Case#: 2, female 4 days (onset), 4 y 3 mo (current), Chinese

CasePresentingHPOs: HP: 0008344, HP: 0012088, HP: 0011968, HP: 0001276, HP: 0001941, HP: 0002543, HP: 0011342 (elevated A keto acids in urine, abnormal urinary odor, feeding difficulties, hypertonia, acidosis, abnormal globus pallidus MRI signals, mild global developmental delay)

HPOsFreeText: Poor response to light and sound, abnormal MRI signals in frontal lobes, Blood ammonia: 95 uM, Hemoglobin: 117 g/L, Leucin: 745.01 uM, Valine: 526.40 uM, Isoleucine: 181.06 uM, Alloisoleucine: 69.45 uM

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo:

CasePreviousTesting: n/a

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_000709.3(BCKDHA): c.659C>T (p.Ala220Val)

ClinVar: 93367

CAID: n/a (because this doesn't need to be included if it is in ClinVar right?)

gnomAD: not in gnomAD

Case#: 7, female, 2 y 5 m (current), Chinese

CasePresentingHPOs: HP: 0008344, HP: 0012751, HP: 0012696 (elevated A keto acids in urine, abnormal signals in cerbral ganglia, abnormal thalamic MRI signal intensity)

HPOsFreeText: leucin: 621.72 uM, valine: 594.15 uM, isoleucine: 225.21 uM, Alloisoleucine: 76.62 uM

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: detected by newborn screening, unsure cis or trans

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_183050.3:c.482T>G (p.Val161Gly), NM_183050.3:c.508C>T (p.Arg170Cys)

ClinVar: not found, 96590

CAID: CA364657700, CA224301

gnomAD: not found, 0.00001759 (European, non-Finnish)

Case# Subject 5, F, 7yo onset, Hispanic

CasePresentingHPOs HP:0001270, HP:0000750, HP:0005184, HP:0001250, HP:0008942, HP:0003236, HP:0001664, HP:0004756, HP:0011675, HP:0001943, HP:0002151, HP:0003201, HP:0001249, HP:0002913, HP:0003324, HP:0001695, HP:0006956

HPOcont: Motor Delay, Speech Delay, Prolonged QTc interval, Seizures, Elevated CPK, Torsade de pointes, Ventricular tachycardia, Arrhythmia, Hypoglycemia, Elevated Lactate, Acute rhabdomyolysis, Intellectual Disability, Myoglobinuria, Generalized Muscle Weakness, Cardiac Arrest, Enlarged lateral ventricles

HPOFreeText: speech and motor delay, prolonged QTc interval, seizures, prior to her acute presentation. (7 years) acute rhabdomyolysis, high CPK and myoglobinuria. (13 years) muscle weakness, cardiac arrest, torsade de pointes from prolonged QTc interval, ventricular tachycardia with recurrent pulseless arrest and arrhythmia, able to ambulate.

CaseNotHPOs n/a

CasePreviousTesting highest CPK (60,000 U/L), 953 U/L for AST, 540 U/L for ALT, and CPK-MB of 291 U/L.

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES and cSNP results confirmed with Sanger

Variant (1) NM_152906.6:c.460G>A (p.Gly154Arg)

ClinVar (1) 208823

CAID (1) CA358646

gnomAD (1) 0.001549(Other), 0.0001208(Overall)

VariantEvidence (Figure 3) using "EBV-transformed B-lymphoblastoid cell lines (BLCLs) from another individual, subject 4 with homozygous c.460G>A (p.Gly154Arg) mutation, and evaluated the Golgi by intracellular staining with WGA, as well as cis Golgi marker, anti-GM130 antibody." WGA stain resolved lower area of golgi bodies in p.Gly154Arg cells than WT. Measured immunoglobulin heavy chain binding protein levels in WT and and patient fibroblasts, BiP levels in patient cells lower than WT after ER induced stress by Brefeldin A.

CaseAddInfo nonconsanguineous, parents confirmed heterozygotes

CasePMIDs n/a

Case# F1_IV:5, M, 6.5yo report, Saudi Arabia

CasePresentingHPOs HP:0001263, HP:0008947, HP:0001257, HP:0000486, HP:0000639, HP:0004326, HP:0000252

HPOcont: Global developmental delay, Infantile muscular hypotonia, Spasticity, Strabismus, Nystagmus, Cachexia, Microcephaly

Free text: "At 4.5 years of age, he was cachectic with a weight of 8.1 kg (−5.2 SD), short with a length of 89 cm (−3.7 SD), and microcephalic with a head circumference of 46 cm (−3.2 SD). He was inattentive and had no visual tracking ability as well as bilateral strabismus and nystagmus. He had severe axial hypotonia and appendicular hypertonia with spasticity."

CaseNotHPOs HP:0001250

NotHPOcont: Seizures

CasePreviousTesting "Plasma lactate, ammonia, uric acid, lipid profile, tandem mass spectrometry (MS), urine organic acids, plasma amino acids, and congenital disorder of glycosylation screenings did not reveal any abnormality. Chromosomal analysis and microarray were unremarkable. Glycosaminoglycans and oligosaccharides in the urine were normal. Lysosomal enzyme analysis was unremarkable. HEXB and SMN1 mutation analysis did not reveal pathogenic mutations. Brain MRI showed mild diffuse brain atrophy, and MRS (magnetic resonance spectroscopy) showed a mild reduction of the N-acetylaspartate peak but a normal lactate peak. Skeletal survey showed diffuse osteopenia."

CaseMethod1 Exome sequencing

CaseMethod2 Sanger

CaseGenotypingMethod autozygome filtering after exome sequencing, confirmed with sanger

Variant NM_032504.1(UNC80):c.3793C>T (p.Arg1265Ter)

ClinVar 219188

gnomAD 0.00004175(Latino), 0.000006613(Overall)

CaseAddInfo His first-cousin parents had two sons who died at 4 and 6 years of age with a reportedly identical phenotype of profound static encephalopathy and no seizures. The index individual has two living brothers and two sisters who are all healthy

Case# Fam1Pat1, F, 21yo onset, Turkish

CasePresentingHPOs HP:0002061, HP:0002066, HP:0002070, HP:0001260, HP:0001310, HP:0000563, HP:0006986,

CasePreviousTesting Neurologic examination revealed dysarthria, spasticity in lower >> upper extremities, mild weakness in proximal leg muscles, Achilles tendon contracture, mild dysmetria, dysdiadochokinesia, and a spastic-ataxic gait. Cranial MRI and nerve conduction studies were unremarkable.

CaseMethod1 Whole Exome

Variant NM_001198868.1:c.994G>A

CAID CA381247865

gnomAD 0.00005842(East Asian), 0.000008204(Overall)

VariantEvidence none

Case# ObeidIndex, F, 13yo report, Palestinian-Emirati

CasePresentingHPOs HP:0006829, HP:0010864, HP:0001263, HP:0000252, HP:0001344, HP:0001250, HP:0002650, HP:0000574, HP:0000414, HP:0000179, HP:0000307, HP:0000218, HP:0040079, HP:0030787, HP:0002136, HP:0001344

HPOcont: Severe muscular hypotonia, Severe intellectual disability, Global developmental delay, Microcephaly, Absent speech, Seizures, Scoliosis, Thick eyebrow, Bulbous nose, Thick lower lip vermilion, Pointed chin, High palate, Irregular dentition, Cerumen abnormality, Broad-based gait, Absent speech

Free Text: "birth weight of 2.6 Kg (< 10th centile), head circumference of 33 cm (< 3rd centile). At the age of 8 months, her developmental delay was noticed as she was unable to sit unsupported. Formally evaluated at one year of age, at which point EEG was suggestive of symptomatic localization-related epilepsy. EEG revealed ill-defined low spikes over the left temporooccipital area, suggesting symptomatic partial epilepsy. At age 11 developed subtle facial dysmorphic features, including bushy eyebrows, bulbous nose, anteverted nostrils, thick lower lip, pointed chin, high arched palate, irregular teeth, and waxy ears. As an eleven years and three months old girl, she is able to sit independently, without support. However, she has difficulty in standing from squat position. She can ambulate independently with a wide based gait with hands on flexion position, but is not able to run, jump, or pedal tricycle. She can climb stairs, but with support. She demonstrated a pincer grasp. She can do purposeful movements; as in the ability to reach, hold and transfer objects, and she can bring food to mouth. She can also dress herself with help, but does not zip or button. She does not have any meaningful speech, but babbles socially."

CaseNotHPOs HP:0002540, HP:0002019, HP:0011968, HP:0002014

NotHPOcont: Inability to walk, Constipation, Feeding difficulties, Diarrhea

CasePreviousTesting Brain MRI, thyroid function tests, metabolic screening, and eye examination were normal; as were the following genetic investigations: chromosomal microarray, karyotyping, FISH for 15q11–13 deletion, subtelomeric FISH, methylation analysis for Angelmann, and molecular analysis for UBE3A gene. "A 186 such variants were looked at individually in order to uncover any connections with the patient’s phenotype in the context of various modes of inheritance in the analyzed trio. For example, heterozygous mutations in NDRG4, RELN, TYRP1, REEP6, FABP2 and others were found and given low priority when looked at in the light of the patient’s phenotype. None of the other variants from that list appeared to have enough functional links to the patient’s condition to merit discussing it along with the UNC80 variant."

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES results confirmed with Sanger sequencing in trio

Variant NM_032504.1:c.8525G>A (p.Arg2842Gln)

CAID CA350413877

gnomAD 0.00006667(European (Non-Finnish), 0.00003230(Overall)

CaseAddInfo parental consanguinity, confirmed in trans

Case17 Female, Finland

CasePresentingHPOs HP:0000347, HP:0002101, HP:0000238, HP:0001341, HP:0007370, HP:0002126, HP:0007260, HP:0007165

(Micrognathia, Defective lung lobation, Hydrocephalus, Olfactory lobe agenesis, Callosal agenesis, Polymicrogyria, Type II lissencephaly, Periventricular neuronal heterotopia)

HPOsFreeText Crown-heel body length 48cm, body weight 2695g, brain weight 249g, abnormal larynx/trachea, hydrocephalus/open-book, occipitotemporal hypoplasia, infratentorial hypoplasia, occipitoschisis/keyhole, leptomeningeal heterotopia, neuroepithelial rosettes, absent developed and identifiable mamillary bodies, absent anterior commissure, difficult to identify nucleus dentatus, (Fig6:) cervical spinal cord shows a polypoid bulge from the posterior part of the cord and a slit-like central canal

CaseNotHPOs HP:0000202, HP:0001161, HP:0001829, HP:0001627, HP:0000157

(Oral cleft, Hand polydactyly, Foot polydactyly, Congenital heart defect, Tongue abnormality)

NotHPOsFreeText Uterus duplex, hydranencephaly/anencephaly, true alobar or semilobar holoprosencephaly

CasePreviousTesting n/a

Variant NM_145014.2(HYLS1):c.632A>G (p.Asp211Gly), homozygous

ClinVar 1143

gnomAD MAF= 0.009594(European(Finnish)), no homozygotes

CaseAddInfo died 5 hours after birth, 36+4wk gestational age

CasePMIDs n/a

Case12 Male, Finland

CasePresentingHPOs HP:0000202, HP:0000347, HP:0001841, HP:0010066, HP:0001627, HP:0000157, HP:0002101, HP:0002323, HP:0000316, HP:0000445, HP:0001162, HP:0030449

(Oral Cleft, Micrognathia, Preaxial foot polydactyly, Duplicated hallux, Congenital heart defect, Tongue abnormality, Defective lung lobation, Anencephaly, Hypertelorism, Broad nose, Postaxial hand polydactyly, Therapeutic abortion)

HPOsFreeText Crown-heel length 19.5cm, body weight 245g, abnormal larynx trachea, uterus duplex, absent developed and identifiable mamillary bodies, absent anterior commissure, difficult to identify nucleus dentatus, gliovascular tissue on the base of the cranium, hypertelorism, broad nose, postaxial polydactyly in hands, and preaxial polydactyly in feet

CaseNotHPOs HP:0001161

(Hand polydactyly)

NotHPOsFreeText true alobar or semilobar holoprosencephaly

CasePreviousTesting n/a

Variant NM_145014.2(HYLS1):c.632A>G (p.Asp211Gly), homozygous

ClinVar 1143

gnomAD MAF= 0.009594(European(Finnish)), no homozygotes

CaseAddInfo induced abortion at 24+0wk gestational age

CasePMIDs n/a

Case4: Female, 74 yrs report

CasePresentingHPOs: HP:0002751, HP:0002540, HP:0100753, HP:0003236, HP:0003089, HP:0003798, HP:0031237, HP:0003555, HP:0012785 (Kyphoscoliosis, Inability to walk, Schizophrenia, Elevated serum creatine phosphokinase, Hamstring contracture, Nemaline bodies, Internally nucleated skeletal muscle fibers, Muscle fiber splitting, Flexion contracture of finger)

HPOsFreeText: Jaw contractures, Pectoral contractures, Quad contractures, Disorganized sarccomeres, Nuclear clumps

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Mother of Case 5 and 6, Proband for Family C

CasePreviousTesting: N/A

CaseGenotypingMethod: The TPM2 gene was sequenced and variants identified. No other information is provided.

Variant: NM_003289.3:c.14_16delAGA (p.Lys7del)

ClinVar: 140486 https://www.ncbi.nlm.nih.gov/clinvar/variation/140486/

gnomAD: Not in gnomAD

Case6: Male, 40 yrs report

CasePresentingHPOs: N/A

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Son of Case 4, Sibling of Case 5

CasePreviousTesting: N/A

CaseGenotypingMethod: The TPM2 gene was sequenced and variants identified. No other information is provided.

Variant: NM_003289.3:c.14_16delAGA (p.Lys7del)

ClinVar: 140486 https://www.ncbi.nlm.nih.gov/clinvar/variation/140486/

gnomAD: Not in gnomAD

Case3: Male, 41 yrs report

CasePresentingHPOs: HP:0012432, HP:0003738, HP:0003236, HP:0003273, HP:0003044, HP:0012785, HP:0006466, HP:0005997, HP:0003798, HP:0100295, HP:0031237, HP:0003201, HP:0012548 (Chronic fatigue, Exercise-induced myalgia, Elevated serum creatine phosphokinase, Hip contracture, Shoulder flexion contracture, Flexion contracture of finger, Ankle contracture, Neck flexion contracture, Nemaline bodies, Muscle fiber atrophy, Internally nucleated skeletal muscle fibers, Rhabdomyolysis, Skeletal muscle fatty infiltration)

HPOsFreeText: Jaw contractures, Core-like regions

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Variant is confirmed de novo via parental testing

CasePreviousTesting: ACTA1 and TPM3 were sequenced and returned negative.

CaseGenotypingMethod: The TPM2 gene was sequenced and variants identified. No other information is provided.

Variant: NM_003289.3:c.14_16delAGA (p.Lys7del)

ClinVar: 140486 https://www.ncbi.nlm.nih.gov/clinvar/variation/140486/

gnomAD: Not in gnomAD

Case2: Male, 14 yrs report

CasePresentingHPOs: HP:0002355, HP:0002527, HP:0000023, HP:0001763, HP:0002942, HP:0001276, HP:0006466, HP:0003089 (Difficulty walking, Falls, Inguinal hernia, Pes planus, Thoracic kyphosis, Hypertonia, Ankle contracture, hamstring contracture)

HPOsFreeText: In-toe gait, Tendo-Achilles release performed

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Son of Case 1, Variant is de novo in mother

CasePreviousTesting: N/A

CaseGenotypingMethod: The TPM2 gene was sequenced and variants identified. No other information is provided.

Variant: NM_003289.3:c.14_16delAGA (p.Lys7del)

ClinVar: 140486 https://www.ncbi.nlm.nih.gov/clinvar/variation/140486/

gnomAD: Not in gnomAD

Case: Family 1 Moynihan Proband, male, Pakistani

CasePresentingHPOs: HP:0000407, HP:0004322, HP:0000135, HP:0100540, HP:0012385, HP:0002716, HP:0034920, HP:0034677, HP:0034391, HP:0030075, HP:0002862

CasePresentingHPOsFreeText: Eyelid swellings due to histiocytic deposits, diverse cytoplasmic inclusions in phagocytes and reticulum cells of bone marrow, Lymph node and eyelid show reactive features with small reactive lymphoid follicles and histiocytes within dilated sinuses resembling RDD. invasive ductal carcinoma grade 3 ER negative breast aged 43 years and carcinoma bladder (grade 3 papillary TCC) age 46 years

CaseNOTHPOs:

CaseNOTHPOSFreeText:

CasePreviousTesting: direct sequencing of PRF1 and UNC5B

CaseGenotypingMethod: autozygosity mapping, genotyping (genome-wide linkage scan was performed using Affymetrix 250k SNP arrays), direct sequencing, PCR

Variant: c.300+1G>A homozygous

ClinVarID: or CAID: 130339/CA155238

gnomAD: This splice site variant in intron 2 is present in gnomAD v4.0.0 at a MAF=0.0002197 (20/91048 alleles) in the South Asian population with 0 homozygotes.

AddCaseInfo: brother is affected as well

PreviouslyPublished: PMID: 9545394

VariantEvidence: n/a

Case# Monnier 2:3, male, French

CasePresentingHPOs HP:0002047

CasePreviousTesting N/A

CaseMethod1 sequenced all cDNA

CaseGenotypingMethod single strand conformation analysis and sequencing

Variant NM_000069.2(CACNA1S):c.3257G>A (p.Arg1086His)

ClinVar 17626

gnomAD 0.00002978 link<br /> gnomAD did not include the G>A mutation, only C>T but it was the same amino acid change

VariantEvidence N/A, all of these case studies claim ICVT verifies the phenotype but that doesn't seem like enough to pass for variant evidence since it is tested in patient muscle tissue.

CaseAddInfo Family not counted, too few segregations for the R1086H variant.

CaseFSIP2_2 male, 52yo report, Tunisian

CasePresentingHPOs HP:0003251, HP:0012207, HP:0012868

(male infertility, asthenospermia, sperm tail anomaly)

HPOsFreeText Sperm volume: 4.7mL, sperm concentration: 1.25 million/mL, total motility: 0h, vitality: 7%, normal spermatozoa: 0%, absent flagella: 16%, short flagella: 50%, coiled flagella: 18%, flagella of irregular caliber: 36%

CaseNotHPOs n/a

CasePreviousTesting Previous genetic analysis of DNAH1, CFAP43, and CFAP44 did not end in diagnosis. "Normal somatic karyotypes 46,XY and were negative for Y chromosome microdeletions."

Variant NM_173651.3(FSIP2):c.2282dup (p.Asn761Lysfs)

ClinVar 586973

gnomAD not in gnomAD

CaseAddInfo Consanguineous parents

CasePMIDs 29449551

CaseFSIP2_1 male, 44yo report, Tunisian

CasePresentingHPOs HP:0003251, HP:0012207, HP:0012868

(male infertility, asthenospermia, sperm tail anomaly)

HPOsFreeText Sperm volume: 2.5mL, sperm concentration: 6.7 million/mL, total motility: 1h, vitality: 47%, normal spermatozoa: 0%, absent flagella: 2%, short flagella: 32%, coiled flagella: 26%, flagella of irregular caliber: 57%

CaseNotHPOs n/a

CasePreviousTesting Previous genetic analysis of DNAH1, CFAP43, and CFAP44 did not end in diagnosis. "Normal somatic karyotypes 46,XY and were negative for Y chromosome microdeletions."

Variant NM_173651.3(FSIP2):c.910del (p.Gln304Lysfs)

ClinVar 586972

gnomAD not in gnomAD

CaseAddInfo Consanguineous parents

CasePMIDs 29449551

Case: Family A Proband AII-8, male, Arabic, Israeli, 13yo at report

CasePresentingHPOs: HP:0000953, HP:0000998, HP:0000054, HP:0001433, HP:0011025, HP:0000365, HP:0000520, HP:0012385, HP:0001684, HP:0000823, HP:0030053, HP:0100324, HP:0100727

CasePresentingHPOsFreeText: Scrotal masses, Dilated scleral vessels

CaseNOTHPOs: HP:0008064, HP:0002619, HP:0007380

CaseNOTHPOSFreeText:

CasePreviousTesting: direct sequencing of AIFM2, ADAMTS14, EIF4EBP2, C10ORF54, PPA1, H2AFY2, LRRC20, NODAL, PRF1, TYSND1, SAR1A, PSAP, NPFFR1, and C10ORF27

CaseGenotypingMethod: microarray, haplotype analysis, direct sequencing of exons of SLC29A3, restriction digestion

Variant: G427S; G437R

ClinVarID: or CAID: 563/CA114349; 565/CA114352

gnomAD: The missense variant G427S is present in gnomAD v4.0.0 with a MAF=0.00005339 (4/74926 alleles) in the African/African American population and 0 homozygotes. The missense variant G437R is present in gnomAD v4.0.0 with a MAF=0.00006666 (4/60002 alleles) in the Admixed American population and 0 homozygotes.

AddCaseInfo: consanguineous parents; mother was het for G427S, but father's genotype was not provided

PreviouslyPublished: PMID: 18410979

VariantEvidence: Functional studies in Xenopus oocytes demonstrated that G427S results in a total loss of transport activity (Kang et al. 2010; PMID: 20595384).

Kang et al. (2010) performed functional characterization of the G437R mutation in Xenopus oocytes and observed transport activity that was approximately half that of wildtype SLC29A3. Studies in NIH 3T3 fibroblasts demonstrated accelerated turnover of the G437R mutant compared to wildtype, suggesting decreased stability.

Case: Family J Proband JII-1, male, 12yo at report

CasePresentingHPOs: HP:0000953, HP:0030053, HP:0000998, HP:0000054, HP:0002240, HP:0031664, HP:0000365, HP:0012385, HP:0034373, HP:0001084, HP:0000771

CasePresentingHPOsFreeText: subcutaneous masses in genital area, dilated lateral scleral vasculature

CaseNOTHPOs: HP:0001822, HP:0000520, HP:0002619, HP:0007380, HP:0001256

CaseNOTHPOSFreeText:

CasePreviousTesting: Direct sequencing of AIFM2, ADAMTS14, EIF4EBP2, C10ORF54, PPA1, H2AFY2, LRRC20, NODAL, PRF1, TYSND1, SAR1A, PSAP, NPFFR1, and C10ORF27

CaseGenotypingMethod: Microarray, homozygosity mapping, haplotype analysis, direct sequencing of exons of SLC29A3

Variant: c.1045delC homozygous

ClinVarID: or CAID: 566/CA351488

gnomAD: The frameshift variant p.Leu349fs, located in exon 6/6, is present in gnomAD v4.0.0 with a MAF=0.000001799 (2/1112010 alleles) in the European Non-Finnish population and 0 homozygotes.

AddCaseInfo: Consanguineous, unaffected parents. 6 unaffected siblings

PreviouslyPublished: n/a

VariantEvidence: Kang et al. (2010; PMID: 20595384) performed functional characterization of the 1045delC mutation in Xenopus oocytes and observed near-total loss of transport activity compared to wildtype SLC29A3. Studies in NIH 3T3 fibroblasts demonstrated mistrafficking of the mutant protein to the endoplasmic reticulum or Gogli apparatus

Case: Family H Proband HII-2, female, 50yo at report

CasePresentingHPOs: HP:0000823, HP:0002240, HP:0001822, HP:0034373, HP:0100490, HP:0002619, HP:0000520, HP:0001838, HP:0007380, HP:0001084, HP:0001871, HP:0004322, HP:0000135, HP:0000141, HP:0012410, HP:0011974

CasePresentingHPOsFreeText: stasis ulcers

CaseNOTHPOs: HP:0000953, HP:0000998, HP:0030053, HP:0001256

CaseNOTHPOSFreeText: dilated lateral scleral vasculature

CasePreviousTesting: Direct sequencing of AIFM2, ADAMTS14, EIF4EBP2, C10ORF54, PPA1, H2AFY2, LRRC20, NODAL, PRF1, TYSND1, SAR1A, PSAP, NPFFR1, and C10ORF27

CaseGenotypingMethod: Microarray, homozygosity mapping, haplotype analysis, direct sequencing of exons of SLC29A3, restriction digestion

Variant: G437R homozygous

ClinVarID: or CAID: 565/CA114352

gnomAD: The missense variant G437R is present in gnomAD v4.0.0 with a MAF=0.00006666 (4/60002 alleles) in the Admixed American population and 0 homozygotes.

AddCaseInfo: Consanguineous parents, not genotyped. 3 unaffected, not genotyped siblings

PreviouslyPublished: n/a

VariantEvidence: Functional characterization of G437R in Xenopus oocytes showed that transport activity was approximately half of WT SLC29A3. Studies in NIH 3T3 fibroblasts demonstrated accelerated turnover of the G437R mutant compared to WT, suggesting decreased stability (Kang et al. 2010; PMID: 20595384)

Article is a PDF so unable to annotate in it, but table 2 shows the pts genotypes.

CasePt11 male, 3yo report, Italian

CasePresentingHPOs HP:0001987 (Hyperammonemia)

HPOsFreeText severe hyperammonemia at 48h of life

CaseNotHPOs n/a

CasePreviousTesting Metabolic testing plasma citrulline(<2[normal 16-40μmol/l]), glutamine(1600[normal 530–913μmol/l]) and ammonia(3400[normal< 75 μg/dl])

CaseMethod1 PCR

CaseMethod2 n/a

CaseGenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

Variant 1. NM_001875.4:c.2440C>T (p.Arg814Trp), 2. NM_001875.4:c.3953T>A (p.Leu1318Ter) compound heterozygous

ClinVar n/a

CAID 1. CA2086638, 2. CA350439297

gnomAD n/a

VariantEvidence n/a

CaseAddInfo n/a

CasePMIDs 21120950

CasePt9 male, 5do death, Italian

CasePresentingHPOs HP:0001987 (Hyperammonemia)

HPOsFreeText Hyperammonemia

CaseNotHPOs n/a

CasePreviousTesting Metabolic testing: ammonia(2750[normal< 75 μg/dl])

CaseMethod1 PCR

CaseMethod2 n/a

CaseGenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

Variant 1. NM_001875.4:c.2429A>G (p.Gln810Arg), 2. NM_001875.4:c.3953T>A (p.Leu1318Ter) compound heterozygous

ClinVar n/a

CAID 1. CA350440293, 2. CA350439297

gnomAD n/a

VariantEvidence n/a

CaseAddInfo n/a

CasePMIDs 12955727

CasePt5 male, 15mo death, Italian

CasePresentingHPOs HP:0001987, HP:0001254, HP:0001252, HP:0003572, HP:0003217 (Hyperammonemia, Lethargy, Hypotonia, Low plasma citrulline, High plasma glutamine)

HPOsFreeText neonatal severe hyperammonemia, mildly hypotonic, lethargy, low plasma citrulline, elevated glutamine

CaseNotHPOs n/a

CasePreviousTesting Metabolic testing plasma citrulline(6[normal 16-40μmol/l]), glutamine(1500[normal 530–913μmol/l]) and ammonia(1214[normal< 75 μg/dl])

CaseMethod1 PCR

CaseMethod2 n/a

CaseGenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

Variant 1. NM_001875.4:c.1440_1441del (p.Thr481CysfsTer?), 2. NM_001122634.3:c.3004C>T (p.Arg1002Trp) compound heterozygous

ClinVar n/a

CAID 1. CA2086366, 2. CA64748170

gnomAD 1. 0.00001802(European (Non-Finnish), 0.000008153(Total), 2. n/a

VariantEvidence n/a

CaseAddInfo Older brother who died with post-mortem suspicion of CPSD or NAGS deficiency.

CasePMIDs 21120950

Family#PresentingHPOs HP:0001987 (Hyperammonemia)

HPOFreeText: Severe hyperammonemia

FamilyNotHPOs n/a

CountryOrigin n/a

Ethnicity Italian

Race n/a

Family#PreviousTesting Elevated plasma ammonia in both siblings (3454 in Pt7 and 1858 in Pt8[normal<75 μg/dl]).

Family#Method1 PCR

Family#Method2 n/a

Family#GenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

Affected 2

Unaffected n/a

Segregations n/a

PublishedLOD n/a

eLOD n/a

AddSegregationInfo n/a

ProbandLabel Pt7, Female, 5mo death

CasePresentingHPOs HP:0002283, HP:0100806, HP:0003572, HP:0003217 (Diffuse brain atrophy, Sepsis, Low plasma citrulline, High plasma glutamine)

CaseHPOsFreeText Severe hyperammonemia(2do), Severe diffuse brain atrophy on MRI(1mo), sepsis(5mo)

CasePreviousTesting Low plasma citruline(0[normal 16-40μmol/l]) and elevated glutamine(2488[normal 530–913 μmol/l])

Variant 1. NM_001875.4:c.1263+5G>C, 2. NM_001875.4:c.2429A>G (p.Gln810Arg)

ClinVar n/a

CAID 1. To register, 2. CA350440293

gnomAD n/a

VariantEvidence c.1263+5G>C causes a splice defect (Table 2)

FamilyAddInfo Brother, Pt8, died with similar clinical features and was diagnosed with CPS1D post-mortem.

FamilyPMIDs 12955727, 12655559

CasePt1 female, 3yo diagnosis, Italian

CasePresentingHPOs HP:0001508, HP:0002014, HP:0000505, HP:0002167, HP:0002013, HP:0001252, HP:0002321, HP:0001987, HP:0003217, HP:0002910, HP:0012747, HP:0100543, HP:0001256 (Failure to thrive, Diarrhea, Visual impairment, Speech impairment, Vomiting, Hypotonia, Vertigo, Hyperammonemia, Hyperglutaminemia, Elevated transaminases, Abnormal brain MRI signal intensity, Cognitive impairment, Mild ID)

HPOsFreeText normal psychomotor dev, failure to thrive and diarrhea(first years), visual/speech impairment, vomiting, hypotonia, vertigo(referred at 3y,2mo), , hyperammonemia, high glutamine, elevated transaminases, normal orotic levels, hyperintense signal in cortical-subcortical frontal region on brain MRI, cognitive impairment:IQ 53(3yo) mild ID(21yo)

CaseNotHPOs n/a

CasePreviousTesting Metabolic testing plasma citrulline(17.3[normal 16-40μmol/l]), glutamine(1244[normal 530–913μmol/l]) and ammonia(300[normal< 75 μg/dl]), elevated transaminases 350 UI/L, normal orotic levels, CPS1 residual enzyme activity "low" in liver biopsy.

CaseMethod1 PCR

CaseMethod2 n/a

CaseGenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

Variant 1. NM_001875.4(CPS1):c.3047A>G (p.Asn1016Ser), 2. NM_001875.4:c.3500C>G (p.Thr1167Arg) compound het

ClinVar 1. 551211

CAID 2. CA350437190

gnomAD 1. 0.00006534(African), 0.000008123(Total) 2. n/a

VariantEvidence enzyme assay showing low CPS1 activity mentioned

CaseAddInfo n/a

CasePMIDs 21120950

Case# Chakarova P, European

CasePresentingHPOs HP:0007675, HP:0001133

CasePreviousTesting no

CaseMethod1 PCR

CaseMethod2 DHPLC and direct sequencing

Variant NM_004698.3(PRPF3):c.1477C>T (p.Pro493Ser)

ClinVar 3353

CasePMIDs 16799052

Case#: Family 1, Individual III-3, Male, 8yo, dx at 6mo

CasePresentingHPOs: HP:0000639, HP:0012389, HP:0001270, HP:0002078, HP:0002070, HP:0001260, HP:0007256

CaseNotHPOs:

CasePreviousTesting: MRI

CaseGenotypingMethod: combination of homozygosity mapping and WES, haplotype analysis

Variant: NM_177400.2(NKX6-2):c.121A>T (p.Lys41Ter)

ClinVar: 430622, https://www.ncbi.nlm.nih.gov/clinvar/variation/430622/

gnomAD: n/a

VariantEvidence:

CaseAddInfo: Wheelchair bound at 8 yo.

CasePMIDs:

Case#: Consequence 14 Table 1 in Data Supplement (1 cases)

DiseaseAssertion: HCM

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: Cardiac magnetic resonance imaging, BSA, NYHA functional class, obstructive HCM, atrial fibrillation, coronary artery disease, NSVT, Syncope, SCD family hitory, wall thickness

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Additional oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing for MYBPC3, TMP1, TNNC1, TNNI2, TNNI3, TNNT2, ACTC1, MYL3

CaseGenotypingMethod: oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing

Variant: NM_000257.4(MYH7):c.1208G>A (p.Arg403Gln)

ClinVar: 14087 https://www.ncbi.nlm.nih.gov/clinvar/variation/14087/

CAID: n/a

gnomAD: absent

Case#: Cluruk_1993_IN-16, male, 13 y.o., Indian ancestry reported (Mandla and Jabalpur districts of Madhya Pradesh)

CasePresentingHPOs: decreased RBCs (3.34), decreased Hb (9.2), elevated HbS (68.2), elevated HbF (21.9), MCH 27.5%, HB A2 4.5%, HB A 5.4%

CaseHPOFreeText: S - B+ - thal (aax/aax) x = variant

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting:

CaseMethod1: Sanger

CaseMethod2: hybridization probing

CaseGenotypingMethod: Sanger + probing

Variant: NM_000558.5(HBA1):c.96-1G>A

ClinVarID: 801169

CAID: CA7770244

gnomAD: allele frequency of 0.0009851 (21/21318 alleles) in the South Asian population (PopMax 0.0006591)

VariantEvidence: Also seen in compound het with 4 patients with a4.2 deletion and 7 patients with 3.7 deletion in this paper. Heterozygotes (aa/aax) had similar levels of Hb S

CaseAddInfo:

CasePMIDs:

Case: Mohlo-Pessach Patient 1, male, 13yo at report, 4yo at onset, Spanish

CasePresentingHPOs: HP:0000953, HP:0000998, HP:0000407, HP:0001596, HP:0003764, HP:0000771, HP:0001744, HP:0002619, HP:0100490, HP:0001935, HP:0003565, HP:0011227, HP:0002716, HP:0100727

CasePresentingHPOsFreeText: Enlarging cutaneous mass over the left thigh with sclerodermoid induration. Hyperpigmentation onset at 4yo; located on thighs, left shin, and left lower abdomen. Alopecia of the scalp. Halo nevi on the trunk. Scrotal masses. Fixed flexion contractures of the proximal interphalangeal joint of his left fifth finger. Skin biopsy included dermal infiltrate consisting of lymphocytes, plasma cells and CD68+ histiocytes, and dermal and subcutaneous fibrosis

CaseNOTHPOs:

CaseNOTHPOSFreeText:

CasePreviousTesting:

CaseGenotypingMethod: SLC29A3 exons and splice junctions were PCR-amplified using intronic primers. PCR products were purified and sequenced on ABI 3700 capillary sequencer.

Variant: c.1087C>T (p.Arg363Trp) homozygous

ClinVarID: or CAID: CA129561

gnomAD: This missense variant, Arg363Trp, is present in gnomAD v4.0.0 with a MAF=0.0001734 (1/5768 alleles) in the Middle Eastern population and 0 homozygotes.

AddCaseInfo: non-consanguineous family

PreviouslyPublished: n/a

VariantEvidence: n/a

Case: Mohlo-Pessach Patient 2, male, 20yo at report, Arab

CasePresentingHPOs: HP:0000365, HP:0000953, HP:0000998, HP:0004322, HP:0001999, HP:0000494, HP:0003196, HP:0000463, HP:0001084, HP:0001433, HP:0100490, HP:0001935, HP:0003565, HP:0011227, HP:0002716, HP:0100727

CasePresentingHPOsFreeText: Cutaneous induration and hyperpigmentation of the thighs appeared at 8yo, spread to genitals, back, and lower limbs. Retrognathism. Scrotal masses. Fixed flexion contractures of the proximal interphalangeal joints of the right fourth and fifth fingers and the left fifth finger. Skin biopsy included dermal infiltrate consisting of lymphocytes, plasma cells and CD68+ histiocytes, and dermal and subcutaneous fibrosis.

CaseNOTHPOs:

CaseNOTHPOSFreeText:

CasePreviousTesting:

CaseGenotypingMethod: SLC29A3 exons and splice junctions were PCR-amplified using intronic primers. PCR products were purified and sequenced on ABI 3700 capillary sequencer.

Variant: c.1088G>A (p.Arg363Gln)

ClinVarID: or CAID: CA129562

gnomAD: This missense variant, Arg363Gln, is present in gnomAD v4.0.0 with a MAF=0.0002666 (16/60010 alleles) in the Admixed American population and 0 homozygotes.

AddCaseInfo: consanguineous parents

PreviouslyPublished: n/a

VariantEvidence: n/a

Proband KH5 was 5yo at report, has the Hurler phenotype, and has this variant in compound heterozygosity with p.Y618X

Case#: Family V, Patient 9, female, 1yo at diagnosis, 5yo at death, Tunisia (Mahdia), black

DiseaseAssertion: MPS1, Hurler

FamilyInfo: Parental consanguinity (first cousins). Age of parents at proband's birth: 50 years (M) 62 years (F). 6 unaffected siblings

CasePresentingHPOs: HP:0010864, HP:0004322, HP:0001537, HP:0000692, HP:0006482, HP:0030812, HP:0001999, HP:0007957, HP:0000943

CaseHPOFreeText: Height=102cm (-3DS). Weight=18kg (-1 DS). IDUA activity in leukocytes=0,020 μKat/kg (Normal values 1.7-3.5 μKat/kg of protein).

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: n/a

GenotypingMethod: Direct sequencing of PCR products from each of 14 exons and flanking intron-exon junctions

PreviouslyPublished: n/a

Variant: p.R628X homozygous. Proband also had the following polymorphisms: A8A, A20A, H33Q, R105Q, A314A, N181N, T410T, V554I, IVS6+21c>a, IVS7+79c>t, IVS7-45g>c, IVS9+36t>c, IVS10+140c>a, IVS11+33c>t, IVS12+13c>t, IVS12-31c>g

ClinVar: 550421

CAID: CA2802462

gnomAD: The highest population minor allele frequency in gnomAD v4.1.0. is 0.00005038 (2/39700 alleles) in the East Asian population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.00025), meeting this criterion (PM2_Supporting).

SupplementalData: n/a

Case# III-1, Female, Caucasian

CasePresentingHPOs HP:0001643

CaseMethod1 WES

CaseMethod2 PCR

Variant NM_001136239.3(PRDM6):c.788G>C (p.Cys263Ser)

ClinVar 243050

VariantEvidence Functional in vitro characterization of PRDM6 p.Cys263Ser in HEK293 cells and human aortic VSMCs showed that the variant protein significantly loses its capability for nuclear localization (Fig 3). DNA overexpression in adenovirus virus infected WT and mutant variants showed MYH11 is also not suppressed by mutant where it is suppressed in WT (Figure 4). Immunoblots of histones in WT human aortic smooth muscle transfected with the variant showed reduced histone modification and and suppression of contractile proteins. (Fig. 5)

Case# B1-3, Male, UK

CasePresentingHPOs HP:0001279

CasePreviousTesting re-sequenicing of genome

CaseGenotypingMethod genotyped for five microsatellite markers spanning TMEM43 on chromosome 3p25

Variant NM_024334.2(TMEM43):c.934C>T (p.Arg312Trp)

ClinVar 36873

gnomAD 0.03553 link

Case: Alonso-Perez_Patient 2, Female, 41yo, Spanish

DiseaseAssertion: Sandhoff Disease

CasePresentingHPOs: HP:0000007, HP:0001260

CaseHPOFreeText:

CaseNOTHPOs: HP:0002380, HP:0001324, HP:0003202

CaseNOTHPOFreeText: No signs of cerebellar or sensory dysfunction, deep tendon reflexes were normal

CasePreviousTesting: Nerve conduction studies and EMG were performed with normal results. Serum CK levels were tested and found to be elevated with the rest of the biochemical analysis normal. MRI was normal with no involvement of the brain. Serum β-hexosaminidase-enzyme activity assay showed low levels.

GenotypingMethod: Sanger sequencing of SMN1, DYNC1H1 and BICD2 genes showed no pathogenic variants. WES revealed HEXB mutations.

PreviouslyPublished: n/a

SupplementalData: n/a

Variant: NM_000521.4, c.171delG (p.Trp57Cysfs7)

CAID: CA3305751

gnomAD: MAF: unavailable in gnomAD, gnomAD variant ID: 5-73981254-TG-T

VariantEvidence: This variant is known to be pathogenic and was previously published only in infantile cases of SD, PMID: 22789865. Total hexosaminidase activity in fibroblasts from the patients with this variant in that paper range from 2.3-9.5% of the normal control levels.

MultipleGeneVariants AR, allele on second allele

Variant: c.1510C>T (p.Pro504Ser)

CAID: CA116493

gnomAD: MAF: 0.0002259, Latino/admixed American, gnomad variant ID: 5-74016469-C-T

VariantEvidence: This variant is known to be pathogenic and was previously published in adult cases of SD, PMID: 9694901. This study concluded the effect of the mutation on ganglioside hydrolysis, combined with its effect on intracellular transport, produces chronic Sandhoff disease.

Case# Postma 3:1, male, 10yo, white

CasePresentingHPOs HP:0004758, HP:0000980, HP:0005184, HP:0000961, HP:0002789

CasePreviousTesting no

CaseMethod1 PCR

CaseGenotypingMethod amplified/screen of CASQ2, SCN5A, HRC, PLN, RYR2, KCNQ1, KCNH2, and KCNK1 genes

Variant NM_001232.3:c.532+1G>A

CAID CA341763774 link

VariantEvidence not in this article

Case#: Family AU-1, 35yo, female, Austrian

DiseaseAssertion: DOA+

FamilyInfo: positive family history, 2 relatives in table 1

CasePresentingHPOs: HP:0000648, HP:0000365, HP:0001251, HP:0000590, HP:0001138

CaseHPOFreeText:

CaseNotHPOs: HP:0003198

CaseNotHPOFreeText:

PreviouslyPublished: n/a

GenotypingMethod: The entire OPA1-coding region and flanking exon–intron boundaries were amplified by the polymerase chain reaction (PCR) and sequenced with BigDye terminator cycle chemistries on an appropriate genetic analyser. All genetic variants were confirmed by reverse sequencing

Variant: c.1635C>G (p.S545R) aka c.1800C>G (p.S600R)

ClinVar: 30461

CAID: CA10575554

SupplementalData:

This case has been added to the VCI and assessed already.

PreviouslyPublished: PMID: 18158317

CaseII-3: Female, 2 years, Turkey

CasePresentingHPOs: HP:0004912, HP:0004322, HP:0002970 (Hypophosphatemic rickets, Short stature, Genu varum)

HPOsFreeText: -2.09 standard deviation score

CaseNotHPOs: HP:0000083, HP:0002024, HP:0001947 (Renal failure, Malabsorption, Renal tubular acidosis)

NotHPOsFreeText: Other tubulopathies that cause secondary hypophosphatemia, Vitamin D-dependent rickets type 1 and 2

CaseAddInfo: Variant is asserted novel, Daughter of II:II-2

CasePreviousTesting: Calcium levels (10.2 mg/dL), Decreased serum phosphate levels (2.1 mg/dL; reference 3.8-6.5), Elevated serum ALP (531 IU/L; reference 90-325), 25OHD3 levels (31.1 ng/ml), PTH levels (52.5 ng/L), TPR levels (62.3), Decreased TmP/GFR levels (1.31; reference 2.9-6.1)

CaseGenotypingMethod: Genomic DNA was isolated from peripheral blood leukocytes, amplified, and directly sequenced in all the coding exons and intron-exon boundaries of PHEX. If no mutations were found, FGF23 followed by consecutive analysis of DMP1, ENPP1, CLCN5, SLC34A3 and SLC34A1 was performed. Significance of found mutations was predicted by computational programs and sorted.

Variant: NM_000444.5:c.979_983dup (p.His329Thrfs*4)

CAID: CA913187410 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913187410

gnomAD: Not in gnomAD

annotating here since this is a PDF

Case#: Yamagishi Case 5, female, 1y at clinical dx, 20y at enzymatic dx, 31y at death

DiseaseAssertion: Hurler/Scheie

FamilyInfo: n/a

CasePresentingHPOs: HP:0002240

CaseHPOFreeText: height=117cm at 21yo. cardiac involvement. CHF caused death

CaseNotHPOs:

CaseNotHPOFreeText: mental delay

PreviouslyPublished: n/a

Variant: 704ins5; R89Q

ClinVar: 11921; 11922

CAID: CA256123; CA256124

SupplementalData: n/a

Case# SAL-399-073, Female, 46yo, French, Hispanic

CasePresentingHPOs HP:0002385, HP:0011448, HP:0001260, HP:0002066, HP:0002015, HP:0002650, HP:0001272

CaseMethod1 Exome

CaseMethod2 Sanger

Variant NM_005186.3:c.463C>T(p.Q155X), NM_005186.3:c.1142C>T(p.R512C)

CAID CA381242841, CA381248914

gnomAD 0.00003567

VariantEvidence nonsense, missense in trans with null variant

CaseAddInfo in article supplement

CaseF9: Female, Italy, 48 years diagnosis

CasePresentingHPOs: HP:0001873 (Thrombocytopenia)

HPOsFreeText: World Health Organization bleeding score is 0 (1 members); Mean platelet count is 117 ×10^9/L; Mean platelet volume is 14.4 fL, Mean platelet diameter is 3.3 μm

CaseAddInfo: N/A

CaseF1:III-1: Female, Italy

CasePresentingHPOs: HP:0001634 (Mitral valve prolapse)

CaseAddInfo: Proband for F1

Case# Subject 2, F, 5mo died, Kurdish

CasePresentingHPOs HP:0001319, HP:0008872, HP:0002033, HP:0003128, HP:0002490, HP:0001531, HP:0040288, HP:0001712, HP:0001410, HP:0002098, HP:0002910, HP:0002126, HP:0000365, HP:0002151 (Neonatal hypotonia, Feeding difficulties in infancy, Poor suck, Hyperlactatemia, Increased CSF lactate level, Failure to thrive in infancy, Nasogastric tube feeding, Left ventricular hypertrophy, Decreased liver function, Respiratory distress, Elevated transaminases, Polymicrogyria, Deafness, Elevated serum lactate)

HPOFreeText: After caesarean delivery, neonatal hypotonia, poor feeding, and sucking. (3 months) failure to thrive, nasogastric feeding, left ventricular hypertrophy and impaired liver function. Brain MRI: bifrontal polymicrogyria and acoustic oto-emissions suggested deafness (4 months). Died of respiratory distress at 5 months.

CaseNotHPOs n/a

CasePreviousTesting Serum lactate (7.4 mmol/L; normal range 0.90–1.70 mmol/L), lactate to pyruvate ratio (170; normal range 30–50), CSF lactate (3.1 mmol/L; control < 2.2 mmol/L), liver function (AST: 84 UI/L, normal range 15–60; ALT: 52 UI/L, normal range 7–40; gGT: 262 UI/L, normal range 6–25 UI/L). Screened panel of known mitochondrial disease genes. Analysis of mtDNA and mtDNA copy number from patient muscle DNA were normal, thus excluding mtDNA rearrangements and point mutations.

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES confirmed with Sanger in patient and parents to confirm in trans

Variant NM_017819.3(TRMT10C):c.542G>T (p.Arg181Leu) -homozygous

ClinVar 224316

gnomAD 0.0003508(Latino), 0.0001121(Total) -no homozygotes on record

VariantEvidence n/a

CaseAddInfo non-consanguineous, healthy older brother, c.542G>T variant in ExAC (10/120,324 alleles) and ESP6500 (1/11,824 alleles)

CaseAddPMIDs n/a

CaseP7 male, 59yo, Tunisia

CasePresentingHPOs HP:0012207, HP:0012865, HP:0012868, HP:0003251

(reduced sperm motility, sperm head anomaly, sperm tail anomaly, male infertility)

HPOsFreeText Patient's sperm volume: 5mL(lower reference limit: 1.5), sperm concentration: 15.5million/mL(reference: 15), total motility after 1hr: 4%(reference: 40), vitality: 47%(reference:53%), normal spermatozoa: 0%(reference: 4), abnormal acrosome: 95%, abnormal head morphology: 7%, abnormal base: 3%, absent flagella: 30.5%, short flagella: 25%, coiled flagella: 27%, flagella of irregular caliber: 33%, multiple anomalies index: 2.56%.

CaseNotHPOs n/a

CasePreviousTesting Previously screened all patients for DNAH1, CFAP43, and CFAP44 variants. Somatic karyotypes were normal.

Variant NM_144668.5:c.3007_3337del

ClinVar 586974

gnomAD not in gnomAD

CaseAddInfo consanguinity

CasePMIDs 29449551

CaseP6 male, 28yo report, Tunisia

CasePresentingHPOs HP:0012207, HP:0003251

(reduced sperm motility, male infertility)

HPOsFreeText Patient's sperm volume: 3mL(lower reference limit: 1.5), sperm concentration: 7.8million/mL(reference: 15), total motility after 1hr: 5%(reference: 40), normal spermatozoa: 0%(reference: 4).

CaseNotHPOs n/a

CasePreviousTesting Previously screened all patients for DNAH1, CFAP43, and CFAP44 variants. Somatic karyotypes were normal.

Variant NM_144668.5:c.3007_3337del

ClinVar 586974

gnomAD not in gnomAD

CaseAddInfo consanguinity

CasePMIDs 29449551

CaseP5 male, 31yo report, Tunisia

CasePresentingHPOs HP:0012207, HP:0012865, HP:0012868, HP:0003251

(reduced sperm motility, sperm head anomaly, sperm tail anomaly, male infertility)

HPOsFreeText Patient's sperm volume: 3.4mL(lower reference limit: 1.5), sperm concentration: 60million/mL(reference: 15), total motility after 1hr: 5%(reference: 40), vitality: 62%(reference:53%), normal spermatozoa: 0%(reference: 4), abnormal acrosome: 80%, abnormal head morphology: 8%, abnormal base: 2%, absent flagella: 24%, short flagella: 50%, coiled flagella: 8%, flagella of irregular caliber: 68%, multiple anomalies index: 2.5%.

CaseNotHPOs n/a

CasePreviousTesting Previously screened all patients for DNAH1, CFAP43, and CFAP44 variants. Somatic karyotypes were normal.

Variant NM_144668.5:c.3007_3337del

ClinVar 586974

gnomAD not in gnomAD

CaseAddInfo nonconsanguineous

CasePMIDs 29449551

Case#: KMP 11, female, 57 yrs, East Slovakia

DiseaseAssertion: HCM

FamilyInfo: yes

CasePresentingHPOs: n/a

CaseHPOFreeText: symptomatic; LVEF 60%; NYHA I.; ECG; echocardiography;

CaseNotHPOs: n/a

CaseNotHPOFreeText: no LVOTO; no ICD

CasePreviousTesting: Additional Sanger sequencing of exons 12, 24, 25 of MYBPC3, exon 12 NEBL, exons 12, 20, 21 of SCN5A, exon 7 of TNNI3, and exon 9 of TNNT2 gene

CaseGenotypingMethod: Sanger sequencing;

Variant: NM_000257.4(MYH7):c.2845G>A (p.Glu949Lys)

ClinVar: 14093 https://www.ncbi.nlm.nih.gov/clinvar/variation/14093/

CAID: n/a

gnomAD: absent

Case1: Female, Italy, Birth onset

CasePresentingHPOs: HP:0003798, HP:0002033, HP:0100703, HP:0000218, HP:0000689, HP:0000297, HP:0003325 (Nemaline bodies, Poor suck, Tongue thrusting, High-arched palate, Dental malocclusion, Facial hypotonia, Limb-girdle muscle weakness)

HPOsFreeText: N/A

CaseNotHPOs: HP:0003560, HP:0003715, HP:0001557, HP:0001270, HP:0002093, HP:0001627, HP:0000602, HP:0001283, HP:0002650, HP:0003306 (Muscular dystrophy, Myofibrillar myopathy, Prenatal movement abnormality, Motor delay, Respiratory impairment, Cardiac abnormality, Ophthalmoplegia, Bulbar palsy, Scoliosis, Spinal rigidity)

NotHPOsFreeText: Congenital myasthenic syndromes

CaseAddInfo: Typical NM presentation, Parental segregation was confirmed

CasePreviousTesting: ACTA1, TPM2 and TPM3 mutations were ruled out via amplification and direct sequencing

CaseGenotypingMethod: Genomic DNA was extracted from peripheral blood leukocytes or fibroblasts. 183 exons of NEB, the relative introns, and the full promoter region was captured via litigation-mediated PCR and high-throughput sequencing of resulting fragments. These were then aligned and filtered for inheritance and pathogenicity. Variants were evaluated for amino acid conservation and confirmed by Sanger sequencing.

Variant1: NM_001164507.1:c.8899A>C (p.Thr2967Pro)

CAID: CA348807784 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_001271208.2%3Ac.8899A%3EC

gnomAD: Not in gnomAD

Variant2: NM_001164507.1:c.23803_23806del (p.Arg7935Serfs*48)

CAID: CA758865527 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_001271208.2%3Ac.23908_23911del

gnomAD: Not in gnomAD

Case: Cecconi_Patient#903, female, 52 yrs old at onset of HCM

CasePresentingHPOs:

CasePresentingHPOsFreeText: In adults, a maximal LV wall thickness (LVWT) ≥15 mm; the maximal LVWT between 10 and 14 mm, in conjunction with other features (i.e., family history, electrocardiogram abnormalities) prompted the diagnosis of borderline HCM.

CaseNOTHPOs:

CaseNOTHPOSFreeText:

CasePreviousTesting: The clinical diagnosis of primary HCM was based on medical history, a physical examination and on the echocardiographic demonstration of a hypertrophied left ventricle (LV) that could not be explained by another cardiac or systemic disease.

CaseGenotypingMethod: NGS, Sanger Targeted NGS panel to simultaneously analyze a total of 19 genes encoding not only TTm proteins, but also other sarcomeric proteins and some non-sarcomeric proteins that cause HCM phenocopies. Sanger sequencing to ensure a depth of coverage >20X for each target nucleotide.

Variant: c.488T>C p.(Leu163Ser)

ClinVarID: or CAID: 45784, CA282614

gnomAD: MAF=0.001724 in African/African Americans (43/24948 alleles), total allele frequency=0.0001521. No homozygotes. v2.1.1

AddCaseInfo: Pt has LVWT of 18, LVEF of 59%, and other medical issues (myasthenia gravis, T2DM, HepC, PVC, PACs, PSVT, and SND

PreviouslyPublished: no

VariantEvidence: none

Case: Zampieri SD1, Male

DiseaseAssertion: Sandhoff Disease

FamilyInfo: patient's genotype was confirmed in parents

CasePresentingHPOs: HP:0000007, HP:0033978

CaseHPOFreeText: neurological symptoms (unspecified)

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: Patients presented with neurological symptoms and diagnosis was confirmed by the demonstration of reduced Hex A and Hex B activity in peripheral white blood cells or cultured fibroblasts.

GenotypingMethod: PCR

PreviouslyPublished: n/a

SupplementalData: n/a

Variant: c.534delAGTT (p.L178fs27X) in both alleles

CAID: CA560766108

gnomAD: MAF 0.000008937, European (non-Finnish), gnomAD variant ID: 5-73992535-CAGTT-C

VariantEvidence: PMID:11292324 previously reported this variant to be associated with the infantile form of SD. Genomic DNA amplification, heteroduplex analysis, cloning and sequencing revealed a 4-bp deletion in exon 4 at position 178. The result is a frameshift mutation that leads to a stop codon in exon 5. This mutation is associated with a dramatic decrease of HEXB mRNA levels.

Annotating here since the article is a PDF.

Case#: Lin ERT Proband, 3yo at dx, male, Taiwan

DiseaseAssertion: MPS1 H/S

FamilyInfo:

CasePresentingHPOs: HP:0002094, HP:0030828, HP:0002870, HP:0001640, HP:0001712, HP:0005133, HP:0001654, HP:0005145, HP:0008155, HP:0002653, HP:0002829, HP:0001376, HP:0002751, HP:0004348, HP:0007957, HP:0007663, HP:0002167, HP:0032341, HP:0410042

CaseHPOFreeText: Positive urine MPS screening test, blood IDUA activity=0.4 umol/h per mg protein (normal range 10-35). ERT improved cardiopulmonary status, joint range of motion, mobility, bone and joint pain, kyphoscoliosis, bone mineral density, sleep quality, corneal clouding and visual acuity, speech fluency, forced vital capacity and liver size, and resulted in 80.2% reduction in urinary GAG excretion. Cardiopulmonary failure

CaseNotHPOs:

CaseNotHPOFreeText:

PreviouslyPublished: n/a

Variant: T364M homozygous

ClinVar: 11925

CAID: CA256126

SupplementalData: n/a

Case# HondaF, female, newborn

CasePresentingHPOs HP:0001640, HP:0006682, HP:0011713, HP:0100572

CaseGenotypingMethod "gene analysis"

Variant NC_000003.10:g.14147425G>A

CAID CA052413

gnomAD 0.001044 link

CaseAddInfo 2 mutations in cis from mom, phenotypes described at birth (usually adult onset)

Case: Family C/Prendiville Patient 2, Lebanese-Australian, 11yo at report

Not scoring this proband since this variant has been reported many times already and parents are consanguineous, from Lebanon which is near many of the other cases

Case# II-4, Female, 14, Ireland

CasePresentingHPOs HP:0002506, HP:0002497, HP:0002061, HP:0011448, HP:0001347

CasePreviousTesting Initial genetic testing (with patient consent) included a screening panel for HSP, as well as SCA 1, 2, 3 and 6, all of which were negative.

CaseMethod1 WES

Variant NM_005186.3:c.1534C>T(p.Arg512Cys)

CAID CA6093457

gnomAD 0.000008977

Case# Travaglini 1, Male, 16 report, Italian

CasePresentingHPOs HP:0006895, HP:0040083, HP:0001347, HP:0003487

CasePreviousTesting Sanger of SPG4 and 89 other known/candid genes by Nextera Custom Enrichment panel

CaseMethod1 Sanger Sequencing

CaseGenotypingMethod CAPN1 variants found in same panel screen

Variant NM_005186.3:c.221G>A (p.G74D), NM_005186.3:c.911C>T(p.T304M), NM_005186.3:c.1418G>T (p.R473L)

CAID CA6092976, CA6093221, CA6093432

gnomAD 0.0006904 , 0.0003415, 0.00003952

CaseAddInfo nonconsanguineous family

Case4: Male, Spain, Post-birth onset

CasePresentingHPOs: HP:0003798, HP:0001324, HP:0000297, HP:0003701, HP:0001252, HP:0001284, HP:0002307, HP:0000218, HP:0001382 (Nemaline bodies, Muscle weakness, Facial hypotonia, Proximal muscle weakness, Muscular hypotonia, Areflexia, Drooling, High palate, Joint hypermobility)

HPOsFreeText: Cephalic support, Sedestation

CaseNotHPOs: HP:0000602, HP:0001249, HP:0001627, HP:0002093, HP:0002307, HP:0003722, HP:0002460, HP:0001283, HP:0002650, HP:0002540, HP:0006466, HP:0011471 (Ophthalmoplegia, Intellectual disability, cardiac abnormality, Ankle contracture, Drooling, Neck flexor weakness, Distal muscle weakness, Bulbar palsy, Respiratory insufficiency, Inability to walk, Scoliosis, PEG-fed in infancy)

NotHPOsFreeText: Bimodal communication, Wheelchair dependence, Mechanic ventilation

CaseAddInfo: Typical variant, Paternity/maternity was confirmed, cDNA analysis confirmed that Variant 1 results in a splice-site donor mutation which skips exon 24 which was confirmed by Sanger sequencing and leads to this deletion: p.His738_Asp770del (c.2212_2310del)

CasePreviousTesting: N/A

CaseGenotypingMethod: A research panel with 751 genes relating to neurological disorders, including the coding and intronic flanking regions of ACTA1, CFL2, KBTBD13, NEB, TNNT1, TNNT3, TPM2 and TPM3, was used to locate any variants in the proband. These variants were then prioritized and confirmed by Sanger sequencing in the probands and their relatives.

Variant1: NM_001164507.1:c.2310+5G>A (p.=)

CAID: CA913203562 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913203562

gnomAD: Not in gnomAD

Variant2: NM_001164507.1:c.17779_17780del (p.Tyr5927Hisfs*17)

CAID: CA913203561 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913203561

gnomAD: Not in gnomAD

Case: TTD218UT

Demographics: Female, 1.5 years at diagnosis. Moroccan origin.

CasePresentingHPOs: HP:0004779, HP:0045055, HP:0008064, HP:0000252, HP:0001263, HP:0004322, HP:0001935, HP:0004840, HP:0040082, HP:0100025

Individual showed recurrent aggravation of hair-loss by tufted breakage at the scalp boundary immediately following episodes of infection-induced fever, and upon long-term exposure to the heat of the sun, she appears to have increased hair-loss. She had an IQ of 54 (at 7 years) and limited physical endurance.

CaseNOTHPOs: Progressive deterioration at 8 years

CasePreviousTesting: None

CaseGenotypingMethod: Whole genome sequencing, confirmed by Sanger sequencing.

Variant: NM_002095.5(GTF2E2):c.C559T [p.Asp187Tyr]

ClinVar ID: 225841

Pathogenic, non-LOF variant gnomAD: hypomorphic, homozygous missense. Not in gnomAD.

AddCaseInfo: The parents of this individual were consanguineous and were heterozygous for the mutation. Of 3 siblings, two (a brother and a sister) were found to be heterozygous carriers, while one was found to have the homozygous wild type alleles (a sister).

VariantEvidence: The variant has been previously reported by Kauschal et al (26996949) in a 16-yr old Moroccan girl. The identification of this variant in four individuals of Moroccan origin suggests the possibility of a founder mutation. Since the variant has been already scored, this proband is not being scored.

Case: Family 11 GC21390 Proband II:1, 49yo at onset (incidental finding), 56yo at report

CasePresentingHPOs:

CasePresentingHPOsFreeText: Prolonged dark adaptation, peripheral visual field loss, BCVA= 6/9, 6/5, retinitis pigmentosa, hypertension, plasma coQ10 level=582.28nmol/L (Reference range: 227- 1432 nmol/L)

CaseNOTHPOs:

CaseNOTHPOSFreeText:

CasePreviousTesting: negative IRD gene panel analysis

CaseGenotypingMethod: genome sequencing, direct Sanger

Variant: c.933delC p.(Tyr311); c.682-7 T > G p.(Gln230); p.(Leu193Phefs*27)

ClinVarID: or CAID: CA6828694; CA6828747

gnomAD: This nonsense variant, Tyr311Ter in exon 7/7, is present in gnomAD v4.1.0 with a MAF=0.00002627 (31/1179996 alleles) in the European NF population with 0 homozygotes. The score has been reduced since NMD is not expected to occur.

This non-canonical splice site variant, c.682-7T>G, is present in gnomAD v4.1.0 with a MAF=0.001031 (66/64040 alleles) in the European Finnish population with 0 homozygotes.

AddCaseInfo: only family member noted to be affected, mother was unaffected and heterozygous for tyr311ter but father is deceased and not genotyped

PreviouslyPublished: n/a

VariantEvidence: RT-PCR of patient blood derived mRNA using oligonucleotide primers targeting COQ5 (Supplementary Table 6) followed by agarose gel electrophoresis showed definite altered transcript length and mis-splicing for the COQ5 c.682-7 T > G variant. ONT sequencing of the full COQ5 transcript from whole blood of individual family 11, II:1 showed skipping of exon 5 to be the predominant effect of the c.682-7 T > G variant leading to early termination and probable nonsense-mediated decay (p.(Gln230)) (Fig. ​(Fig.4).4). In addition, exon 4–5 skipping was identified in a low proportion of reads (3%) leading to a reading-frame shift and early termination (p.(Leu193Phefs27)).

Case# Baskin RW, Female, 31

CasePresentingHPOs HP:0004756, HP:0011841, HP:0002013

CasePreviousTesting patients referred to our high-risk hereditary heart disorders clinic for assessment of possible ARVC, as well as DNA-bearing blood or tissue samples sent for clinical ARVC gene-testing from other physicians, clinics or institutions to our CLIA-approved molecular genetics laboratory at the Hospital for Sick Children (listed on www.genetests.org).

CaseMethod1 PCR

CaseGenotypingMethod direct sequence analysis of all exons and flanking intron sequences of DSP (MIM 125647), PKP2 (MIM 602861), DSC2 (MIM 125645), DSG2 (MIM 125671) and TMEM43.

Variant NM_024334.2(TMEM43):c.934C>T (p.Arg312Trp)

ClinVar 36873

gnomAD 0.03553 link

This variant was found in homozygosity in patient #184 from Uzbekistan. The maximum point total for homozygosity has already been reached for this variant.

Case#: Hadalin_2021_Family_1_Patient_III-1, male, 31 years old at first examination, family origin in Slovenia

CasePresentingHPOs: HP:0011463 (Childhood onset), HP:0000545 (Myopia), HP:0008020 (Cone dystrophy), HP:0007663 (Reduced visual acuity), HP:0012230 (Rhegmatogenous retinal detachment), HP:0000603 (Central scotoma), HP:0007814 (Retinal pigment epithelial mottling), HP:0008043 (Retinal arteriolar constriction), HP:0000543 (Optic disc pallor), HP:0030602 (Abnormal fundus autofluorescence imaging), HP:0200070 (Peripheral retinal atrophy), HP:0030465 (Undetectable light-adapted electroretinogram), HP:0000613 (Photophobia), HP:0011504 (Bull's eye maculopathy), HP:0007737 (Bone spicule pigmentation of the retina),

CaseHPOFreeText: The patient received a diagnosis of cone dystrophy. Myopia was present from childhood, while visual loss occurred in the early 30's.

CaseNotHPOs: N/A

CaseNotHPOFreeText: Dark-adapted ERG was normal at the time of the study.

CasePreviousTesting: The patient and an apparently unrelated proband from another family were subjected to whole-exome sequencing.

CaseMethod1: Whole-exome sequencing

CaseMethod2: Haplotype analysis using SNPs on the X chromosome

CaseGenotypingMethod: The patient and a proband from another family not known to be related were subjected to whole-exome sequencing, followed by haplotype analysis using SNPs on the X chromosome.

Variant: The patient harbors the NM_001034853.2(RPGR):c.3457T>A (p.Ter1153Lys) variant in the hemizygous state.

ClinVar: 931960

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

VariantEvidence: NM_001034853.2(RPGR):c.3457T>A (p.Ter1153Lys) is a stop-loss variant that triggers an extension of the C-terminus of RPGR by 38 amino acids. It is not predicted to undergo nonsense-mediated decay, and its inheritance pattern with largely unaffected female carriers is consistent with loss-of-function.

CaseAddInfo: The proband is a member of Family 1, with the mother being a female carrier with mild myopia, and an apparently affected maternal grandfather. Two other patients not known to be close relatives but harboring the same founder variant within a 29-megabase shared region received the same diagnosis of cone dystrophy.

CasePMIDs: N/A

Case#: Jespersgaard_2019_Patient_165, gender and age not specified, origin likely to be Danish based on cohort

CasePresentingHPOs: N/A

CaseHPOFreeText: The proband has been diagnosed with retinitis pigmentosa, as part of a larger group of generalized non-syndromic retinal dystrophies. Detailed phenotypes are not described.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Next-generation sequencing was performed focusing on a targeted panel of 125 genes known to be linked to inherited retinal disease.

CaseMethod1: NGS panel

CaseMethod2: N/A

CaseGenotypingMethod: Next-generation sequencing was performed focusing on a targeted panel of 125 genes known to be linked to inherited retinal disease. It is not clear whether Sanger sequencing was used to validate the genotyping of this particular case.

Variant: The proband harbors the NM_000440.3(PDE6A):c.1620+1G>A variant in the homozygous state.

ClinVar: 636054

gnomAD: The NM_000440.3(PDE6A):c.1620+1G>A variant is found in gnomAD v2.1.1 at a frequency of 0.00003267 (1/30608) in the South Asian population https://gnomad.broadinstitute.org/variant/5-149275918-C-T

VariantEvidence: The NM_000440.3(PDE6A):c.1620+1G>A variant disrupts a canonical splice site in intron 12, but does not have experimental confirmation of exon skipping or frameshift.

CaseAddInfo: N/A

CasePMIDs: N/A

Case#: Pattnaik_2015_Proband, male, age 10 years, family national origin described as Jordanian

CasePresentingHPOs: Nyctalopia HP:0000662, Childhood onset HP:0011463, Severely reduced visual acuity HP:0001141, Granular macular appearance HP:0007793, Retinal arteriolar constriction HP:0008043, Retinal degeneration HP:0000546, Abnormal choroid morphology (hypertrophy) HP:0000610

CaseHPOFreeText: The proband has been diagnosed at different times with Stargardt disease, retinitis pigmentosa, cone-rod dystrophy, and Leber congenital amaurosis, first presenting with night vision difficulties at age 2 years. Small focal sub-RPE deposits were observed.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The proband was initially genotyped by PCR-based screening for known LCA-associated variants and next-generation sequencing focused on a 19-gene LCA panel.

CaseMethod1: PCR-based screening for known LCA-associated variants as well as next-generation sequencing of a 19-gene LCA panel

CaseMethod2: Sanger sequencing of gaps and low-coverage regions as well as for confirmation of the variants detected by other methods.

CaseGenotypingMethod: The proband was initially genotyped by PCR-based screening for known LCA-associated variants and next-generation sequencing focused on a 19-gene LCA panel. Sanger sequencing of gaps and low-coverage regions as well as for confirmation of the variants detected by other methods.

Variant: The individual is homozygous for the NM_002242.4(KCNJ13):c.158G>A (p.Trp53Ter) variant.

ClinVar: 224857

gnomAD: The variant is not found in gnomAD version 4.1.0.

VariantEvidence: Heterologous expression of the NM_002242.4(KCNJ13):c.158G>A (p.Trp53Ter) variant in CHO-K1 cells revealed that the variant channel retained very little ability to enable the flow of current, with the measurement of -68.8pA more comparable to the negative control (-42.4pA) than to the wild-type control (-588.7pA).

CaseAddInfo: The family history does not reportedly indicate consanguinity.

CasePMIDs: N/A

Case#: Pusch_2000_Familly_9606_Proband, male, age and race not mentioned

CasePresentingHPOs: HP:0030640 (Complete congenital stationary night blindness), HP:0007663 (Reduced visual acuity), HP:0031624 (Moderate myopia), HP:0007984 (Electronegative electroretinogram)

CaseHPOFreeText: ERG with absent oscillatory-potential wavelets

CaseNotHPOs: HP:0001098 (Abnormal fundus morphology), HP:0030473 (Abnormal light-adapted flicker electroretinogram)

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

CaseMethod1: Sanger sequencing of PCR amplified exons from NYX

CaseMethod2: N/A

CaseGenotypingMethod: The proband and family members were subjected to Sanger sequencing of NYX to identify the variant.

Variant: The proband harbors the NM_001378477.3(NYX):c.90C>A (p.Cys30Ter) variant on the X chromosome.

ClinVar: 11422

gnomAD: NM_001378477.3(NYX):c.90C>A (p.Cys30Ter) was not found in gnomAD.

VariantEvidence: This nonsense variant is located in exon 2/3 and is predicted to trigger NMD. It introduces a premature stop codon that would truncate 93% of the protein product.

CaseAddInfo: This variant appears not only in Family 9606, but also in Family 2438T, yet is not suspected to be a founder alelle.

CasePMIDs: N/A

Case#: Ashkenazy_2023_Proband, female, age 18 at time of report, family origin unknown due to adoption but reported in the United States

CasePresentingHPOs: Snowflake vitreoretinal degeneration HP:0011533, High myopia HP:0011003, Retinoschisis HP:0030502, Rhegmatogenous retinal detachment HP:0012230, Abnormal vitreous humor morphology HP:0004327, Full-thickness macular hole HP:0031152

CaseHPOFreeText: The patient exhibited fibrillar vitreous structure, crystalline retinopathy, and optic nerve flattening.

CaseNotHPOs: Corneal guttata HP:0012038, Presenile cataracts HP:0007819

CaseNotHPOFreeText: Perivascular sheathing was absent.

CasePreviousTesting: Genotyping of the proband was not described in detail, but reportedly did not include whole exome sequencing, due to the specificity of the phenotype. Genes implied to have been possibly examined were COL2A1, COL11A1, and CSPG2.

CaseMethod1: Sanger sequencing of KCNJ13

CaseMethod2: N/A

CaseGenotypingMethod: Genotyping of the proband was not described in detail, but reportedly did not include whole exome sequencing, due to the specificity of the phenotype. Genes implied to have been possibly examined were COL2A1, COL11A1, and CSPG2. Sanger sequencing of KCNJ13 was performed.

Variant: The individual harbors the NM_002242.4(KCNJ13):c.484C>T (p.Arg162Trp) variant in the heterozygous state.

ClinVar: 6585

gnomAD: The variant is found in gnomAD version 4.1.0 at a frequency of 0.0000008536 (1 / 1,171,470) in the European (non-Finnish) population https://gnomad.broadinstitute.org/variant/chr2-232768790-G-A?dataset=gnomad_r4

VariantEvidence:NM_002242.4(KCNJ13):c.484C>T (p.Arg162Trp) is a missense variant that has functional evidence of electrophysiological abnormalities and loss of sensitivity to different K+ concentrations, when exogenously expressed in CHO cells (PMID: 18179896, Figure 2).

CaseAddInfo: The proband may or may not be a relative of the family previously reported with the same variant in PMID: 18179896, as both appear to have received medical care in the United States.

CasePMIDs: N/A

Case#: Kelsell_1998_CORD6_Family_2_Proband, female, age 45 at time of report, nationality listed as British

CasePresentingHPOs: HP:0007401 (Macular atrophy), HP:0000548 (Cone/cone-rod dystrophy)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

CaseMethod1: Sanger sequencing of PCR products from each of the 18 exons of the GUCY2D locus

CaseMethod2: HhaI restriction digest of the PCR-amplified exon 13

CaseGenotypingMethod: The proband and her family members were subjected to sequencing of PCR products from each of the 18 exons of the GUCY2D locus. The PCR-amplified product from exon 13 was then subjected to HhaI restriction digest and resolved by agarose gel electrophoresis.

Variant: The proband harbors the NM_000180.4(GUCY2D):c.2512C>T (p.Arg838Cys) variant in the heterozygous state.

ClinVar: 9355

gnomAD: The variant is present in gnomAD at a frequency of 0.000007744 (1/129124) in the European non-Finnish population, with no homozygotes. https://gnomad.broadinstitute.org/variant/17-7918018-C-T

VariantEvidence: NM_000180.4(GUCY2D):c.2512C>T (p.Arg838Cys) is a missense variant located within the coiled-coil domain that mediates GUCY2D dimerization. Codon 838 has proven to be a hot spot disrupted in other families similarly affected with autosomal dominant cone-rod dystrophy (PMID: 11115851, PMID: 12552567, PMID: 26298565). The p.Arg838Cys substitution has been shown to disrupt the calcium sensitivity of GUCY2D and to trigger the inability to inactivate cyclase activity at high physiological calcium ion concentrations (PMID: 11115851).

CaseAddInfo: N/A

CasePMIDs: N/A

Case: Gliem_2000_Family_1_patient_II.1, female, country of origin Germany, onset at 47 years of age

DiseaseAssertion: Sorsby's fundus dystrophy

FamilyInfo: The variant was inherited by the proband rather than acquired de novo.

CasePresentingHPOs: HP:0000662 (Nyctalopia), HP:0007663 (Reduced visual acuity), HP:0011510 (Drusen), HP:0000533 (Chorioretinal atrophy)

CaseHPOFreeText: Presentation at age 47 with nyctalopia. Evaluation at age 61 showed drusen deposits in macular area, near optic disk and along vascular arcades, central and midperipheral atrophy, and reduced choroidal thickness.

CaseNOTHPOs: HP:0011506 (Choroidal neovascularization)

CaseNOTHPOFreeText: N/A

CasePreviousTesting: Phenotypic characterization only

GenotypingMethod: Sanger sequencing of PCR products from all 5 exons and flanking splice junctions of the TIMP3 gene.

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: Proband harbors the NM_000362.5(TIMP3):c.530A>G (p.Tyr177Cys) missense variant.

CAID: CA411540328

gnomAD: Variant is absent from gnomAD.

VariantEvidence: This missense variant within exon 5 of TIMP3 results in an unpaired Cys residue.

Case#: Olivier_2021_Family_K_Proband_II:3, male, age 43 years at the time of onset, national origin reported as Spanish

CasePresentingHPOs: HP:0000662 (Nyctalopia), HP:0001099 (Fundus atrophy), HP:0007737 (Bone spicule pigmentation of the retina)

CaseHPOFreeText: The proband has onset of retinitis pigmentosa at the age of 43 years.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: It is not clear whether previous testing methods included systematic genotyping of loci associated with VMD or RP.

CaseMethod1: Screening of IMPG1 using either gene panel testing or exome sequencing

CaseMethod2: Sanger sequencing-based confirmation

CaseGenotypingMethod: Genotyping is not entirely clear but has at least included panel-based analysis of the IMPG1 locus and Sanger sequencing-based confirmation.

Variant: The proband harbors the NM_001563.4(IMPG1):c.1982G>A (p.Arg661His) variant in the homozygous state.

ClinVar ID: 1056230

gnomAD: The NM_001563.4(IMPG1):c.1982G>A (p.Arg661His) variant is found in gnomAD v2.1.1 at a frequency of 0.00004006 (1/24964) in the African / African-American population, with 0 homozygotes https://gnomad.broadinstitute.org/variant/6-76657093-C-T

VariantEvidence: NM_001563.4(IMPG1):c.1982G>A (p.Arg661His) is a missense variant, which does not have experimental evidence of a functional effect on the protein product.

CaseAddInfo: The patient's affected sister shares the same homozygous genotype.

CasePMIDs: N/A

Case#: Olivier_2021_Family_H_Proband_II:1, male, age 53 years at the time of diagnosis, national origin reported as French

CasePresentingHPOs: HP:0007401 (Macular atrophy), HP:0007737 (Bone spicule pigmentation of the retina)

CaseHPOFreeText: The proband has been diagnosed with maculopathy at the age of 53 years, and exhibits retinal discoloration.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: It is not clear whether previous testing methods included systematic genotyping of loci associated with VMD or RP.

CaseMethod1: Screening of IMPG1 using either gene panel testing or exome sequencing

CaseMethod2: Sanger sequencing-based confirmation

CaseGenotypingMethod: Genotyping is not entirely clear but has at least included panel-based analysis of the IMPG1 locus and Sanger sequencing-based confirmation.

Variant: The proband harbors the NM_001563.4:c.2083G>T (p.Glu695Ter) variant in the heterozygous state.

CAID: CA364770054

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

VariantEvidence: NM_001563.4:c.2083G>T (p.Glu695Ter) is a nonsense variant in exon 15 of 17, which is predicted to trigger nonsense-mediated decay or to at least truncate the C-terminal 13% of the protein product.

CaseAddInfo: The patient's brother is an unaffected carrier of the variant.

CasePMIDs: N/A

Case#: Ebenezer_2005_Family_B_Patient_IV:11, male, age 44, family origin reported to be British

CasePresentingHPOs: HP:0003581 (Adult onset), HP:0000654 (Decreased light- and dark-adapted electroretinogram amplitude), HP:0000662 (Nyctalopia), HP:0007663 (Reduced visual acuity), HP:0000613 (Photophobia), HP:0000545 (Myopia), HP:0000483 (Astigmatism), HP:0007803 (Monochromacy), HP:0007722 (Retinal pigment epithelial atrophy), HP:0025159 (Hypoautofluorescent retinal lesion), HP:0007814 (Retinal pigment epithelial mottling)

CaseHPOFreeText: The proband has been diagnosed with progressive retinal degeneration / cone-rod dystrophy, with the family exhibiting an X-linked pattern of inheritance.

CaseNotHPOs: HP:0000639 (Nystagmus)

CaseNotHPOFreeText: N/A

CasePreviousTesting: The proband and family members were not genotyped outside of the RPGR locus.

CaseMethod1: Sanger sequencing of exon 15 of RPGR

CaseMethod2: N/A

CaseGenotypingMethod: The proband and family members were genotyped by Sanger sequencing of exon 15 of RPGR, but not by genome-wide methods.

Variant: The proband harbors the NM_001034853.2(RPGR):c.2929G>T (p.Gly977Ter) variant in the hemizygous state.

ClinVar: 9918

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

VariantEvidence: NM_001034853.2(RPGR):c.2929G>T (p.Gly977Ter) is a nonsense variant in the final exon (exon 15) that is not predicted to trigger nonsense-mediated decay, but disrupts ~15% of the C-terminus of the protein product.

CaseAddInfo: The proband is a member of Family B (shown in Figure 1), which includes four other affected genotype-positive males and as well as four carrier females who showed reduced visual acuity and golden tapetal reflex.

CasePMIDs: N/A

Case#: Ebenezer_2005_Family_A_Patient_III.4, male, age not specified, family origin reported to be British

CasePresentingHPOs: HP:0025710 (Late young adult onset), HP:0000662 (Nyctalopia), HP:0007663 (Reduced visual acuity), HP:0000613 (Photophobia), HP:0007803 (Monochromacy), HP:0031624 (Moderate myopia), HP:0001103 (Abnormal macular morphology), HP:0000533 (Chorioretinal atrophy), HP:0500087 (Peripapillary atrophy), HP:0025159 (Hypoautofluorescent retinal lesion), HP:0030844 (Undetectable pattern electroretinogram), HP:0000654 (Decreased light- and dark-adapted electroretinogram amplitude)

CaseHPOFreeText: The proband has been diagnosed with retinitis pigmentosa, with the family exhibiting an X-linked pattern of inheritance. Cone ERG was more severely reduced than rod ERG.

CaseNotHPOs: HP:0007769 (Peripheral retinal degeneration), HP:0000639 (Nystagmus)

CaseNotHPOFreeText: N/A

CasePreviousTesting: The proband and family members were not genotyped outside of the RPGR locus.

CaseMethod1: Sanger sequencing of exon 15 of RPGR

CaseMethod2: N/A

CaseGenotypingMethod: The proband and family members were genotyped by Sanger sequencing of exon 15 of RPGR, but not by genome-wide methods.

Variant: The proband harbors the NM_001034853.2(RPGR):c.2847_2848inv (p.Glu949_Glu950delinsAspTer) variant in the hemizygous state.

ClinVar: 9917

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

VariantEvidence: NM_001034853.2(RPGR):c.2847_2848inv (p.Glu949_Glu950delinsAspTer) is an indel in the final exon (exon 15) that introduces a premature stop codon. Although it is not predicted to trigger nonsense-mediated decay, it at least disrupts ~18% of the C-terminus of the protein product.

CaseAddInfo: The proband is a member of Family A (shown in Figure 1), which includes four other affected genotype-positive males and four carrier females who showed RPE abnormalities.

CasePMIDs: N/A

Case#: Georgiou_2024_Family_JP01_Proband_P12, male, reported at age 6 years, family origin reported as from Japan

CasePresentingHPOs: HP:0011003 (High myopia), HP:0030558 (Best corrected visual acuity 0.5 LogMAR)

CaseHPOFreeText: BCVA began at 0.20 logMAR and progressed to 0.57 logMAR.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Previous genotyping was by either next-generation sequencing panel, whole exome sequencing, or whole genome sequencing, but was unspecified.

CaseMethod1: NGS panel / WES / WGS

CaseMethod2: Sanger sequencing of RBP3

CaseGenotypingMethod: Previous genotyping by either next-generation sequencing panel, whole exome sequencing, or whole genome sequencing was followed by Sanger sequencing of RBP3.

Variant: The individual harbors the NM_002900.3(RBP3):c.632G>A (p.Trp211Ter) and NM_002900.3(RBP3):c.345_349del (p.Trp116AlafsTer7) variants in the compound heterozygous state.

ClinVar ID: 838965

CAID CA2953902720

gnomAD: The NM_002900.3(RBP3):c.345_349del (p.Trp116AlafsTer7) variant was not found in gnomAD version 4.1.1. The NM_002900.3(RBP3):c.632G>A (p.Trp211Ter) variant is found in gnomAD version 4.1.1 at a frequency of 0.00008913 (4 / 44878) in the East Asian population https://gnomad.broadinstitute.org/variant/chr10-47349116-G-A?dataset=gnomad_r4

VariantEvidence: NM_002900.3(RBP3):c.632G>A (p.Trp211Ter) is a nonsense variant within exon 1 of 4 that is predicted to trigger nonsense-mediated decay. NM_002900.3(RBP3):c.345_349del (p.Trp116AlafsTer7) is a frameshift variant within exon 1 of 4 that is predicted to trigger nonsense-mediated decay.

CaseAddInfo: Potential consanguinity within the proband's family has not been commented on.

CasePMIDs: N/A

Case#: Georgiou_2024_Family_NY01_Proband_P10, female, reported at age 56 years, family origin not reported

CasePresentingHPOs: HP:0011003 (High myopia), HP:0030558 (Best corrected visual acuity 0.5 LogMAR), HP:0000518 (Cataract)

CaseHPOFreeText: BCVA began at 0.51 logMAR and progressed to 0.54 logMAR. The proband had posterior chamber intraocular lenses. Myopia developed by age 7 years.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Previous genotyping was by either next-generation sequencing panel, whole exome sequencing, or whole genome sequencing, but was unspecified.

CaseMethod1: NGS panel / WES / WGS

CaseMethod2: Sanger sequencing of RBP3

CaseGenotypingMethod: Previous genotyping by either next-generation sequencing panel, whole exome sequencing, or whole genome sequencing was followed by Sanger sequencing of RBP3.

Variant: The individual harbors the NM_002900.3(RBP3):c.2824C>T (p.Gln942Ter) variant in the homozygous state.

ClinVar ID: 1069291

gnomAD: The variant is found in gnomAD version 4.1.1 at a frequency of 0.00001332 (1 / 75072) in the African / African-American population https://gnomad.broadinstitute.org/variant/chr10-47351308-C-T?dataset=gnomad_r4

VariantEvidence: NM_002900.3(RBP3):c.2824C>T (p.Gln942Ter) is a nonsense variant within exon 1 of 4 that is predicted to trigger nonsense-mediated decay.

CaseAddInfo: Potential consanguinity within the proband's family and their geographic origin have not been commented on.

CasePMIDs: N/A

Case

Case#: Meindl_1996_Family_F50_Proband, male, age not specified, family origin either German or British

CasePresentingHPOs: HP:0000510 (Rod-cone dystrophy)

CaseHPOFreeText: The proband has been diagnosed with retinitis pigmentosa. Disease onset was reported as early.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The family members previously underwent linkage analysis to map the underlying genetic cause to the region on chromosome Xp21.1 between the CYBB and OTC genes.

CaseMethod1: Hybridization analysis of amplified cDNA fragments from the RPGR locus to look for deletions, and SSCP analysis to look for point mutations

CaseMethod2: Sanger sequencing of the RPGR locus

CaseGenotypingMethod: The family members previously underwent linkage analysis to map the underlying genetic cause to the region on chromosome Xp21.1 between the CYBB and OTC genes. Amplified cDNA fragments from the RPGR locus were then screened by hybridization analysis to look for deletions and SSCP analysis to look for point mutations. The presence of the variant was confirmed by Sanger sequencing of the RPGR locus.

Variant: The affected family members harbor the NM_001034853.2(RPGR):c.581G>A (p.Trp194Ter) variant in the hemizygous state.

ClinVar: 98790

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

VariantEvidence: NM_001034853.2(RPGR):c.581G>A (p.Trp194Ter) is a nonsense variant predicted to trigger nonsense-mediated decay or to at least disrupt the C-terminal 76% of the protein product.

CaseAddInfo: The proband is a member of Family F50.

CasePMIDs: N/A

Case#: Gupta_2021_Proband_1, female, age 25 years at time of report, ethnic origin not reported

CasePresentingHPOs: HP:0000575 (Scotoma), HP:0007663 (Reduced visual acuity), HP:0030500 (Yellow/white lesions of the macula, specifically small foveal yellow spots), HP:0030627 (Foveal hyporeflective spaces on macular OCT), HP:0008323 (Abnormal light- and dark-adapted electroretinogram, specifically reduced response in the center of one retina)

CaseHPOFreeText: The patient has been diagnosed with foveomacular vitelliform dystrophy with adult onset.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Previous testing appears to have included genotyping of the

CaseMethod1:

CaseMethod2:

CaseGenotypingMethod: Genotyping appears to have included

Variant: The proband harbors the NM_001563.4(IMPG1):c.461T>C (p.Leu154Pro) variant in the heterozygous state.

ClinVar: 162136

gnomAD: This variant was found in gnomAD v2.1.1 at a frequency of 0.00007924 (9/113576) in the European non-Finnish population, with 0 homozygotes https://gnomad.broadinstitute.org/variant/6-76744345-A-G

VariantEvidence: NM_001563.4(IMPG1):c.461T>C (p.Leu154Pro) is a missense variant that does not have evidence confirming an impact on the gene product. However, another study has reported apparently unrelated affected patients harboring this variant in the compound heterozygous state (PMID: 23993198), in trans with the NM_001563.4(IMPG1):c.1519C>T (p.Arg507Ter) variant.

CaseAddInfo: The variant is paternally inherited in this case, and the patient's father has been diagnosed with central serous chorioretinopathy but lacks other features of vitelliform macular dystrophy. This indicates that central serous chorioretinopathy is part of the spectrum of monoallelic disease.

CasePMIDs: N/A

Case#: Qin_2005_patient_8, female, age 14 years at report, national origin reported as Japanese

CasePresentingHPOs: HP:0001103 (Abnormal macular morphology), HP:0004349 (Reduced bone mineral density), HP:0003621 (Juvenile onset)

CaseHPOFreeText: The patient has been diagnosed with simplex FEVR, with bilateral dragged macula.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Genotyping appears to have been limited to the LRP5 and FZD4 loci.

CaseMethod1: Sanger sequencing of PCR-amplified exons and flanking regions of the LRP5 and FZD4 loci

CaseMethod2: N/A

CaseGenotypingMethod: Genotyping appears to have been limited to Sanger sequencing of PCR-amplified exons and flanking regions of the LRP5 and FZD4 loci.

Variant: The patient harbors the NM_002335.4(LRP5):c.804_813del (p.Gly269fs) and NM_002335.4(LRP5):c.1828G>A (p.Gly610Arg) variants in the compound heterozygous state.

ClinVar: 6295, 6294

gnomAD: The NM_002335.4(LRP5):c.804_813del (p.Gly269fs) variant was not found in gnomAD v2.1.1. The NM_002335.4(LRP5):c.1828G>A (p.Gly610Arg) variant was found in gnomAD v2.1.1 at a frequency of 0.00002644 (3/113484) in the European non-Finnish population https://gnomad.broadinstitute.org/variant/11-68174018-G-A

VariantEvidence: NM_002335.4(LRP5):c.1828G>A (p.Gly610Arg) is a missense variant in exon 9 that does not have experimental evidence of an impact on the protein product. NM_002335.4(LRP5):c.804_813del (p.Gly269fs) is a frameshift variant in exon 4 of 23 that is predicted to trigger nonsense-mediated decay or to at least disrupt the C-terminal 83% of the protein product.

CaseAddInfo: The patient has no family history of FEVR in her parents and brother, although bone mineral density was reduced in both parents. The mother is a carrier for p.Gly610Arg, while the father and brother are heterozygous for p.G268fsX272.

CasePMIDs: N/A

Case#: Harville_2010_Patient_A2885–II2, sex and age not reported, family origin reportedly from Saudi Arabia

CasePresentingHPOs: HP:0000510 (Rod-cone dystrophy), HP:0010442 (Polydactyly), HP:0001513 (Obesity), HP:0000077 (Abnormality of the kidney), HP:0001249 (Intellectual disability), HP:0004322 (Short stature), HP:0001263 (Global developmental delay), HP:0000823 (Delayed puberty)

CaseHPOFreeText: The proband has an initial clinical diagnosis of Bardet-Biedl syndrome.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The proband was initially subjected to homozygosity mapping to identify parts of the genome to search for the basis of recessive disease.

CaseMethod1: homozygosity mapping

CaseMethod2: Sanger sequencing of the exons of any of the 14 BBS-associated loci (BBS1, BBS2, ARL6, BBS4, BBS5, MKKS, BBS7, TTC8, BBS9, BBS10, TRIM32, BBS12, MKS1, and CEP290) that showed homozygosity.

CaseGenotypingMethod: The proband was initially subjected to homozygosity mapping to identify parts of the genome to search for the basis of recessive disease. This was followed by Sanger sequencing of the exons of any of the 14 BBS-associated loci (BBS1, BBS2, ARL6, BBS4, BBS5, MKKS, BBS7, TTC8, BBS9, BBS10, TRIM32, BBS12, MKS1, and CEP290) that showed homozygosity.

Variant: The proband harbors the NM_024649.5(BBS1):c.124+1G>A variant in the homozygous state.

ClinVar ID: 557428

gnomAD: The NM_024649.5(BBS1):c.124+1G>A variant was not found in gnomAD v2.1.1.

VariantEvidence: NM_024649.5(BBS1):c.124+1G>A is a canonical splice site variant in intron 2 that is predicted but not confirmed to disrupt BBS1 splicing.

CaseAddInfo: The proband's family is reportedly consanguineous and includes a similarly affected sibling sharing the same homozygous genotype.

CasePMIDs: N/A

Case#: Lebrun_2009_Patient_2, male, age 2-3 at onset, age 15 at death, family ethnicity reported as Afghan

CasePresentingHPOs: HP:0001251 (Ataxia), HP:0002474 (Expressive language delay), HP:0001250 (Seizure), HP:0011463 (Childhood onset), HP:0011421 (Death in adolescence)

CaseHPOFreeText: Onset was at age 2-3, with the first presenting phenotypes being ataxia and delay in speech development. Seizures began at age 4. Death occurred at age 15.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The extent of previous testing within this patient is unclear.

CaseMethod1: N/A

CaseMethod2: N/A

CaseGenotypingMethod: CLN5 mRNA was reverse transcribed, PCR-amplified, and subjected to Sanger sequencing. This process was performed for both affected and control individuals (parents).

Variant: The patient is homozygous for the NM_006493.4(CLN5):c.990G>T (p.Trp330Cys) variant, (although this variant is referred to in the article as c.1137G>T (p.Trp379Cys)).

ClinVar: 56530

gnomAD: The variant is reported to have a maximum allele frequency of 0.00006484 (in the European non-Finnish population, with no homozygous individuals). https://gnomad.broadinstitute.org/variant/13-77575017-G-T

VariantEvidence: The missense variant introduces an additional cysteine into the protein product, potentially disrupting folding and three-dimensional structure. Immunofluorescent detection of the exogenously expressed variant in COS7 cells shows aberrant localization to the ER in contrast to the wild-type localization to the lysosome (Figure 3).

CaseAddInfo: The patient's family is consanguineous, as parents are described as first degree cousins. Parents were heterozygous for the variant. Family relationships between individuals were verified.

CasePMIDs: N/A

Case#: Lebrun_2009_Patient_1, male, age 5 at onset, U.K. origin with family ethnicity reported as Pakistani

CasePresentingHPOs: HP:0007010 (Poor fine motor coordination), HP:0007015 (Poor gross motor coordination), HP:0100952 (Enlarged sylvian cistern), HP:0001251 (Ataxia), HP:0001250 (Seizure), HP:0002465 (Poor speech), HP:0007064 (Progressive language deterioration), HP:0011463 (Childhood onset), HP:0000572 (Visual loss), HP:0030511 (Bradyopsia), HP:0000550 (Undetectable electroretinogram), HP:0003208 (Fingerprint intracellular accumulation of autofluorescent lipopigment storage material), HP:0002120 (Cerebral cortical atrophy), HP:0001272 (Cerebellar atrophy)

CaseHPOFreeText: Onset was at age 5, with the first presenting phenotypes being motor problems. Marked cerebellar sulcal widening with subarachnoidal space expansion was seen by brain MRI at age 5. Ataxia and language degradation were observed at age 6. Cortical and cerebellar atrophy presented by brain MRI scan at age 7. Visual problems presented at age 7.5, specifically with inability to focus on moving objects. Seizures first presented at age 8.5, along with bilaterally extinguished ERG. Skin biopsy showed fingerprint-type intralysosomal inclusions.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Genome-wide methods were not initially used, as clinical phenotypes were consistent with diagnosis of neuronal ceroid lipofuscinosis (NCL). Enzymatic tests ruled out defects in the CLN1, CLN2, and CLN10 loci, while CLN3, CLN6, and CLN8 defects were ruled out by Sanger sequencing of the coding regions. SNP array-based homozygosity mapping was performed, revealing 7 homozygous candidate regions in the affected members from the (consanguineous) family. These regions were analyzed for candidate NCL genes, finding CLN5 as the most likely locus to harbor the causative variant.

CaseMethod1: SNP array-based homozygosity mapping was performed, revealing 7 homozygous candidate regions in the affected members from the (consanguineous) family. These regions were analyzed for candidate NCL genes, finding CLN5 as the most likely candidate for further genotyping.

CaseMethod2: N/A

CaseGenotypingMethod: CLN5 mRNA was reverse transcribed, PCR-amplified, and subjected to Sanger sequencing. This process was performed for both affected and control individuals (parents and unaffected sibling).

Variant: Patient is homozygous for NM_006493.4(CLN5):c.924_925del (p.Leu309fs), (although this variant is referred to in the article as c.1072_1073delTT (p.Leu358AlafsX4)).

ClinVar: 56526

gnomAD: The variant is reported to have a maximum allele frequency of 0.0002603 (in the Latino / Admixed American population, with no homozygous individuals). https://gnomad.broadinstitute.org/variant/13-77574801-AAT-A

VariantEvidence: The frameshift variant results in premature truncation and disrupts approximately 14% of the protein product at the C-terminus. Immunofluorescent detection of the exogenously expressed variant in COS7 cells shows aberrant localization to the ER in contrast to the wild-type localization to the lysosome (Figure 3).

CaseAddInfo: The patient's family has some degree of consanguinity, as parents are described as distantly related. Parents were heterozygous for the variant. Family relationships between individuals were verified.

CasePMIDs: N/A

Case#: Wang_2013_Proband_741, female, age 30 years at time of report, family origin not reported

CasePresentingHPOs: Retinal dystrophy HP:0000556, Attenuation of retinal blood vessels HP:0007843, Retinal pigment epithelial mottling HP:0007814, Patchy atrophy of the retinal pigment epithelium HP:0007791, Abnormality of macular pigmentation HP:0008002, Perifoveal ring of hyperautofluorescence HP:0030629, Abnormal retinal morphology on macular OCT HP:0030612, Mildly reduced visual acuity HP:0032037, Subretinal deposits HP:0031528

CaseHPOFreeText: The proband has a diagnosis of juvenile retinitis pigmentosa.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The proband was subjected to capture-based next-generation sequencing panel that included 163 known retinal disease genes.

CaseMethod1: next-generation sequencing panel

CaseMethod2: SNP array and Sanger sequencing of PRPH2

CaseGenotypingMethod: The proband was genotyped by capture-based next-generation sequencing panel that included 163 known retinal disease genes. Sanger sequencing of PRPH2 was subsequently used to confirm the presence of the variant.

Variant: The proband harbors the NM_000322.5(PRPH2):c.554T>C (p.Leu185Pro) variant in the homozygous state.

ClinVar ID: 13165

gnomAD: The NM_000322.5(PRPH2):c.554T>C (p.Leu185Pro) variant is found in gnomAD v4.0.0 at a frequency of 0.00003587 in the European (non-Finnish) population, with 15 alleles / 418142 total alleles (0 homozygotes) https://gnomad.broadinstitute.org/variant/6-42721781-A-G?dataset=gnomad_r4

VariantEvidence: NM_000322.5(PRPH2):c.554T>C (p.Leu185Pro) is a missense variant with mouse knock-in evidence of a disease-causing effect in the heterozygous state (PMID: 11427722). Mouse phenotypes from PMID: 11427722 included reduced amplitude of dark-adapted bright flash electroretinogram a-wave HP:0030483 (Figure 4), Reduced OCT-measured macular thickness HP:0030607 (Figure 2), and immunoblot analysis showing reduced L185P in retinas, indicating instability or reduced transport to the outer segment (Figure 5b). Other experiments from PMID: 11297544 showed that the p.Leu185Pro variant successfully forms dimers but fails to assemble into higher order oligomers, particularly in the absence of wild-type PRPH2 (Figures 3, 5).

CaseAddInfo: The proband's parents are each heterozygous carriers of the variant who appear to be sub-clinically affected. The 56-year-old father showed macular pattern dystrophy with clear foveal changes, but normal visual acuity.

CasePMIDs: N/A

Case#: Sergouniotis_2011_Proband_B-3, male, age 33 years, family ethnic origin described as European

CasePresentingHPOs: Reduced visual acuity HP:0007663, Constriction of peripheral visual field HP:0001133, Infantile onset HP:0003593, Strabismus HP:0000486, Nystagmus HP:0000639, Progressive night blindness HP:0007675, Moderate myopia HP:0031624, Decreased light- and dark-adapted electroretinogram amplitude HP:0000654, Presenile cataracts HP:0007819, Nummular pigmentation of the fundus HP:0030505, Retinal pigment epithelial loss on macular OCT HP:0030611

CaseHPOFreeText: The proband received a diagnosis of Leber congenital amaurosis. His phenotype is described as similar to the other affected individuals, including "a distinct and unusual retinal appearance and a similar early onset of visual loss, suggesting both impaired retinal development and progressive retinal degeneration, involving both rod and cone pathways". The disease was described as mildly progressive. OCT showed distorted retinal microanatomy even in areas without cell death, possibly indicating disturbance of the early development of the neurosensory retina.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The proband was previously genotyped by screening for previously-reported LCA-causing variants by microarray chip, with no molecular diagnosis.

CaseMethod1: screening for previously-reported LCA-causing variants by microarray chip

CaseMethod2: Sanger sequencing of the KCNJ13 exons and intron-exon boundaries

CaseGenotypingMethod: The proband was previously genotyped by screening for previously-reported LCA-causing variants by microarray chip, with no molecular diagnosis. Sanger sequencing of the KCNJ13 exons and intron-exon boundaries was subsequently performed.

Variant: The individual is homozygous for the NM_002242.4(KCNJ13):c.722T>C (p.Leu241Pro) variant.

ClinVar: 30332

gnomAD: The variant was not found in gnomAD version 4.1.0.

VariantEvidence: NM_002242.4(KCNJ13):c.722T>C (p.Leu241Pro) is a missense variant that has no experimental evidence in this study but has separately been shown to severely decrease expression and abolish complex glycosylation of KCNJ13 (PMID: 30257863, Figure 10).

CaseAddInfo: The proband's family history is not known to include consanguinity but heterozygous parents originate from the same isolated geographic area.

CasePMIDs: N/A