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Prepair 1000+ v1.9 ATRX Andrew Coventry reviewed gene: ATRX: Rating: GREEN; Mode of pathogenicity: None; Publications: 16813605, 16955409, 15350606, 23681356; Phenotypes: Alpha thalassemia X-linked intellectual disability syndrome MONDO:0010519; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Prepair 1000+ v1.9 ASAH1 Lucy Spencer reviewed gene: ASAH1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Spinal muscular atrophy with progressive myoclonic epilepsy, MIM#159950, Farber lipogranulomatosis, MIM#; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.5 ADPRHL2 Zornitza Stark changed review comment from: Fourteen unrelated families reported with stress-induced childhood-onset neurodegeneration with variable ataxia and seizures (CONDSIAS), an autosomal recessive neurodegenerative disorder with onset in the first years of life following normal early development. The disorder is characterised by cyclic episodic deterioration in response to stress, such as infection or febrile illness. The severity is highly variable: some individuals develop seizures early in life that are associated with loss of developmental milestones and early sudden death in childhood, whereas others present at a later age with muscle weakness, gait ataxia, impaired speech, more subtle clinical deterioration, and cognitive decline. Neurologic involvement includes gait ataxia, cerebellar signs associated with cerebellar atrophy, generalized brain atrophy, impaired intellectual development, hearing loss, and peripheral neuropathy.

New HGNC approved name is ADPRS.; to: Fourteen unrelated families reported with stress-induced childhood-onset neurodegeneration with variable ataxia and seizures (CONDSIAS), an autosomal recessive neurodegenerative disorder with onset in the first years of life following normal early development. The disorder is characterised by cyclic episodic deterioration in response to stress, such as infection or febrile illness. The severity is highly variable: some individuals develop seizures early in life that are associated with loss of developmental milestones and early sudden death in childhood, whereas others present at a later age with muscle weakness, gait ataxia, impaired speech, more subtle clinical deterioration, and cognitive decline. Neurologic involvement includes gait ataxia, cerebellar signs associated with cerebellar atrophy, generalized brain atrophy, impaired intellectual development, hearing loss, and peripheral neuropathy.

New HGNC approved name is ADPRS.

To be upgraded to GREEN in next version of panel.
Prepair 1000+ v1.3 TF Seb Lunke Added phenotypes Atransferrinemia, 209300 (3) for gene: TF
Prepair 1000+ v1.3 TBCD Seb Lunke Added phenotypes Encephalopathy, progressive, early-onset, with brain atrophy and thin corpus callosum, 617193 (3), Autosomal recessive for gene: TBCD
Prepair 1000+ v1.3 SMN1 Seb Lunke Added phenotypes Spinal muscular atrophy-1, 253300 (3) for gene: SMN1
Prepair 1000+ v1.3 MED17 Seb Lunke Added phenotypes Microcephaly, postnatal progressive, with seizures and brain atrophy, 613668 (3) for gene: MED17
Prepair 1000+ v1.3 ITGB4 Seb Lunke Added phenotypes Epidermolysis bullosa, junctional, with pyloric atresia, 226730 (3) for gene: ITGB4
Prepair 1000+ v1.3 GDF1 Seb Lunke Added phenotypes Right atrial isomerism, 208530 (3) for gene: GDF1
Prepair 1000+ v1.3 ATRX Seb Lunke Added phenotypes Mental retardation-hypotonic facies syndrome, X-linked, 309580 (3) for gene: ATRX
Prepair 1000+ v1.3 ATR Seb Lunke Added phenotypes Seckel syndrome 1, 210600 (3) for gene: ATR
Prepair 1000+ v1.2 ATRX Zornitza Stark Phenotypes for gene: ATRX were changed from Mental retardation-hypotonic facies syndrome, X-linked, 309580 (3) to ATR-X-related syndrome MONDO:0016980
Prepair 1000+ v0.178 RPGR Zornitza Stark Phenotypes for gene: RPGR were changed from Macular degeneration, X-linked atrophic, 300834 (3) to Retinitis pigmentosa 3 (MIM#300029)
Prepair 1000+ v0.157 OAT Zornitza Stark reviewed gene: OAT: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Gyrate atrophy of choroid and retina with or without ornithinemia, MIM# 258870; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v0.85 PYGM Crystle Lee gene: PYGM was added
gene: PYGM was added to Reproductive Carrier Screen_VCGS. Sources: Literature
Mode of inheritance for gene: PYGM was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: PYGM were set to McArdle disease (MIM#232600)
Review for gene: PYGM was set to AMBER
Added comment: Gene-disease association for bi-allelic variants is well established.

McCardle disease: glycogen storage disease type V (GSD5), characterized by onset of exercise intolerance and muscle cramps in childhood or adolescence. Transient myoglobinuria may occur after exercise, due to rhabdomyolysis. Severe myoglobinuria may lead to acute renal failure. Patients may report muscle weakness, myalgia, and lack of endurance since childhood or adolescence. Later in adult life, there is persistent and progressive muscle weakness and atrophy with fatty replacement. McArdle disease is a relatively benign disorder, except for possible renal failure as a complication of myoglobinuria

Clinical heterogeneity exists; about 10% of all affected individuals have mild manifestations (e.g., fatigue or poor stamina without contractures) and remain virtually asymptomatic during daily activities of living(Gene Reviews)
Sources: Literature
Prepair 1000+ v0.85 OAT Crystle Lee gene: OAT was added
gene: OAT was added to Reproductive Carrier Screen_VCGS. Sources: Literature
Mode of inheritance for gene: OAT was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: OAT were set to 33463379; 34340878
Phenotypes for gene: OAT were set to Gyrate atrophy of choroid and retina with or without ornithinemia (MIM#258870)
Review for gene: OAT was set to AMBER
Added comment: Biallelic variants associated with deficiency of mitochondrial enzyme ornithine aminotransferase and elevation of plasma ornithine levels without elevation of ammonia. Characterized by ocular anomalies; however, neurological and muscular features may also be present.

There is evidence of intra-familial variability.
Sources: Literature
Prepair 1000+ v0.50 UBA1 Crystle Lee reviewed gene: UBA1: Rating: GREEN; Mode of pathogenicity: None; Publications: 18179898, 32181232, 31932168, 29034082, 23518311, 26028276; Phenotypes: Spinal muscular atrophy, X-linked 2, infantile (MIM#301830); Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Prepair 1000+ v0.49 ITGA6 Crystle Lee reviewed gene: ITGA6: Rating: GREEN; Mode of pathogenicity: None; Publications: 31502654, 27607025, 9158140, 34525201, 20301336; Phenotypes: Epidermolysis bullosa, junctional 6, with pyloric atresia (MIM#619817); Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v0.31 SGO1 Crystle Lee reviewed gene: SGO1: Rating: RED; Mode of pathogenicity: None; Publications: 25282101; Phenotypes: Chronic atrial and intestinal dysrhythmia, MIM# 616201; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v0.0 TRAPPC6B Zornitza Stark gene: TRAPPC6B was added
gene: TRAPPC6B was added to Reproductive Carrier Screen_VCGS. Sources: Expert Review
Mode of inheritance for gene: TRAPPC6B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TRAPPC6B were set to 28397838; 28626029; 31687267
Phenotypes for gene: TRAPPC6B were set to Neurodevelopmental disorder with microcephaly, epilepsy, and brain atrophy, MIM# 617862
Prepair 1000+ v0.0 TRAPPC12 Zornitza Stark gene: TRAPPC12 was added
gene: TRAPPC12 was added to Reproductive Carrier Screen_VCGS. Sources: Expert Review
Mode of inheritance for gene: TRAPPC12 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TRAPPC12 were set to 32369837; 28777934
Phenotypes for gene: TRAPPC12 were set to Encephalopathy, progressive, early-onset, with brain atrophy and spasticity, MIM# 617669
Prepair 1000+ v0.0 VARS Zornitza Stark gene: VARS was added
gene: VARS was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: VARS was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: VARS were set to Neurodevelopmental disorder with microcephaly, seizures, and cortical atrophy, 617802 (3), Autosomal recessive
Prepair 1000+ v0.0 UBA1 Zornitza Stark gene: UBA1 was added
gene: UBA1 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: UBA1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Phenotypes for gene: UBA1 were set to Spinal muscular atrophy, X-linked 2, infantile, 301830 (3)
Prepair 1000+ v0.0 TMEM126A Zornitza Stark gene: TMEM126A was added
gene: TMEM126A was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: TMEM126A was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: TMEM126A were set to Optic atrophy 7, 612989 (3)
Prepair 1000+ v0.0 TF Zornitza Stark gene: TF was added
gene: TF was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: TF was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: TF were set to Atransferrinemia, 209300 (3)
Prepair 1000+ v0.0 TBCD Zornitza Stark gene: TBCD was added
gene: TBCD was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: TBCD was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: TBCD were set to Encephalopathy, progressive, early-onset, with brain atrophy and thin corpus callosum, 617193 (3), Autosomal recessive
Prepair 1000+ v0.0 SMN1 Zornitza Stark gene: SMN1 was added
gene: SMN1 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: SMN1 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: SMN1 were set to Spinal muscular atrophy-1, 253300 (3)
Prepair 1000+ v0.0 SGO1 Zornitza Stark gene: SGO1 was added
gene: SGO1 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: SGO1 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: SGO1 were set to Chronic atrial and intestinal dysrhythmia, 616201 (3)
Prepair 1000+ v0.0 RTN4IP1 Zornitza Stark gene: RTN4IP1 was added
gene: RTN4IP1 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: RTN4IP1 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: RTN4IP1 were set to Optic atrophy 10 with or without ataxia, mental retardation, and seizures, 616732 (3), Autosomal recessive
Prepair 1000+ v0.0 RPGR Zornitza Stark gene: RPGR was added
gene: RPGR was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: RPGR was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Phenotypes for gene: RPGR were set to Macular degeneration, X-linked atrophic, 300834 (3)
Prepair 1000+ v0.0 QARS Zornitza Stark gene: QARS was added
gene: QARS was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: QARS was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: QARS were set to Microcephaly, progressive, seizures, and cerebral and cerebellar atrophy, 615760 (3)
Prepair 1000+ v0.0 PLEC Zornitza Stark gene: PLEC was added
gene: PLEC was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: PLEC was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: PLEC were set to Epidermolysis bullosa simplex with pyloric atresia, 612138 (3)
Prepair 1000+ v0.0 NBAS Zornitza Stark gene: NBAS was added
gene: NBAS was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: NBAS was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: NBAS were set to Short stature, optic nerve atrophy, and Pelger-Huet anomaly, 614800 (3)
Prepair 1000+ v0.0 MED17 Zornitza Stark gene: MED17 was added
gene: MED17 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: MED17 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: MED17 were set to Microcephaly, postnatal progressive, with seizures and brain atrophy, 613668 (3)
Prepair 1000+ v0.0 ITGB4 Zornitza Stark gene: ITGB4 was added
gene: ITGB4 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: ITGB4 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: ITGB4 were set to Epidermolysis bullosa, junctional, with pyloric atresia, 226730 (3)
Prepair 1000+ v0.0 GDF1 Zornitza Stark gene: GDF1 was added
gene: GDF1 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: GDF1 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: GDF1 were set to Right atrial isomerism, 208530 (3)
Prepair 1000+ v0.0 ATRX Zornitza Stark gene: ATRX was added
gene: ATRX was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: ATRX was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Phenotypes for gene: ATRX were set to Mental retardation-hypotonic facies syndrome, X-linked, 309580 (3)
Prepair 1000+ v0.0 ATR Zornitza Stark gene: ATR was added
gene: ATR was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: ATR was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: ATR were set to Seckel syndrome 1, 210600 (3)
Prepair 1000+ v0.0 ASCC1 Zornitza Stark gene: ASCC1 was added
gene: ASCC1 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: ASCC1 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: ASCC1 were set to Spinal muscular atrophy with congenital bone fractures 2, MIM#616867