Case#: a 46-year-old male

DiseaseAssertion: Pseudoxanthoma elasticum (PXE)

FamilyInfo: NR

CasePresentingHPOs: HP:0200034, HP:0011506, HP:0001102, HP:0025533, HP:0007401, HP:0200056, HP:0007754, HP:0031526, HP:0007663

CaseHPOFreeText: skin papules, CNV in right eye, angioid steaks, peau d'orange, peripheral comet lesions and macular atrophy at the poseterior pole (more severe in left eye). Juxtafoveal pigmented scar in right eye and fibrotic tissue at the interpapillomacular region in left eye. Pattern dystrophy-like changes were evident at posterior pole. OCT scan showed subretinal fluid with ellipsoid zone abnormalities at the fovea with juxtafoveal hyperreflective alteration corresponding to the fundus scar in the right eye. At the interpapillomacular region, the atrophy of the outer retinal layer and RPE was evident (hypertransmission phenomenon). In left eye, OCT scan showed widespread RPE atrophy with atrophy of the outer retinal layers. 6/10 visual acuity in right eye and 1/20 in left eye.

CaseNotHPOs: NR

CaseNotHPOFreeText: NR

Genotyping Method: Whole exome sequencing analysis focusing on 340 genes associated with the calcification process or inherited retinal diseases

PreviouslyPublished: NR

Variant: c.6647C>T, p.Ala2216Val, NM_000350.3

ClinVar: 236149

CAID: CA10602405

SupplementalData: NR

Case#: a 56-year-old female

DiseaseAssertion: Pseudoxanthoma elasticum (PXE)

FamilyInfo: NR

CasePresentingHPOs: HP:0200034, HP:0001102, HP:0025533, HP:0011506, HP:0500087

CaseHPOFreeText: Papules on neck and axillae, marked skin laxity and redundance in neck, axillae, periumbilican area, groyne, and inner thighs, angioid streaks, peau d'orange. In right eye, a CNV, a large peripapillary atrophy, a small iuxafoveal scar, and RPE-Bruch's membrane complex normalities nasally to the fovea.

CaseNotHPOs: NR

CaseNotHPOFreeText: NR

Genotyping Method: Next generation sequencing focusing on 362 genes associated with calcification-related diseases and inherited retinal diseases

PreviouslyPublished: NR

Variant: c.1928T>G, p.Val643Gly, NM_000350.3

ClinVar: 99102

CAID: CA226958

SupplementalData: This variant has been reported likely pathogenic in VarSome and literature.

Case#: a 29-year-old man

DiseaseAssertion: Stargardt Disease

FamilyInfo: NR

CasePresentingHPOs: HP:0007663

CaseHPOFreeText: 20/70 visual acuity in both eyes

CaseNotHPOs: NR

CaseNotHPOFreeText: NR

Genotyping Method: ABCA4 microarray (ABCR5000 chip)

PreviouslyPublished: NR

Variant: NM_000350.3:c.5882G>A, p.G1961E and c.5018+2C>T (rare splice variant)

ClinVar: 7888, NR

CAID: CA119132, NR

SupplementalData: No CAID or ClinVar ID were found for the rare splice variant c.5018+2C>T

Case#: a 45-year-old man from Sardinia, Italy

DiseaseAssertion: Cone rod dystrophy

FamilyInfo: Five members, this patient is the only one affected by CRD

CasePresentingHPOs: HP:0000505, HP:0007663, HP:0000603, HP:0001123, HP:0000608, HP:0007401, HP:0011504, HP:0000548, HP:0030329, HP:0000543

CaseHPOFreeText: 1998: Subacute central vision loss in both eyes, choroidal and RPE atrophy surrounding left fovea and small white patches of atrophy around right fovea. Pale appearance of optic disc in both eyes. Punctate retinal pigment epitheliopathy observed bilaterally in midperipheral retina, hyperfluorescent macular regions suggesting bull's eye maculopathy. Paracentral ring scotoma, surrounded by a relative annular scotoma, early and predominant involvement of photopic over scotopic responses; 2018: BCVA was bilateral light perception with visual field extinction. FAF showed a central round area of decreased autofluorescence corresponding to area of macular atrophy, surrounded by an area of relatively increased autofluorescence. Several roundish areas of reduced autofluorescence in midperipheral retina. Severe macular atrophy surrounded by a ring of preserved RPE in both eyes. Sparse pigmentary deposits in midperipheral retina of both eyes. Severe bilateral retinal thinning with disappearance of external retinal layers. Outer retina tubulations

CaseNotHPOs: HP:0025148

CaseNotHPOFreeText: No pigment deposits on optic disc, no dark choroid

Genotyping Method: Candidate gene approach on ABCA4 followed by whole exome sequencing

PreviouslyPublished: NR

Variant: NM_000350, c.4535C>G, p.P1512R

ClinVar: 99291

CAID: CA227203

SupplementalData: Patient's healthy brother showed the same molecular condition for ABCA4. Patient also has 2 novel frameshift mutations in C2orf71.

Case#: 14-year-old, female, asian (Chinese) patient

DiseaseAssertion: ABCA-4 associated retinal dystrophy

FamilyInfo: The effect of the deep intronic variant on splicing was validated by a minigene assay in our previous study (Tian et al., 2022). Co-segregation analysis result exhibited that the variant c.1222C>T p.(Arg408Ter) came from the female parent, and the deep intronic variant c.2919-884G>T p.[Phe973LeufsTer3,=] from the male parent

ParentalTesting: Co-segregation analysis result exhibited that the variant c.1222C>T p.(Arg408Ter) came from the female parent, and the deep intronic variant c.2919-884G>T p.[Phe973LeufsTer3,=] from the male parent

CasePresentingHPOs: HP:0000556

CasePhenotypeFreeText: ABCA4-associated retinal dystrophy

CaseNotHPOs: NR

CaseNotPhenotypeFreeText: NR

CasePreviousTesting:NR

GenotypingMethod:

In the present study, we recruited a 14-year-old female patient diagnosed with ABCA4-RD. Biallelic variants were found in this patient, including the nonsense variant c.1222C>T p.(Arg408Ter) detected by Sanger sequencing and the deep intronic variant c.2919-884G>T p.[Phe973LeufsTer3,=] identified by next-generation sequencing.

We isolated peripheral blood mononuclear cells (PBMCs) from the patient’s peripheral venous blood and introduced three episomal plasmids containing transcription factors OCT4, SOX2, NANOG, LIN28, c-MYC, KLF4, and SV40LT into PBMCs. The reprogramming iPSC line, named BIOi003-A, showed stabilized morphology (Fig. 1A) and a normal karyotype in culture (Fig. 1B). Then, the endogenous expression of two pluripotent biomarkers, POU5F1 and NANOG, was detected (Table 2). The expression levels were compared with human embryonic stem cell line H1(hESC-H1) and mesenchymal stem cell line P3 (MSC-P3) by qRT-PCR (Fig. 1C). Surface markers SSEA4 and TRA-1–81 were analyzed by flow cytometry (Fig. 1D). the ABCA4 compound heterozygous variants c.(1222C>T;2919-884G>T) p.[Arg408Ter;Phe973LeufsTer3,=] were verified by Sanger sequencing (Fig. 1E). Furthermore, the teratoma assay exhibited the differentiation capacity of this iPSC line in vivo (Fig. 1F). Short tandem repeats (STR) analysis exhibited that the PBMCs and the iPSC line came from the same patient. PCR proved negative for mycoplasma contamination

Variant: NM_000350.3(ABCA4):c.1222C>T (p.Arg408Ter) and NM_000350.3(ABCA4):c.2919G>T (p.Leu973Phe)

LegacyVariant: c.1222C>T (p.Arg408Ter) and c.2919G>T (p.Leu973Phe)

ClinVar: 99035 and NR

CAID: CA179692 and CA341275270

gnomeAD: 1:94544895 G / A and NR

MultipleGeneVariants: No

PreviouslyPublished:No

AdditionalInfo: One patient was homozygous at the ABCA-4 gene, so there is information about both variants in one annotation because there is only one patient.

Case#: two siblings (female) were from one consanguineous family (case 1, 11 years and case 2, 9 years)

DiseaseAssertion: Stargardt’s Disease

FamilyInfo: NR

ParentalTesting: NR

CasePresentingHPOs: HP:0030500, HP:0011507

CasePhenotypeFreeText: LogMAR visual acuity for the right and left eye of cases 1–4 was 0.3 and 0.2, 0.1 and 0.1, 0.5 and 0.4, and 0.3 and 0.4, respectively. Gross disruption of the outer retinal layers at the macula in all cases; in two (cases 2 and 4), the presumed external limiting membrane (ELM) peak was broadened with the inner segment ellipsoid band (ISe) missing. Subtle white-yellowish fine dots at the macula and numerous white-yellowish flecks extending anterior to the arcade are shown in the colour fundus photograph of case 1. Autofluorescence (AF) imaging of case 1 detected well-defined dots with high signal at the central macula surrounded by a ring of increased signal and numerous foci with high or low signal extending to the peripheral retina. Case 2 also had subtle white-yellowish fine dots at the central macula and numerous white-yellowish flecks extending anterior to the arcade, both associated with high signal on AF imaging. In addition, case 3 had white-yellowish fine dots at the macula and numerous white-yellowish flecks extending to the periphery, both of which had high or low signal on AF imaging. Case 4 showed subtle fine macular dots mainly in a para-foveal location, which are well-defined on AF imaging.

CaseNotHPOs: HP:0007401, HP:0000505

CaseNotPhenotypeFreeText: Most cases with STGD have central macular atrophy with numerous more peripheral flecks (Michaelides et al. 2003). Given their relatively good visual acuity, it is likely that the central macular dots observed in our cases may be an early sign of macular dysfunction before the development of macular atrophy. Similar fine macular dots or a ‘mottled macula’ have also been reported in other inherited retinal diseases

CasePreviousTesting: The age of disease onset in cases 1–4, defined as either the age at which visual loss was first noted by the subject or in the asymptomatic subjects when abnormal retinal appearance was first detected, was 5, 7, 8, and 6 years old, respectively.

GenotypingMethod: After informed consent was obtained, blood samples were taken from probands of 2/3 families for ABCA4 screening. A full medical history was obtained, and a full ophthalmologic examination was performed in all cases. Mutation screening of ABCA4 was performed in two probands of the three families, and two likely disease-causing variants were identified in each case; c.768G > T, p.V256V (a previously reported splicing-altering synonymous variant) and c.4363T > C, p.C1455R (a missense variant) in case 1, and c.1906C > T, p.Q636* (a non-sense variant) and c.5461-10 T > C (a disease-associated intronic variant with uncertain effect) in case 3. A blood sample was not available in one proband (case 4).

Variant: NM_000350.3(ABCA4):c.768G>T (p.Val256=) and NM_000350.3(ABCA4):c.4363T>C (p.Cys1455Arg)

LegacyVariant: c.768G>T (p.Val256=) and c.4363T>C (p.Cys1455Arg)

ClinVar: 99505 and 377404

CAID: CA227458 and CA957621

gnomeAD: 1:94564350 C / A and 1:94495177 A / G

MultipleGeneVariants:No

PreviouslyPublished: No

AdditionalInfo: Some symptoms/diagnoses are consistent with Stargardt’s Disease 3, however the probands in the study were younger in age, so many of the symptoms hadn’t progressed much. Also, all of the cases had decent visual acuity, which contradicts a symptom of Stargardt’s Disease 3.

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#: 34 year-old Chinese male.

DiseaseAssertion: HAE-C1INH Type 1.

FamilyInfo: Family history of edema (mother passed away due to laryngeal edema, older sister experienced buttock swelling after prolonged sitting, maternal uncle experienced episodic abdominal pain and unilateral upper-limb swelling). Family testing for serum C4 and C1INH concentration and C1INH functional activity indicate that proband’s maternal uncle and asymptomatic daughter exhibit low values for all three of these biochemical markers, consistent with Type 1 HAE. The proband’s daughter and maternal uncle also tested positive for the variant identified in the proband. Pedigree included in figures.

ParentalTesting: Mother passed away before study. Father tested for C4 and C1INH concentration and C1INH function with all values falling in normal ranges.

CasePresentingHPOs: Edema (HP:0000969), Edema of the dorsum of hands (HP:0007514), Edema of the upper limbs (HP:0010742), Non-pitting edema (HP:6000507), Abdominal pain (HP:0002027)

CasePhenotypeFreeText: Onset at approximate age of 26. Episodes of localized edema of limbs, skin, and buttocks lasting two to three days regardless of treatment. Episodes became more frequent at age 34 and were accompanied by abdominal pain triggered by fatigue. Non-pitting edema of right hand observed on physical examination.. The proband’s C4 level was 0.02 g/L (reference range: 0.1–0.4 g/L), C1INH concentration was 0.07 g/L (reference range: 0.21–0.39 g/L), and C1INH functional activity was 4.3% (reference range: ≥68.0%).

CaseNotHPOs: N/A

CaseNotPhenotypeFreeText: N/A

CasePreviousTesting: N/A

GenotypingMethod: PCR amplification with Sanger sequencing.

Variant: NM_000062:c.1067T>A p.(Val356Glu)

LegacyVariant: N/A

ClinVar: N/A

CAID: CA380702482

gnomAD: N/A

MultipleGeneVariants: N/A

PreviouslyPublished: N/A

AdditionalInfo: N/A

-Gene: DICER1 -PMID: 29343557 -Inheritance Pattern: DICER1 is inherited as an autosomal dominant condition with decreased penetrance -Disease Entity: earlier onset disease, multisite disease, 0-2 site disease, cystic lung disease, familial disease, bilateral disease, stage IA/IB, bilateral disease -mutation: germline loss-of-function mutation, missense mutation, Intronic mutations, hotspot mutation, second somatic mutation, truncating mutations, biallelic mutation -zygosity: heterozygosity -Family History: -testing should be considered for those with a family history of DICER1-associated conditions so that appropriate surveillance can be undertaken. -Individuals at 50% risk of a germline pathogenic variant based on family history who do not pursue genetic testing should follow surveillance guidelines as -if they have a DICER1 mutation unless/until genetic testing confirms that they did not inherit the familial mutation When a pulmonary cyst is identified in a young child with a pathogenic germline -DICER1 variant or family history of a DICER1-associated condition, it should be assumed to be Type I PPB until proven otherwise

Other Information: -Case: Risk for most DICER1-associated neoplasms is highest in early childhood and decreases in adulthood -affected phenotype may simply result from probabilities of generating the characteristic “loss-of-function plus hotspot” two hit typical of a DICER1 syndrome neoplasm. -Caseprevioustesting: presymptomatic testing of a minor child, should be discussed and factored into the decision process, as some individuals may choose, and have the right to choose, not to know their/their child’s genetic status. -gnomAD: n/a