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 1, Male, 4 y/o, German and Thai

DiseaseAssertion:FOXG1 syndrome

FamilyInfo: Non-consanguineous parents. De novo. Patient 1 has maternally inherited duplications at 15q21.12(47292250-47309868)x3 and Xp22.31(6451676-8115124)x3 of unknown clinical significance.

ParentalGenotype:Not provided

CasePresentingHPOs:HP:0002197, HP:0005484, HP:0011344, HP:0001252, HP:0020045,HP:0000540, HP:0010808, HP:0002019, HP:0003781, HP:0012741, HP:0002421, HP:0000748, HP:0003763, HP:5200017, HP:0025112, HP:0000957

CaseHPOFreeText: At 19 months, could not sit independently and no speech development. Stereotypic hand and head movements. High pain tolerance. X-ray at age 2 showed broad ribs. Improved head control by age 4.

CaseNotHPO:HP:0410263, HP:0002376

CaseNotHPOFreeText:Dysmorphic features. breathing abnormalities

CasePreviousTesting:No previous testing

PreviouslyPublished:Not previously published

GenotypingMethod:Mate-pair sequencing, Sanger sequencing

Gene:FOXG1

Variant:46,XY,t(9;14)(q22.3;q11.2)dn

HGVS:Not provided

ClinVarID:426096

gnomAD:Not provided

Case:Patient 3, Male, 1 y/o, Brazilian

DiseaseAssertion: FOXG1 syndrome

FamilyInfo: Non-consanguineous parents

ParentalGenotype: No family testing mentioned.

CasePresentingHPOs: HP:0000252, HP:0001252, HP:0000486

CaseHPOFreeText: Developed microcephaly within 1 year. Developmental delay, unable to sit without assistance at 1 year old. Central Nervous System (CNS) MRI showed a volumetric reduction of the cerebral parenchyma, hypomyelination, and hypoplasia of corpus callosum mainly involving the anterior part and prominent lateral ventricles

CaseNotHPO: HP:0030917

CaseNotHPOFreeText: Normal length, weight, HC at birth. No retinal abnormalities.

CasePreviousTesting: Not asserted.

PreviouslyPublished: Not previously published.

GenotypingMethod: Sanger sequencing, mate-pair sequencing

Gene: FOXG1

Variant: 46,XY,t(2;14)(q37;q11.2)dn

HGVS: Not provided.

ClinVarID:426094

gnomAD:Not provided

Case:Patient 2, Female, 5 y/o, Brazilian

DiseaseAssertion:quadriplegic cerebral palsy with axial hypotonia and distal spasticity

FamilyInfo: Non-consanguineous parents. Parents had normal karyotypes. Older sister was clinically normal.

ParentalGenotype: Normal karyotypes for both parents.

CasePresentingHPOs: HP:0002098, HP:0010959, HP:0008755, HP:0002090, HP:0032661, HP:0001274, HP:0011344, HP:0001249, HP:0001344, HP:0000748, HP:0034435, HP:0000486, HP:0000483, HP:0200136

CaseHPOFreeText: Dilated superficial blood vessels seen on brain MRI.

CaseNotHPO:N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Not asserted

PreviouslyPublished: Not previously published

GenotypingMethod:Mate-pair sequencing, Sanger sequencing, chromosome analysis

Gene: FOXG1

Variant: 46,XX,t(4;14)(q27;q13)dn

HGVS: Not provided

ClinVarID: 426095

gnomAD: Not provided

Case#:Patient 52, female, 3 years old

DiseaseAssertion:Neonatal/Infantile Epileptic Encephalopathy (NIEE)

FamilyInfo:DeNovo. The family is Chinese

ParentalGenotype:The authors only conducted singleton and not trio-based exome sequencing so the parents' exomes were not sequenced.

CasePresentingHPOs:HP:0011344, HP:0002069, HP:0007359, HP:0011097, HP:0100704, HP:0001332, HP:0002072, HP:0012171.

CaseHPOFreeText:Patient 52 presents with severe global developmental delay and epilepsy.

Patient 52 has generalized tonic/clonic/tonic-clonic seizures, focal seizures and spasms. Patient 52's seizure onset occurred at 3 months old.

Patient 52 has cortical visual impairment (CVI), dystonia, chorea, and hand-washing sterotypies.

Patient History

@ 3 months - Patient 52 had generalized tonic/clonic/tonic-clonic seizures.

Patient 52 was on 3 antiepileptic drugs at most recent follow-up 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:CDKL5

Variant:NM_003159.2 c. 1849delC (p. Arg617Valfs*4)

The authors state that the variant is a heterozygous frameshift deletion.

The authors state that this is a novel variant and is pathogenic.

HGVS:Not provided

ClinVarID:Not found

CAID:Not found.

gnomAD:Not found

MultipleGeneVariants:Not provided

Case: Patient 1, female, 2 years old

DiseaseAssertion: Rett Syndrome

FamilyInfo: DeNovo. Patient 1 was the second child of a nonconsanguineous Chinese couple. Patient 1 was born at full term with a birth weight of 3.83 kg.

ParentalGenotype(s):Not provided

CasePresentingHPOs:HP:0011344, HP:0001250, HP:0001252, HP:0000252, HP:0000748, HP:0003763, HP:0005469, HP:0000486, HP:0012171.

CaseHPOFreeRext:Patient 1 presents with severe global developmental delay, epilepsy, and hypotonia. The Patient History contains all of Patient 1's phenotypes along with the progression of her condition.

Patient History

@ 3 months - Patient 1 had microcephaly (head circumference was less than 3rd percentile with a body weight and body height at 75th percentile). Patient 1 had hypotonia.

Patient 1 was given a metabolic screening, a muscle enzyme, and a brain tomography with normal results.

@ 6 months - Patient 1 had microcephaly, flat occiput, right divergent squint, and hypotonia. No syndromal diagnosis could be ascertained at that time.

@ 2 years - Patient 1 had epilepsy.

Patient 1 had severe global development delay.

Patient 1 was given an EEG which showed nonspecific background slowing, but no epileptiform abnormalities. Patient 1 was also given a brain MRI which showed mild thinning of corpus callosum without major structural defect. Patient 1 had no developmental regression but she developed stereotypical hand movements, bruxism, and occasional outburst of laughter.

Based on these phenotypes, Angelman/Rett Syndrome was suspected.

CaseNOTHPOs: HP:0002353.

CaseNOTHPOFreeText: Patient 1 was given an EEG which detected no epileptic abnormalites.

CasePreviousTesting: Genetic investigations (including methylation-specific multiplex ligation-dependent probe amplification (MS-MLLPA)) was conducted for Angelman Syndrome, UBE3A gene, MECP gene, and array CGH. These studies were negative. A FOXG1 related disease was suspected

PreviouslyPublished:Not previously published

GenotypingMethod: A FOXG1 gene test showed a de novo frameshift pathogenic mutation FOXG1 {NM_005249.3} c. 396_397ins26; FOXG1{NP_005240.3} :(p. Gly133TRPfs*68) which confirmed the diagnosis of a FOXG1 related congenital variant of Rett Syndrome.

Gene:FOXG1

Variant: (NM_005249.3) c. 396_397ins26 (p. Gly133Trpfs*68)

HGVS:Not provided

ClinVarID:Not found

CAID:Not found

gnomAD:Not found

Case:Patient 2, female, Chinese

DiseaseAssertion:Global delay

FamilyInfo:Patient 2 was the first child of nonconsanguineous Chinese couple born at 38-week gestation. The mother had gestational diabetes mellitus that required insulin therapy.

ParentalGenotype:Not provided

CasePresentingHPOs:HP:0000365, HP:0020049, HP:0000252, HP:0001263, HP:0012171, HP:0000154, HP:0000708, HP:0003763, HP:0002376, HP:0012433.

CaseHPOFreeText:

Patient History

@ birth - Patient 2 presented with mild grade bilateral hearing impairment and left divergent squint diagnosed at birth.

@ Follow-up visit - Patient 2 had microbrachycephaly and global developmental delay. Brain MRI, metabolic screening and array CGH were normal.

@ 1 year - Patient 2 had stereotypical handwashing movement.

There was no clinical or electrical seizure.

Patient 2 has craniofacial features like microbrachycephaly, wide mouth, divergent squint, and behavioral phenotype.

@ 1.5 years - Patient 2 had bruxism and developmental regression. Patient 2 also had loss of some motor and social skills.

CaseNotHPOs:HP:0001250

CaseNotHPOFreeText:Patient 2 has no seizures.

CasePreviousTesting:Not provided

PreviouslyPublished:Not previously published

GenotypingMethod:Not provided

Gene:MECP2 (MN_004992.3) (NP_004983.1)

Variant:c. 808C>T (p. Arg270*)

HGVS:Not provided

ClinVarID:Not found

CAID:CA172577

gnomAD:Not found

MultipleGeneVariants:NA

Case:Patient 1, female, 11 years old

DiseaseAssertion:Rett Syndrome - Atypical Variant

FamilyInfo:De Novo. Patient 1's parents were healthy. When Patient 1 was clinically examined, the head circumferences of her mother and father were 53 cm (P25) and 59 cm (P90), respectively. The parents had normal weight.

ParentalGenotype:Both parents were sequenced for Patient 1's mutation, and the deletion was not detected.

CasePresentingHPOs:HP:0001249, HP:0001513, HP:0001626, HP:0000256, HP:0010465, HP:0012758, HP:0000750, HP:0012433, HP:0002591, HP:0001250, HP:0020174, HP:0000316, HP:0000336, HP:0000431, HP:0000377, HP:0000470, HP:0001156, HP:0001500.

CaseHPOFreeText:

Patient history

@ birth - Patient 1 was born at 38 weeks of gestation after an uncomplicated pregnancy. Her weight was 3,390 g (P69), height 51 cm (P60), and her head circumference was 36 cm (P90).

@ 6 months - Patient 1 experienced developmental delay.

@ 9 months - Patient 1 sat without support.

@ 2 years - Patient 1 began to walk.

@ later on - Patient 1 presented with speech delay and behavioral disturbances. The behavioral disturbances were reduced by the drug risperidone.

@ early childhood - Patient 1 has been obese and appeared to display hyperphagia.

@ 8 years - Patient 1 developed precocious puberty.

@ 10 years - Patient 1 had her first epileptic seizure. Treatment with lamotrigine prevented further seizures. The seizures later became refractory to this treatment.

@ 10 years - Patient 1 presented with a height of 160 cm (P>97) and a head circumference of 59 cm (P>97). She had hypertelorism and prominent eyebrows. Her nasal bridge was broad and auricles were fleshy. In addition, Patient 1's neck was short and the fingers were short and wide.

Patient 1 has an intellectual disability, metabolic syndrome, and macrocephaly.

CaseNotHPOs:HP:0002540.

CaseNotHPOFreeText:Patient 1 sat without support at 9 months old. She walked at 2 years.

CasePreviousTesting:Patient 1 was given a conventional cytogenetic analysis. The chromosomal analyses (46,XX) and array CGH results (BlueGnome CytoChip ISCA 4×180K v1.0; Agilent Human Genome CGH Microarray 180K) were normal. Patient 1 was also given a methylation-specific MLPA to exclude a Temple syndrome, which is also characterized by weight gain and precocious puberty. In addition, Prader-Willi syndrome was ruled out by methylation testing. This syndrome is another imprinting disease causing obesity and intellectual disability.

PreviouslyPublished:Not previously published

GenotypingMethod:Whole-exome sequencing analysis of the entire exome was conducted for Patient 1. Whole-genome sequencing showed heterozygosity in Patient 1, which was confirmed by Sanger sequencing. Macrocephalic syndrome genes including PTEN, NSD1, NFIX, SETBP1, RAI1, and PHF6 were analyzed, and no additional variants of interest (pathogenic, likely pathogenic, or variants of uncertain significance) were observed.

Gene:MECP2

Variant:c. 1162_1172del (p. Pro388*), heterozygosity, frameshift.

HGVS:NM_004992.3

ClinVarID:Not found

CAID:CA1139667881

gnomAD:Not found

MultipleGeneVariants:Not provided

Case:Patient 2, female, 2.5 years old

DiseaseAssertion:CDKL5 Disorder

FamilyInfo:De Novo with an unremarkable family history.

ParentalGenotype:Not provided

CasePresentingHPOs:HP:0032792, HP:0007359, HP:0011154, HP:0002194, HP:0010862, HP:0000750, HP:0012434, HP:0000710, HP:0100023, HP:0000252, HP:0009062, HP:0010845, HP:0020174, HP:0010841.

CaseHPOFreeText:

Patient history

@ 2 months to 2.5 years - Patient 2 experienced tonic and focal seizures with autonomic symptoms.

@ 2 years - Patient 2 was diagnosed with CDKL5 disorder.

Patient 2 had severe delayed gross motor development, severe delayed fine motor development, severe delayed language development and delayed social development. Patient 2 had hyperoral and hand flapping stereotypies. She also had microcephaly (< 2 SD) and axial hypotonia.

Patient 2 was given a brain EEG which detected Delta slowing of the background followed by generalized attenuation during seizures and multifocal interictal epileptiform abnormalities.

@ 2.5 years - Patient 2 experienced seizures in clusters.

Treatments

Antiepleptic treatments included:Phenobarbital, Topirimate, Clobazam, Valproate, Keppra, Vitamin B6, Phenytoin, Lamotrigine, Nitrazepam, Oxcarbazepine, Mirtazipine, KCI, Levetiracetam, ant ketogenic diet.

Patient 2 was also treated with Carnitine. Patient 2's seizures seem to have changed in type over time but continued.

Other testing

Tests were conducted on Patient 2 to obtain data in the following areas: NBS, lactate, lipoprotein profile, plasma and urine amino acids, urine organic acids, acylcarnitine profile, total and free serum carnitine levels, plasma ammonia, total plasma homocysteine, serum CK, liver enzymes, urine alpha-AASA, creatine, biotinidase, VLCFA, Batten disease screen, CSF analysis (amino acids, lactate, glucose, protein, cell count, neurotransmitters), MRI-brain with spectroscopy, and karyotype.

CaseNotHPOs:Not provided

CaseNotHPOFreeText:Not provided

CasePreviousTesting:Patient 2 was given a gene sequence test for the genes SCNIA and MECP2. No gene mutation was found for these two genes.

PreviouslyPublished:Not previously published

GenotypingMethod:Patient 2 was given a CDKL5 gene sequence test. The test detected a mutation in the CDKL5 gene.

Gene:CDKL5

Variant:c. 2480_2486dupCAGATCT. frameshift

The authors state that CDKL5 gene sequencing detected a de novo duplication in exon 17, c. 2480_2486dupCAGATCT, resulting in a frameshift (Boston University School of Medicine, Center for Human Genetics, Boston, MA). This is a novel change that has not been reported before in ExAC. Only pathogenic point mutations in exon 17 have previously been reported. In a patient with a previously reported frameshift mutation in exon 18, a truncated CDKL5 transcript was detected. A truncated protein would lack the C-terminus and would not localize correctly in the cell, as demonstrated in vitro. Accordingly, any reading frame altering mutations proximal to exon 18 are null-variants. Therefore, this mutation is classified as pathogenic according to ACMG criteria.

HGVS:Not provided

ClinVarID:547188

NM_001323289.2 (CDKL5): c. 2480_2486dup (p. Gln830fs)

Allele ID: 538303

CAID:Not found

gnomAD:Not found

MultipleGeneVariants:Not provided

Case#: 7-year-old boy

DiseaseAssertion: Atrial flutter (AFL), sick sinus syndrome (SSS), Brugada syndrome (BrS)

FamilyInfo: Family history of sudden death in maternal grandfather at age 30 years. Family testing identified the same SCN5A variant in the proband's mother and sister. The mother was asymptomatic but had a coved type ST elevation in V1 lead recorded at the 3rd intercostal position (Fig. 1e) and remained free of cardiac events until age 37 years. His sister's ECG was normal, and she remained free of cardiac events for 10 months

ParentalTesting: Mother was found to have the same LOF variant

CasePresentingHPOs: HP:0004749, HP:0011712, HP:0011704, HP:0011654

CaseHPOFreeText: AFL detected on ECG with right bundle branch block but no history of arrhythmia, congenital heart disease, or cardiomyopathy. Post-RFCA, patient had sinus arrest lasting up to 7s, leading to diagnosis of sick sinus syndrome (SSS). Post-ablation ECG following a second RFCA revealed Brugada-type patterns, raising suspicion of Brugada syndrome (BrS) which eventually lead to a diagnosis.

CaseNotHPOs: HP:0001638, HP:0001279, HP:0011675

CaseNotHPOFreeText: Cardiomyopathy, syncope, arrhythmia

CasePreviousTesting: NR

Genotyping Method: NR

FunctionalAnalysis: NR

Variant: c.2678G > A p.Arg893His

ClinVar: 67749

CAID: CA016396

gnomAD: https://gnomad.broadinstitute.org/variant/3-38585800-C-T?dataset=gnomad_r4 (v4.1.0 GrpMax FAF: 0.000003390 (European non-Finnish) )

Case#: 55-year-old man

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

FamilyInfo: Unremarkable

ParentalTesting: NR

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

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

CaseNotHPOs: NR

CaseNotHPOFreeText: Stenosis

CasePreviousTesting: See NGS results in Supplementary Table 1

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

FunctionalAnalysis: NR

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

ClinVar: 67694

CAID: CA015449

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

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