38 years old at the time of clinical diagnosis, 40.6 yeras old at the time of genetic diagnosis, alive at the time of publication

DiseaseAssertion: severly affected based on a CHAI score of 52.38%

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: ENST00000295854.10:c.356T>G

ClinVar ID: not found

CAID:CA350138616

gnomAD: not found

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P12, sex: n/a, age: n/a, ethnicity: n/a

DiseaseAssertion: n/a

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.326G>A (p.Gly109Glu)

ClinVar ID: 542071

gnomAD: 0.0002354 https://gnomad.broadinstitute.org/variant/2-203870802-G-A?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P11, Female, German, age: n/a, alive at the time of publication

DiseaseAssertion: Severely affected based on a CHAI score of 18.75%

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.326G>A (p.Gly109Glu)

ClinVar ID: 542071

gnomAD: 0.0002354 https://gnomad.broadinstitute.org/variant/2-203870802-G-A?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P10, Female, German, 24 years old at the time of clinical diagnosis, 25 years old at the time of genetic diagnosis, alive at the time of publication

DiseaseAssertion: Severely affected based on a CHAI score of 33.33%

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.326G>A (p.Gly109Glu)

ClinVar ID: 542071

gnomAD: 0.0002354 https://gnomad.broadinstitute.org/variant/2-203870802-G-A?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P09, Male, age: n/a, ethnicity: n/a, alive at the time of publication

DiseaseAssertion: n/a

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.265T>C (p.Tyr89His)

ClinVar ID: 1391402

gnomAD: 0.000003717 https://gnomad.broadinstitute.org/variant/2-203870741-T-C?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P08, Female, Canadian, age: n/a, alive at the time of publication

DiseaseAssertion: N/A

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.257C>T (p.Ala86Val)

ClinVar ID: 661941

gnomAD: 0.00001859

https://gnomad.broadinstitute.org/variant/2-203870733-C-T?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P07, Male, German, 18 years old at the time of clinical diagnosis and 24.2 years old at the time of genetic diagnosis, alive at the time of publication

DiseaseAssertion: Mildly affected based on a CHAI score of 17.65%

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: <br /> NM_005214.5(CTLA4):c.224G>A (p.Arg75Gln)

ClinVar ID: 943305

gnomAD: 0.000008673

https://gnomad.broadinstitute.org/variant/2-203870700-G-A?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P06. Female, German, 52 years old at the time of clinical diagnosis, Alive at the time of publication

DiseaseAssertion: classified as "Severely affected" based on a CHAI score of 47.37%

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.214A>C (p.Thr72Pro)

ClinVar ID: 546886

gnomAD: not found

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P04, male, genetic diagnosis at the age of 71.4, ethnicity: N/A, Dead at the time of article's publication

DiseaseAssertion: N/A

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.160G>A (p.Ala54Thr)

ClinVar ID: 430905

gnomAD: not found

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P03, Male, Age: N/A, ethnicity: N/A, Alive at the time of article's publication

DiseaseAssertion: N/A

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.155G>A (p.Gly52Asp)

ClinVar ID: 871301

gnomAD: not found in any gnomAD version.

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P22, Female, German, age: n/a , alive at the time of publication

DiseaseAssertion: Severely affected based on a CHAI score of 42.86%

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: ENSP00000497102.1:p.Leu163Ser

ClinVar ID:

CAID: PA2850594025

gnomAD: Not found

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P21, female, American, age: n/a, alive at the time of publication

DiseaseAssertion: n/a

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NM_005214.5(CTLA4):c.467C>T (p.Pro156Leu)

ClinVar ID: 1035066

gnomAD: 0.00002292 https://gnomad.broadinstitute.org/variant/2-203871387-C-T?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P20, male, German, 22 years old at the time of clinical diagnosis, 22.7 years old at the time of genetic diagnosis, dead at the time of publication

DiseaseAssertion: Severely affected based on a CHAI score of 42.11%

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: NP_001032720.1:p.Thr147Arg

ClinVar ID:

CAID: PA2850594024

gnomAD: Not found

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: P19, Female, Italian, age: n/a, alive at the time of diagnosis

DiseaseAssertion: n/a

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The percentage of transendocytosis using either CD80-GFP or CD80-mScarlet CHO cells was determined in eight LRBA-deficient patients. No difference in the percentage of transendocytosis was observed between CTLA4-variant carriers (GFP median=5.4%; mScarlet median= 49.8%) and LRBA-deficient patients (GFP median=9.9%; mScarlet median, 48.6%). However, significantly lower percentages of transendocytosis were observed in LRBA-deficient patients compared to healthy donors (HD) when using CD80-mScarlet CHO cells (median, 48.6% vs. 65.5% in HD) (Fig. ​(Fig.4e),4e). This difference was not observed with CD80-GFP CHO cells (patients median of 9.9% in patients vs. 13.9% in HD). In conclusion, the CTLA4 transendocytosis method using CD80-mScarlet CHO cells enables the functional verification of LRBA deficiency, but it cannot differentiate between LRBA deficiency and CTLA4 insufficiency.

GenotypingMethod: NGS and Sanger sequencing

PreviouslyPublished: N/A

Variant: ENST00000295854.10:c.434A>G

ClinVar ID:

CAID: CA350138791

gnomAD: 6.197e-7 https://gnomad.broadinstitute.org/variant/2-203870910-A-G?dataset=gnomad_r4

SupplementalData: Yes, all data regarding the patient was found in Table1.

Case#: Angulo_2014_P9, M, 15 months (onset), Irish/Danish ancestry reported

DiseaseAssertion: APDS

FamilyInfo: mother genotype/phenotype positive

CasePresentingHPOs: Recurrent respiratory infection, HP:0002205 Recurrent ear infection, HP:0410018 Splenomegaly, HP:0001744 Increased serum IgM, HP:0003496 Decreased IgG, HP:0004315 Decreased IgA, HP:0002720 Decreased tetanus antibodies, HP:0410295 Low levels of anti-pneumococcal antibodies, HP:0012476 Low levels of anti-Haemophilus Influenzae type B antibodies, HP:0410303 Decreased circulating T cells, HP:0005403 Decreased circulating B cells, HP:0010976 Increased circulating transitional B cells, HP:0030381 Decreased circulating class switched memory B cells, HP:0030388 Bronchiectasis, HP:0002110 lymphadenopathy, HP:0002716

CaseHPOFreeText: n/a

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

CasePreviousTesting: n/a

GenotypingMethod: WES and Sanger

PreviouslyPublished: not reported

Variant: heterozygous NM_005026.5:c.3061G>A (p.E1021K)

ClinVarID: 88675

CAID: CA145460

gnomAD: Not present in gnomAD

SupplementalData: Phenotypic info in table S2

Case#: Angulo_2014_P8, M, 6 months (onset), origin in Slovenia

DiseaseAssertion: APDS

FamilyInfo: de novo confirmed

CasePresentingHPOs: HP:0002783, HP:0410018, HP:0002716, HP:0002014, HP:0032247, HP:0031693, HP:0001433, HP:0000620, HP:0030877, HP:0002720, HP:0003496, HP:0410303, HP:0032218, HP:0010976, HP:0030374, HP:0030388, HP:0030381 (recurrent LRTI, recurrent ear infections, massive generalized lymphadenopathy, cryptosporidium parvum diarrhoea, CMV and EBV infections, hepatosplenomegaly, chronic dacriocystitis requiring surgical intervention, mixed obstructive/restrictive FEV1/FVC, decreased IgA, increased IgM, decreased haemophilus B antibodies, decreased CD4+ T cells, decreased B cells, decreased IgM memory B cells; CD19+ CD27+ IgD+, decreased Class-switched memory B cells; CD19+ CD27+ IgD–, as % of CD19+, increased transitional B cells; CD19+ CD38+ IgM+, as % of CD19+

CaseHPOFreeText: decreased CD25+ as % CD3+, mastocytoma, increased CD8+ T cells, CD4+ CD25– CD127– as % of CD4+ T cells, increased CD8+ CD25– CD127– as % of CD8 T cells, as % of CD19+)

CaseNotHPOs:

CaseNotHPOFreeText: malignancy, abnormal CD4+ CD25+ CD127- as % of CD4+ regulatory T cells

CasePreviousTesting: fibroblast and blood samples taken to evaluate somaticism. Findings indicate the mutation was germline.

GenotypingMethod: WES and Sanger, followed by genome for parental confirmation.

PreviouslyPublished: not reported

Variant: heterozygous NM_005026.5:c.3061G>A (p.E1021K)

ClinVarID: 88675

CAID: CA145460

gnomAD: Not present in gnomAD

SupplementalData: Phenotypic info in table S2

Note: could lacrimal gland obstruction be considered atopy for phenotype scoring?

Case#: Angulo_2014_P5, M, 12 months old (onset), origin in England

DiseaseAssertion: APDS

FamilyInfo: Pedigree in figure 1. Affected sister, son, and niece

CasePresentingHPOs: HP:0002783, HP:0410018, HP:0003496, HP:0005403, HP:0032218, HP:0005415, HP:0010976, HP:0020112, HP:0000365, HP:0002878, HP:0033537, HP:0011950, HP:0001744, HP:0025289, HP:0030387, HP:0030381, HP:0030877 (recurrent lower respiratory tract infection, recurrent ear infection, elevated IgM, decreased T cells, decreased CD4+ T cells, decreased CD8+ T cells, decreased B cells, Increased proportion of CD4+CD25+ regulatory T cells, hearing impairment, type 2 respiratory failure, mosaic attenuation, inflammatory bronchiolitis, splenomegaly, cervical lymphadenopathy, increased class switched memory B cells, increased transitional B cells, mixed obstructive/restrictive FEV1/FVC,

CaseHPOFreeText: increased CD25+ as a percentage of CD3+, increased CD3+CD56+ as % of CD3+, increased proportion of CD4+ CD25+ CD127– CD45RA- regulatory T cells, increased proportion of CD8+ CD25+ CD127– CD45RA+ regulatory T cells, increased CD4+ CD25- CD127– CD45RA- as % of CD4+ peripherally expanded T cells, increased CD8+ CD25- CD127– CD45RA+ as % of CD8+ peripherally expanded t cells, severe necrotising pneumonia, hypoperfused right lung, recurrent salivar gland abscesses, CD

CaseNotHPOs: HP:0410242, HP:0410240 (abnormal IgG, abnormal IgA)

CaseNotHPOFreeText: malignancy

CasePreviousTesting:

GenotypingMethod: WES and Sanger

PreviouslyPublished: not reported

Variant: heterozygous NM_005026.5:c.3061G>A (p.E1021K)

ClinVarID: 88675

CAID: CA145460

gnomAD: Not present in gnomAD

SupplementalData: Phenotypic info in table S2

Case#: Schwab_2018_Patient_129, 16 y.o. (onset) and 19 y.o. (death), male, origin in Germany

DiseaseAssertion: CTLA4 Haploinsufficiency

FamilyInfo: mother (patient 128) was heterozygous with same variant. This patient was recored as 'affected' but type-1 diabetes was the only phenotype reported.

CasePresentingHPOs: HP:0001973, HP:0001945, HP:0001744, HP:0001058, HP:0004313, HP:0004315, HP:0002720, HP:0031378, HP:0002240, HP:0002716, HP:0002093, HP:0000964, HP:0001047 (ITP, fever, splenomegaly, wound healing disorder, hypogammaglobulinemia, low IgG, Low IgA, lymphoproliferation, hepatomegaly, lymphadenopathy, respiratory involvement, eczema, atopic dermatitis)

CaseHPOFreeText: organ infiltration (brain and lung), GLILD, neurological involvement,

CaseNotHPOs: large phenotype table with unreported symptoms in table S1

CaseNotHPOFreeText: n/a

CasePreviousTesting: unknown

GenotypingMethod: unknown

PreviouslyPublished: n/a

Variant: NM_005214.5(CTLA4):c.151C>T (p.Arg51Ter)

ClinVarID: 161109

CAID: CA173992

gnomAD: not found

SupplementalData: extensive data in S1

Note: functionally tested using transendocytosis

Case#: U.II.1, subject 50. Male. Age of Onset: 3.75 y.o. Age of evaluation: 9 y.o. Origin in Japan, Asian

DiseaseAssertion: Diagnosis with CVID (later with CTLA4 insufficiency)

FamilyInfo: Patient is oldest of three siblings. All three have been genotyped, but only this proband is affected. Variant inherited from the father, who is also unaffected (pedigree in Figure 1).

CasePresentingHPOs: HP:0001873, HP:0001973, HP:0004313, HP:0002720, HP:0004315, HP:0002719, HP:0005353

CaseHPOFreeText: Cytopenia, Autoimmune cytopenia, hypogammaglobulinemia, low IgG, low IgA, Clinically reactivated/apparent Infections, Herpes Infection, clinical EBV infection (possibly chronic?), ITP, positive Coombs test

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: Unpublished

Variant: NM_005214.5(CTLA4):c.494G>A (p.W165*)

ClinVarID: N/A

CAID: CA350138939

gnomAD: This variant is not found in gnomAD v2.1.1.

SupplementalData: Extensive data in S1, including some phenotypes that were tested for but found to be absent.

Note: Not functionally tested using transendocytosis.

Case#: 27-month-old girl Iranian girl

DiseaseAssertion: Combined immunodeficiency.

FamilyInfo: Table2 Mother is a carrier for the variant . CasePresentingHPOs: Annotate with the HPOs presenting specifically in the proband of interest . Case#: 27-month-old girl Iranian girl

DiseaseAssertion: Combined immunodeficiency

FamilyInfo: Table2 Mother ,who has hypothyroidism and a history of frequent respiratory infections in childhood, is a carrier for the variant. Father doesn't carry the variant.

CasePresentingHPOs: HP:0001954 (Recurrent fever) HP:0001369 (Arthritis) HP:0012219 (Erythema nodosum) HP:0031936 (Delayed ability to walk) HP:0000750 (Delayed speech and language development) HP:0001698 (Pericardial effusion) HP:0002205 (Recurrent respiratory infections) HP:0002007 (Frontal bossing) HP:0004315 (Decreased circulating IgG level) HP:0033222 (Decreased CD4:CD8 ratio) HP:0001953 (Diabetic ketoacidosis) HP:0000821 (Hypothyroidism) HP:0100651 (Type I diabetes mellitus)

CaseHPOFreeText: Patient has recurrent hospitalizations. 1) 2mo fever and elevated ESR, CRP 2) 8mo massive pericardial effusion 3) 10mo recurrent pericardial effusion 4) 13 mo high-grade fever and elevated ESR, CRP 5) 18 mo high-grade fever and elevated ESR, CRP 6) 24 mo COVID-19 positive with fever 7) 28 mo COVID-19  gastrointestinal manifestations without any adverse effects.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Whole-exome sequencing was performed on the patient's whole blood sample.

GenotypingMethod: Whole-exome sequencing was performed on the patient’s whole blood sample.

PreviouslyPublished: No

Variant: NM_005026:c.1429G>A p.E477K

ClinVar: Was not found on ClinVar

CAID: CA577192

gnomAD: 0.0003597 https://gnomad.broadinstitute.org/variant/1-9780259-G-A

Case#: P3, 9 year old girl

DiseaseAssertion: APDS

CaseHPOFreeText: presented with growth retardation since 6 months of age (currently −3 SD of height and −2.5 SD of weight). Lymphadenopathy and splenomegaly were noted at the age of 8 years, and adenoidectomy and tonsillectomy were performed. She had decreased IgA but normal IgG and IgM serum levels. Her mother had a similar clinical phenotype and died from Hodgkin lymphoma.

CasePreviousTesting: Thus, mutations known to cause APDS1 or APDS2 were searched and excluded by Sanger sequencing

GenotypingMethod: For P2 and P3, a targeted Next-Generation sequencing of a primary immunodeficiencies gene panel including PIK3CD and PIK3R1 was performed

Variant: A heterozygous G to A mutation at position 9775907 (GRCh37; NM_005026.3) in the PIK3CD gene was detected. The mutation leads to an amino acid substitution from glycine to aspartic acid at position 124 (G124D) located in the linker region between the ABD and the RBD at the N-terminal part of p110δ (Figure 1A).

CAID: CA338300460

gnomAD: absent from gnomAD v2.1.1

Case#: P2, 10 year old boy

DiseaseAssertion: APDS

CaseHPOFreeText: presented with recurrent otitis media and sinusitis since his first year of life. He had an adenoidectomy at 3 years of age. He presented with high IgM but normal IgG and IgA serum levels (Table 1). The serum levels of IgG2 (0.23; N: 0.56) and IgG4 (<0.002; N: 0.018) subclasses were low.

CasePreviousTesting: Thus, mutations known to cause APDS1 or APDS2 were searched and excluded by Sanger sequencing

GenotypingMethod: For P2 and P3, a targeted Next-Generation sequencing of a primary immunodeficiencies gene panel including PIK3CD and PIK3R1 was performed

Variant: A heterozygous G to A mutation at position 9775907 (GRCh37; NM_005026.3) in the PIK3CD gene was detected. The mutation leads to an amino acid substitution from glycine to aspartic acid at position 124 (G124D) located in the linker region between the ABD and the RBD at the N-terminal part of p110δ (Figure 1A).

CAID: CA338300460

gnomAD: absent from gnomAD v2.1.1

Case#: Ayrignac_2020_Patient_3, female, 42 y.o. (onset), origin unknown

DiseaseAssertion: CTLA4-related haploinsufficiency

FamilyInfo: unremarkable family history

CasePresentingHPOs: HP:0001138, HP:0000009, HP:0000572, HP:0020036, HP:0002015, HP:0002167, HP:0001285, HP:0002346, HP:0001272, HP:0002719, HP:0002720, HP:0004315, HP:0002923, HP:0002110 (bilateral axonal optic neuropathy, bladder urgency, vision loss, upper limb dysmetria, speech/swallowing disorder, spastic tetra paresis, head tremor, cerebellar atrophy, recurrent infections, IgA and IgG deficiency, autoantibodies [rheumatoid factor], bronchiectasis)

CaseHPOFreeText: white matter and deep basal ganglia FLAIR hyperintensities

CaseNotHPOs: lymphoproliferation

CaseNotHPOFreeText: abnormal CSF analysis

CasePreviousTesting: CSF analysis, "multiple panel gene excluded the main known causes of inherited leukoencephalopathy, cerebellar ataxia, and mitochondrial diseases."

GenotypingMethod: mini-exome analysis

PreviouslyPublished: n/a

Variant: NM_005214.5(CTLA4):c.151C>T (p.Arg51Ter)

ClinVarID: 161109

CAID: CA173992

gnomAD: not reported

SupplementalData: n/a

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#: Collen_2022_Patient_2, female, <1 y.o. (onset) 14 y.o. (report), Ethnicity reported: Hispanic

DiseaseAssertion: CTLA4 haploinsufficiency

FamilyInfo: reported de novo, but no evidence

CasePresentingHPOs: HP:0002014, HP:0002013, HP:0001508, HP:0001508, HP:0001510, HP:0002018, HP:0002027, HP:0032249, HP:0031035, HP:0005263, HP:0010783, HP:0004313, (diarrhea, vomiting, failure to thrive, lack of growth, chronic nausea, abdominal pain, lung coccidiomycosis, persistent villous atrophy, diffuse stomach inflammation, erythema, mucus plaques, hypogammaglobulinemia)

CaseHPOFreeText: Patient is from an endemic coccidiomyosis region. Increased intra-epithelial lymphocytes, mucoid plaque, scalloping of the duodenum, lamina proprietor expansion, poor response to polysaccharide pneumoccal vaccine

CaseNotHPOs: HP:0002608 (celiac serologies)

CaseNotHPOFreeText: TTG, IgA, EMA, HLA, DQ2, and DQ8 were negative. Bowel wall thickening. abnormal ileocolonoscopy

CasePreviousTesting: Primary immunodeficiency gene panel testing by Invitae

GenotypingMethod: Primary immunodeficiency gene panel testing by Invitae

PreviouslyPublished: not reported

Variant: de novo heterozygous c.71_72del (p.Leu24Profs*35) in exon 1 (NM_005214.5:c.71_72del)

ClinVarID: 1439020

CAID: CA2573320555

gnomAD: not reported

SupplementalData: n/a

MultipleGeneVariants: A heterozygous variant in PLCG2 (c.802C>T, p.Arg268Trp) detected (ClinVarID:403319, CAID:CA8193460). It is not usually reported in the panel. The authors ruled it out because the variant was found in 5 of 66 patients with disseminated coccidiomycosis in PMID:PMC7776098. The variant has been associated with autoimmune diseases according to OMIM. It is present in gnomAD (MAF: 0.101, Ashkenazi Jewish). It has been classified as benign in ClinVar.

Case#: Collen_2022_Patient_1, female, infancy (onset) 23 y.o. (report), Ethnicity reported: white

DiseaseAssertion: CTLA4 haploinsifficiency

FamilyInfo: Mutation inherited from father, who had melanoma and was asymptomatic for autoimmunity. Paternal first cousin had type-1 diabetes. Mother and brother had no autoimmune symptoms to report.

CasePresentingHPOs: HP:0002014, HP:0001510, HP:0002608, HP:0003261, HP:0033637, HP:0011473, HP:0002900, HP:0001903, HP:0001944, HP:0002246, HP:0001973, HP:0000872, HP:0008207, HP:0003765, HP:0004315, HP:0410240, HP:0030374 (diarrhea, low growth, celiac disease, elevated TTG IgA, endomyosial antibody, absence of duodenal villi, secondary hypokalemia, anemia, dehydration, scalloping of duodenal folds, cytopenias, hashimoto thyroiditis, Addison disease, psoriasis, low IgG, low IgA, low memory B cells)

CaseHPOFreeText: possible lichen sclerosis, negative titers to varicella-zoster virus and mumps despite vaccination. Patient showed switched memory B cells 1.4%, unswitched memory B cells 4.9%, and intraepithelial lymphocytes. Additional diagnosis's: Celiac disease, Hashimoto thyroiditis, Addison disease, CVID

CaseNotHPOs: HP:0002718 (recurrent bacterial infections)

CaseNotHPOFreeText: abnormal stool culture

CasePreviousTesting: none

GenotypingMethod: Whole exome sequencing (research based)

PreviouslyPublished: not reported

Variant: NM_005214.5:c.457+2T>C

ClinVarID: not found

CAID: CA350138849

gnomAD: not found

SupplementalData: n/a

Note: Functional information present. Immunophenotyping using flow cytometery revealed diminished expression of CTLA4 on CD4+/Foxp3+/CD45RA− memory regulatory T cells (Tregs) (Figure 3A).

Case#: 20-year-old male, Race: White (ancestry unavailable) DiseaseAssertion: The patient is asserted to have "CTLA4 haploinsufficiency" manifesting as aplastic anemia. FamilyInfo: Patient's father has disease variant Case PresentingHPOs: HP:0012378 (Fatigue), HP:0001962 (Palpitations), HP:0002875 (Exertional dyspnea), HP:0001903 (Anemia), HP:0001873 (Thrombocytopenia), HP:0002608 (Celiac disease), HP:0000608 (Macular degeneration), HP:0001876 (pancytopenia), HP:0001915 (aplastic anemia), CaseHPOFreeText: ** Diagnosis at age 20 when patient presented with persistent and profound incapacitating fatigue. Bone marrow biopsy was consistent to aplastic anemia. Table 1 summarizes presenting labs and flow cytometry results. Patient was first treated with high-dose IVIG, cyclosporine, and systemic corticosteroids. He initially responded well, but 6 months into therapy he developed renal impairment and was transitioned to sirolimus. His aplastic anemia relapsed. Patient underwent haploidentical (sibling, variant negative) hematopoietic stem cell transplantation, which was curative. CaseNotHPOs: HP:4000129 (Recent blood transfusion), CaseNotHPOFreeText: N/A CasePreviousTesting: The following studies were negative: Bone marrow chromosome analysis; FISH hybridization for BCR/ABL1, monosomy 5, monosomy 7, trisomy 8, and 20q deletion; myelodysplastic syndrome mutation sequencing. GenotypingMethod: A primary immunodeficiency NGS panel was run (gene content not specified) and identified a paternally inherited heterozygous missense variant in CTLA4. Variant: The patient is heterozygous for the NM_005214.5(CTLA4):c.385T>A (p.Cys129Ser). ClinVar: 1414930 CAID: N/A gnomAD**: This variant was not found in gnomAD v.4.1.0

Case#: Case 1, male, Brazilian

DiseaseAssertion: APDS1

FamilyInfo: We identified a kinship that included 3 half-siblings with symptoms typical for APDS1. The patient's father (I.4), a truck driver, reported that in addition to the index case, he had 4 additional children with 3 other women living in different Brazilian cities along his truck route and that 2 of these children (II.4 and II.5) had symptoms similar to the index case (Fig 1A). Of his 5 children, 1 had died at 3 years of age (II.1) with clinical symptoms similar to the index case, including hepatosplenomegaly, fever, and recurrent infections; immunologic studies were not performed. The other symptomatic half-brother (II.5) was evaluated at 5 years of age with a history of 5 episodes of pneumonia, recurrent oral candidiasis, several upper respiratory infections, and hepatosplenomegaly. The pedigree suggested that the father (I.4) carried the same autosomal-dominant PIK3CD mutation that affected 3 sons born to different mothers. However, neither he nor the mothers of the affected boys had any symptoms suggestive of APDS. Sanger sequencing demonstrated that neither the father nor the mothers of the affected boys carried the identified PIK3CD mutation in blood. This raised the possibility of germline or gonadal mosaicism in the father. To test this hypothesis, genomic DNA was extracted from his semen. As illustrated in Figure 1F, semen-derived DNA carried the heterozygous p.E1021K mutation identified in the affected sons. Based on relative peak heights, we estimated that 20% to 25% of the semen carried the mutation.

CaseHPOFreeText: The index case (II.4 in Fig 1A) had 10 episodes of pneumonia, 2 episodes of sepsis, several upper respiratory infections, and oral moniliasis within the first year of life. He subsequently developed hepatosplenomegaly, lymphadenopathy, and an axillary abscess owing to Candida albicans. At 3 years of age, laboratory investigation showed increased immunoglobulin (Ig) M (368 mg/dL) and IgG (1,450 mg/dL) levels, normal IgA level (107 mg/dL), low CD4 (330/mm3) and increased CD8 (1,229/mm3) counts, and low CD19 B cells (17/mm3). IgG subclasses showed normal absolute levels of IgG1 (1,020 mg/dL), IgG2 (79.0 mg/dL), IgG3 (78.3 mg/dL), and IgG4 (28.1 mg/dL); however, their ratio showed a proportional decrease of IgG2.

GenotypingMethod: Sanger sequencing. Unclear if entire PIK3CD gene was sequenced across intron/exon boundaries.

Variant: a heterozygous PIK3CD hotspot mutation (c.3061G→A, p.E1021K) was identified by Sanger sequencing.

CAID: CA145460

gnomAD: absent from gnomAD v2.1.1

Case#:Patient 7, male, 5 years old

DiseaseAssertion:Neonatal/Infantile Epileptic Encephalopathy (NIEE)

FamilyInfo:The family is French/Chinese

ParentalGenotype:The variant was inherited from Patient 7's asymptomatic mother.

CasePresentingHPOs:HP:0010864, HP:0012758, HP:0000729, HP:0007359, HP:0002069, HP:0032794, HP:0001250, HP:0000252.

CaseHPOFreeText:Patient 7 presents with severe intellectual disability, developmental slowdown, and various seizure types. Patient 7 has Autistic Spectrum Disorder (ASD) and microcephaly.

Patient History

@ 12 months - Patient 7 presented with seizures.

Patient 7 developed additional seizure types including: focal seizures with/without generalization, generalized tonic/clonic/tonic-clonic seizures, myoclonic seizures, and hypomotor seizures.

Patient 7 was on two antiepileptic drugs at most recent followup visit which reduced seizure frequency by >50%.

CaseNotHPOs:Not provided

CaseNotHPOFreeText:Not provided

CasePreviousTesting:The authors selected a cohort of 31 patients with seizure cryptogenic Neonatal/Infantile Epileptic Encephalopathy (NIEE) and seizure onset before 24 months.

Exclusion criteria included: (1) Patients with a definite history of brain insult, malformation of cortical development, neurocutaneous and syndromal disorders, and confirmed or highly suspected neurometabolic disorders based on clinical and biochemical markers. (2) Patients with Dravet syndrome and epilepsy at infancy with migrating focal seizure were also excluded because the majority of variants are detected in the SCN1A (>85%) and KCNT1 (approximately 50%) genes.

Formal neuropsychological testing or best clinical assessment was used to classify patient development or intelligence.

PreviouslyPublished:Not previously published

GenotypingMethod:Whole Exome Sequencing (WES) variant results were filtered in a panel of 430 epilepsy-associated genes. After selection of variants from the 430-gene panel, the synonymous variants, variants with variant frequency <10%, and variants with allele frequency >1% were removed.

Gene:SLC9A6

Variant:Hemizygous splice site NM_001042537.1 c. 794-2A>G was assessed by the authors to be likely pathogenic.

HGVS:Not provided

ClinVarID:Not found

CAID:CA414750320

gnomAD:Not found

MultipleGeneVariants:Not provided

Case#: Buchbinder_2019_Patient 1, female, 11 y.o. (onset) 21 y.o. (report), Caucasian

DiseaseAssertion: cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) haploinsufficiency

FamilyInfo: "maternal history of vitiligo, hypothyroidism, a maternal grandmother with hypothyroidism, and a maternal great grandmother with multiple sclerosis." mutation was present in the mother, maternal grandmother, and absent in the father.

CasePresentingHPOs: HP:0002113, HP:0001085, HP:0032070, HP:0000988, HP:0002027, HP:0002017, HP:0002014, HP:0001433, HP:0001973, HP:0004313, HP:0001888, HP:0001875, HP:0033608, HP:0002716, HP:0033583, HP:0002729, HP:0001945, HP:0032154, HP:0002829, HP:0032366, HP:0032296, HP:0005479, HP:0100633, HP:0004295, HP:0100279, HP:0032203, HP:0002633, HP:0030374, HP:0045080, HP:0005415, HP:0001882, HP:0002315, HP:0000505, HP:0001250, HP:0000225, HP:0001873

(nodular pulmonary infiltrates, papilledema, leptomeningeal enhancement, recurrent rashes, abdominal pain, vomiting, diarrhea, hepatosplenomegaly, immune cytopenias, hypogammaglobulinemia, lymphopenia, neutropenia, pulmonary nodules, adenopathy, lymphocytic pleocytosis, follicular bronchiolitis, follicular lymphoid hyperplasia, fevers, aphthous ulcerations, arthralgias, presence of direct antiglobulin, elevated IgG level, decreased IgE level, chronic esophagus inflammation, gastric mucosa inflammation, colon inflammation, intramucosal lymphoid nodules in colon, vasculitis, decreased memory B cells, decreased CD3+T, decreased CD8+T, decreased WBC, headache, decreased vision, seizures, gum bleeding, thrombocytopenia)

CaseHPOFreeText: autoantibodies were absent except for a positive direct antiglobulin test. Improvement with corticosteroids, faint oligoclonal bands documented yet absent on subsequent evaluation. brain lesions, elevated CD19+B, decreased NK,

CaseNotHPOs: abnormal bone marrow, abnormal bronchoscopy, abnormal IgA, abnormal IgM, positive anti neuronal antibody test

CaseNotHPOFreeText: n/a

CasePreviousTesting: none

GenotypingMethod: Sanger sequencing of CTLA4

PreviouslyPublished: not reported

Variant: heterozygous for NM_005214.5:c.151C>T

ClinVarID: 161109

CAID: CA173992

gnomAD: not found

SupplementalData: none

Case#: 15-year-old boy

DiseaseAssertion: SHORT syndrome and Immunodeficiency 36

FamilyInfo: Table2 Father is wild type, mother was unavailable for testing. Consanguinity was reported at Table 4. No affected family members Table4.

CasePresentingHPOs: HP:0001511(Intrauterine growth retardation) HP:0004322(Short stature) HP:0000325(Triangular face) HP:0010751(Dimple chin) HP:0000684(Delayed eruption of teeth) HP:0000347(micrognathia) HP:0100750(Atelectasis) HP:0004469(chronic bronchitis) HP:0002110(bronchiectasis) HP:0002720(Decreased circulating IgA level) HP:0011342(Mild global developmental delay) HP:0004279(short hands) HP:0000954(Single transverse palmar crease) HP:0002205(Recurrent respiratory infections)

CaseHPOFreeText:

CaseNotHPOs: Height -5.5 to -6.1 SDS

CaseNotHPOFreeText: N/A

CasePreviousTesting: CMA and MS-MLPA for chromosomes 6,14,20 was performed.

GenotypingMethod: Whole-exome sequencing was performed on the patient’s whole blood sample.

PreviouslyPublished: No

Variant: NM_001242466.2:c.68G > A p.Arg23Gln

ClinVar: 1361868

CAID: CA3290343

gnomAD: 0.00005439 https://gnomad.broadinstitute.org/variant/5-67589169-G-A

CTLA4 Alteration and Neurologic Manifestations: A New Family with Large Phenotypic Variability and Literature Review

Case#: 36 y.o male European

DiseaseAssertion: Limb Girdle

FamilyInfo: None

CasePresentingHPOs: HP:0003701,HP:0003560, HP:0006785, HP:0003236,HP:0003325, HP:0008981,

CaseHPOFreeText: Experienced two episodes of atrial fibrillation. High CADD scores. Exercise-induced myalgia and/or rhabdomyolysis

CaseNotHPOs:

CaseNotHPOFreeText:

MotorAchievement: Age 20 he developed exercise intolerance and sporadic myoglobinuria after intense exercise. Able to walk and cycle for long distances with little muscle pain.

CreatineKinase: Ranging from 1700 to 8000 UI/L), at the age of 10 years

CasePreviousTesting: Last neurological examination there was moderate calf hypertrophy.

GenotypingMethod: Muscle Biopsy using next generation sequencing and multiple gene panel. Minimal myopathic changes on histological assessment and normal immunofluorescence staining for muscle proteins including α-sarcoglycan

PreviouslyPublished:

Variant: NM_000023.4(SGCA):c.850C>T (p.Arg284Cys)

ClinVar: 9439

CAID:

gnomAD: 0.0007716