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Prepair 1000+ v1.1811 PDHX Andrew Coventry gene: PDHX was added
gene: PDHX was added to Prepair 1000+. Sources: Literature
Mode of inheritance for gene: PDHX was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PDHX were set to 20002125; 34873726; 33092611; 30981218; 25087164; 22766002; 12557299; 14518830; 15303005; 16566017; 27343776
Phenotypes for gene: PDHX were set to Lacticacidemia due to PDX1 deficiency MIM#245349; Mitochondrial disease MONDO:0044970
Review for gene: PDHX was set to GREEN
Added comment: Established gene-disease association.
Clingen definitive for mitochondrial disease: "While various names have been given to the constellation of features seen in those with PDHX-related disorders, including pyruvate dehydrogenase complex deficiency or PDCD, pathogenic variants in this gene ultimately cause a primary mitochondrial disease. Therefore, the PDHX phenotype has been lumped into one disease entity according to the ClinGen Lumping and Splitting Framework."

Condition is a metabolic disorder associated with abnormal function of the mitochondria in cells, thus depriving the body of energy. Progressive neurological symptoms usually start in infancy but may be evident at birth, or in later childhood; these symptoms may include developmental delay, intermittent ataxia, poor muscle tone (hypotonia), abnormal eye movements, or seizures. Severe lethargy, poor feeding, and tachypnea (rapid breathing) commonly occur, especially during times of illness, stress, or high carbohydrate intake.

Clingen: Age of onset ranges from the first days of life to later in childhood, with some individuals living well into adulthood. Clinical features in affected individuals include neonatal lactic acidosis, LSS, seizures, spasticity, agenesis of the corpus callosum, cerebral atrophy, vomiting, and optic atrophy.

Note:
PDHX c.1336C>T (p.Arg446Ter) is a Roma founder variant;
c.1182+2T>C (p.Ile386SerfsTer13) is a Moroccan founder variant.
Sources: Literature
Prepair 1000+ v1.1566 SLC6A5 Andrew Coventry changed review comment from: Affected individuals cab present with neonatal hypertonia, an exaggerated startle response to tactile or acoustic stimuli, and life-threatening neonatal apnea episodes. In some cases, symptoms resolved in the first year of life (PMID: 16751771).
Well established gene-disease association, especially for bi-allelic variants, including animal model.

AD association also reported, however, limited evidence in literature for mono-allelic cause of disease.; to: Affected individuals can present with neonatal hypertonia, an exaggerated startle response to tactile or acoustic stimuli, and life-threatening neonatal apnea episodes. In some cases, symptoms resolved in the first year of life (PMID: 16751771).
Well established gene-disease association, especially for bi-allelic variants, including animal model.

AD association also reported, however, limited evidence in literature for mono-allelic cause of disease.
Prepair 1000+ v1.1459 ABCA4 Lisa Norbart reviewed gene: ABCA4: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Retinitis pigmentosa 19, MIM#601718, Retinal dystrophy, early-onset severe, MIM#248200, Stargardt disease 1, MIM#248200, Cone-rod dystrophy 3, MIM#604116; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.633 IMPG2 Andrew Coventry changed review comment from: Retinitis pigmentosa 56 - is an early-onset form of RP with progressive visual-field loss and deterioration of visual acuity. Features include night blindness, progressive visual loss, macular retinal pigment epithelium (RPE) mottling / atrophy, decreased ERG amplitudes (affecting rods more severely than cones), colour vision defect, peripheral visual field loss, central scotoma, retinal blood vessel attenuation, and/or optic disc pallor. These features are largely distinct from the vitelliform macular dystrophy phenotype (MIM#616152).
- biallelic loss-of-function consistently associates with retinitis pigmentosa, while monoallelic loss-of-function consistently associates with vitelliform macular dystrophy.
PMID: 20673862 - 2 families each with 3 affected sibs. Additional 10 index cases identified.
- Those with nonsenses showed early-onset RP, patient with missense variants had a milder maculopathy phenotype.

Further studies and evidence:
Mouse models present exhibiting RP phenotype. (PMID: 38217426 - indicates missense variants had minimal retinal pathology in mice)
Functional study present using patient derived iPS (PMID: 36206764) - confirmed LoF due to lack of expression or lack os post-translational modifications - destabilising outer segments of rods and cones.

ClinGen - curation definitive for AR RP phenotype in association with gene IMPG2, with 10 suspected disease-causing variants scored as part of their curation (five nonsense, one frameshift, one canonical splice site disruption, one in-frame exon deletion, and two missense). Variants curated were in 8 probands (PMID: 24876279, PMID: 20673862, PMID: 31264916, PMID: 34990796).

RP genes already screened for by 1000+, consider above adequate evidence to upgrade to green status for inclusion in v2.; to: Retinitis pigmentosa 56 - is an early-onset form of RP with progressive visual-field loss and deterioration of visual acuity. Features include night blindness, progressive visual loss, macular retinal pigment epithelium (RPE) mottling / atrophy, decreased ERG amplitudes (affecting rods more severely than cones), colour vision defect, peripheral visual field loss, central scotoma, retinal blood vessel attenuation, and/or optic disc pallor. These features are largely distinct from the vitelliform macular dystrophy phenotype (MIM#616152).
- biallelic loss-of-function consistently associates with retinitis pigmentosa, while monoallelic loss-of-function consistently associates with vitelliform macular dystrophy.
PMID: 20673862 - 2 families each with 3 affected sibs. Additional 10 index cases identified.
- Those with nonsenses showed early-onset RP, patient with missense variants had a milder maculopathy phenotype.

Age of onset:
PMID 34990796 - 16yo had night blindness and photophobia. Had 22y.o. sibling that was severely affected. Age of initial onset of visual symptoms said to be ~2-4 years of age.
PMID 31264916 - 8y.o. with photophobia and myopia, 4y.o. with light sensitivity. 17yo with poor vision 'since childhood', 17yo with poor vision since birth and poor night vision, 45yo with poor night vision - starting at 6yo and progressing loss of central vision.
PMID 24876279 - age of onset of patients studied: 1, 5, 6, 1, 2, 3, 2, 3, 1, 4, 1, 2, 1, 2, 6, 1, 1. Symptoms variable, including night blindness, decrease of visual acuity, loss of visual field.

Further studies and evidence:
Mouse models present exhibiting RP phenotype. (PMID: 38217426 - indicates missense variants had minimal retinal pathology in mice)
Functional study present using patient derived iPS (PMID: 36206764) - confirmed LoF due to lack of expression or lack os post-translational modifications - destabilising outer segments of rods and cones.

ClinGen - curation definitive for AR RP phenotype in association with gene IMPG2, with 10 suspected disease-causing variants scored as part of their curation (five nonsense, one frameshift, one canonical splice site disruption, one in-frame exon deletion, and two missense). Variants curated were in 8 probands (PMID: 24876279, PMID: 20673862, PMID: 31264916, PMID: 34990796).

RP genes already screened for by 1000+, consider above adequate evidence to upgrade to green status for inclusion in v2.
Prepair 1000+ v1.344 POMGNT1 Lilian Downie Added comment: Comment when marking as ready: Isolated RP presentation can start with night blindness in childhood.
Prepair 1000+ v1.324 STAR Lilian Downie Marked gene: STAR as ready
Prepair 1000+ v1.324 STAR Lilian Downie Gene: star has been classified as Green List (High Evidence).
Prepair 1000+ v1.324 STAR Lilian Downie Publications for gene: STAR were set to
Prepair 1000+ v1.322 STAR Andrew Coventry reviewed gene: STAR: Rating: GREEN; Mode of pathogenicity: None; Publications: 7892608 8634702 9326645 8948562 9097960 11061515 11297612 14764819 16968793; Phenotypes: Lipoid adrenal hyperplasia MIM#201710; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.229 DYSF Marta Cifuentes Ochoa commented on gene: DYSF: Miyoshi myopathy (MM) is the most common form of recessive distal myopathy in populations with founder mutations such as Libyan and Israeli Jewish population, Italian and Spanish populations.The typical age of onset of MM lies between 15 and 30 years

Autosomal recessive limb-girdle muscular dystrophy type 2B (LGMD2B) is a subtype of autosomal recessive limb-girdle muscular dystrophy characterized by an onset in late adolescence or early adulthood of slowly progressive, proximal weakness and atrophy of shoulder and pelvic girdle muscles. Cardiac and respiratory muscles are not involved. Hypertrophy of the calf muscles and highly elevated serum creatine kinase levels are frequently observed.

Myopathy, distal, with anterior tibial onset is a rare genetic neuromuscular disease with characteristics of a progressive muscle weakness starting in the anterior tibial muscles, later involving lower and upper limb muscles, associated with an increased serum creatine kinase levels and absence of dysferlin on muscle biopsy. Patients become wheelchair dependent.

HGNC approved symbol/name: DYSF
Is the phenotype(s) severe and onset <18yo ? ? chidhood, early adulthood to late onset
Known technical challenges? N but large‐scale copy number variants have been identified.
Gene reported in >3 independent families

Unsure due genotype/phenotype correlation and onset
Prepair 1000+ v1.9 AGL Marta Cifuentes Ochoa commented on gene: AGL: Current Treatment high-fat, high-protein and low-carbohydrate diet with cornstarch supplementation
Prepair 1000+ v1.3 STAR Seb Lunke Added phenotypes Lipoid adrenal hyperplasia, 201710 (3) for gene: STAR
Prepair 1000+ v0.0 ABCA4 Zornitza Stark gene: ABCA4 was added
gene: ABCA4 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Red
Mode of inheritance for gene: ABCA4 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: ABCA4 were set to Cone-rod dystrophy 3 MIM#604116; Stargardt disease 1 MIM#248200; Retinal dystrophy, early-onset severe MIM#248200
Prepair 1000+ v0.0 STAR Zornitza Stark gene: STAR was added
gene: STAR was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: STAR was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: STAR were set to Lipoid adrenal hyperplasia, 201710 (3)