Activity

Filter

Cancel
Date Panel Item Activity
67 actions
Prepair 1000+ v1.2151 DBR1 Zornitza Stark Phenotypes for gene: DBR1 were changed from to Xerosis and growth failure with immune and pulmonary dysfunction syndrome MIM#620510
Prepair 1000+ v1.1956 XRCC4 Lilian Downie Phenotypes for gene: XRCC4 were changed from Short stature, microcephaly, and endocrine dysfunction, 616541 (3), Autosomal recessive to Short stature, microcephaly, and endocrine dysfunction MIM#616541
Prepair 1000+ v1.1938 IBA57 Zornitza Stark Phenotypes for gene: IBA57 were changed from Multiple mitochondrial dysfunctions syndrome 3, 615330 (3), Autosomal recessive to Multiple mitochondrial dysfunctions syndrome 3 MIM#615330
Prepair 1000+ v1.1868 IBA57 Andrew Coventry reviewed gene: IBA57: Rating: GREEN; Mode of pathogenicity: None; Publications: 23462291, 25971455, 25609768, 28913435, 28671726, 30258207; Phenotypes: Mitochondrial disease MONDO:0044970, Multiple mitochondrial dysfunctions syndrome 3 MIM#615330; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.1868 POLE Andrew Coventry gene: POLE was added
gene: POLE was added to Prepair 1000+. Sources: Literature
Mode of inheritance for gene: POLE was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: POLE were set to 30503519; 23230001; 25948378; 36071887
Phenotypes for gene: POLE were set to IMAGE-I syndrome MIM#618336; FILS syndrome MIM#615139
Review for gene: POLE was set to GREEN
Added comment: IMAGE-I Syndrome
Autosomal recessive disorder characterised by intrauterine growth retardation, metaphyseal dysplasia, adrenal hypoplasia congenita, genital anomalies, and immunodeficiency. Patients exhibit distinctive facial features and variable immune dysfunction with evidence of lymphocyte deficiency.
Well established gene-disease association. Reported in greater than 10 families.
Note recurrent intronic variant, c.1686+32C-G (intron 15) in IMAGE-I, found in combination with multiple other variants.

FILS syndrome
FILS syndrome is characterised by mild facial dysmorphism, mainly malar hypoplasia, livedo on the skin since birth, immunodeficiency resulting in recurrent infections, and short stature.
PMID: 23230001 - French consanguineoius kindred: 11 affected individuals displayed mild facial dysmorphism, immunodeficiency, livedo, and short stature. 3 additional members displayed two or three of these four features. Homozygous for splicing site variant: c.4444+3A>G.
PMID: 25948378 - Palestinian girl, with same homozygous variant as reported in French family.
PMID: 36071887 - 4y.o. Chinese boy with c.5811 + 2T > C and c.2006G > A variants.
PMID: 32705701 - 6y.o. hispanic boy reported with homozygous c.100C>T(p.Arg34Cys
Total of 14 affected individuals across 4 families.
Sources: Literature
Prepair 1000+ v1.1845 VPS33B Zornitza Stark Phenotypes for gene: VPS33B were changed from Arthrogryposis, renal dysfunction, and cholestasis 1, 208085 (3) to Arthrogryposis, renal dysfunction, and cholestasis 1 MIM#208085; Cholestasis, progressive familial intrahepatic, 12 MIM#620010; Keratoderma-ichthyosis-deafness syndrome, autosomal recessive MIM#620009
Prepair 1000+ v1.1826 VPS33B Michelle Torres reviewed gene: VPS33B: Rating: GREEN; Mode of pathogenicity: None; Publications: 31479177, 30561130, 28017832; Phenotypes: Arthrogryposis, renal dysfunction, and cholestasis 1 MIM#208085, Cholestasis, progressive familial intrahepatic, 12 MIM#620010, Keratoderma-ichthyosis-deafness syndrome, autosomal recessive MIM#620009; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.1822 VIPAS39 Michelle Torres reviewed gene: VIPAS39: Rating: GREEN; Mode of pathogenicity: None; Publications: 20190753, 35151346; Phenotypes: Arthrogryposis, renal dysfunction, and cholestasis 2 MIM#613404; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.1822 XRCC4 Michelle Torres reviewed gene: XRCC4: Rating: GREEN; Mode of pathogenicity: None; Publications: 24389050, 25728776, 25872942; Phenotypes: Short stature, microcephaly, and endocrine dysfunction MIM#616541; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.1811 MTPAP Andrew Coventry gene: MTPAP was added
gene: MTPAP was added to Prepair 1000+. Sources: Literature
Mode of inheritance for gene: MTPAP was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MTPAP were set to 20970105; 33340416; 32376682; 15769737; 31779033; 35235001; 27391121
Phenotypes for gene: MTPAP were set to Mitochondrial disease MONDO:0044970
Review for gene: MTPAP was set to GREEN
Added comment: Definitive disease-gene classification by ClinGen - "Identified in five individuals from four publications (PMIDs: 20970105, 31779033, 35235001, 27391121). Supported by a biochemical function (mitochondrial translation) shared with other genes associated with primary mitochondrial disease, early embryonic lethality and failure of developmental progression in a knockout mouse model, and disrupted expression of mitochondrial proteins and mitochondrial dysfunction following gene knockdown in HeLa cells (PMIDs: 33340416, 32376682, 15769737)."

Note that 6 individuals with spastic ataxia all had same founder variant and were traced as distantly related (Amish community - c.1432A>G (p.Asn478Asp).
Further additional families reported with a much more severe phenotype of lethal encephalopathy.

Phenotypes previous reported to be associated with MTPAP are likely to represent a continuum of severity associated with a mitochondrial disorder.
Clingen "While various names have been given to the constellation of features seen in those with MTPAP-related disease, including autosomal recessive spastic ataxia 4 (SPAX4) (MIM 613672) in additional to other mitochondrial disorders, pathogenic variants in this gene cause a primary mitochondrial disease.... lumped into one disease entity..."
Sources: Literature
Prepair 1000+ v1.1611 DBR1 Lilian Downie Added comment: Comment when marking as ready: Green for the immune condition in OMIM Xerosis and growth failure with immune and pulmonary dysfunction syndrome MIM#620510 although evidence is from a single paper but includes 4 unrelated families, 2 papers regarding encephalopathy, again enough evidence for inclusion >3 unrelated families.

UPGRADE TO GREEN
Prepair 1000+ v1.1596 PEX1 Kate Scarff changed review comment from: Characterized clinically by severe neurologic dysfunction, craniofacial abnormalities, and liver dysfunction, and biochemically by the absence of peroxisomes. Most severely affected individuals with classic Zellweger syndrome phenotype die within the first year of life.
~98% of variants detectable by sequencing. The PEX1 variants c.2097_2098insT/p.Ile700YfsX42 and c.2528GRA/p.Gly843Asp are the most common.
Homozygosity for p.Ile700TyrfsTer42 is associated with a more severe phenotype. Homozygosity for p.Gly843Asp has to date been associated with a milder ZSD phenotype and sometimes with an intermediate phenotype.

Other phenotypes:
Peroxisome biogenesis disorder 1B (NALD/IRD), MIM #601539, characterised by overlapping phenotypes of neonatal adrenoleukodystrophy (NALD) and infantile Refsum disease (IRD), which represent the milder manifestations of the Zellweger syndrome spectrum. Many children presenting as newborns, whereas others do not come to attention until later. Many can communicate, and although language is rare, there have been children who have near normal language for age. Craniofacial anomalies are similar to but less pronounced than in Zellweger syndrome. In some individuals a leukodystrophy develops, with degeneration of myelin, loss of previously acquired skills, and development of spasticity; this may stabilize, or progress and be fatal. Associated with p.Gly843Asp variant?

Heimler syndrome-1 (MIM #234580) represents the mildest end of the peroxisomal biogenesis disorder spectrum, characterized by sensorineural hearing loss, enamel hypoplasia of the secondary dentition, and nail abnormalities. Not severe enough to report for P1000? See PMID: 26387595.; to: Characterized clinically by severe neurologic dysfunction, craniofacial abnormalities, and liver dysfunction, and biochemically by the absence of peroxisomes. Most severely affected individuals with classic Zellweger syndrome phenotype die within the first year of life.
~98% of variants detectable by sequencing. The PEX1 variants c.2097_2098insT/p.Ile700YfsX42 and c.2528GRA/p.Gly843Asp are the most common.
Homozygosity for p.Ile700TyrfsTer42 is associated with a more severe phenotype. Homozygosity for p.Gly843Asp has to date been associated with a milder ZSD phenotype and sometimes with an intermediate phenotype.

Other phenotypes:
Peroxisome biogenesis disorder 1B (NALD/IRD), MIM #601539, characterised by overlapping phenotypes of neonatal adrenoleukodystrophy (NALD) and infantile Refsum disease (IRD), which represent the milder manifestations of the Zellweger syndrome spectrum. Many children presenting as newborns, whereas others do not come to attention until later. Many can communicate, and although language is rare, there have been children who have near normal language for age. Craniofacial anomalies are similar to but less pronounced than in Zellweger syndrome. In some individuals a leukodystrophy develops, with degeneration of myelin, loss of previously acquired skills, and development of spasticity; this may stabilize, or progress and be fatal. Associated with p.Gly843Asp variant?

Heimler syndrome-1 (MIM #234580) represents the mildest end of the peroxisomal biogenesis disorder spectrum, characterized by sensorineural hearing loss, enamel hypoplasia of the secondary dentition, and nail abnormalities. Not severe enough to report for P1000? See PMID: 26387595.

MONDO:0100259 - Any Zellweger spectrum disorder in which the cause of the disease is a mutation in the PEX1 gene.
Prepair 1000+ v1.1596 PEX1 Kate Scarff changed review comment from: Characterized clinically by severe neurologic dysfunction, craniofacial abnormalities, and liver dysfunction, and biochemically by the absence of peroxisomes. Most severely affected individuals with classic Zellweger syndrome phenotype die within the first year of life.
~98% of variants detectable by sequencing. The PEX1 variants c.2097_2098insT/p.Ile700YfsX42 and c.2528GRA/p.Gly843Asp are the most common.
Homozygosity for p.Ile700TyrfsTer42 is associated with a more severe phenotype. Homozygosity for p.Gly843Asp has to date been associated with a milder ZSD phenotype and sometimes with an intermediate phenotype.

Other phenotypes:
Peroxisome biogenesis disorder 1B (NALD/IRD), MIM #601539, characterised by overlapping phenotypes of neonatal adrenoleukodystrophy (NALD) and infantile Refsum disease (IRD), which represent the milder manifestations of the Zellweger syndrome spectrum. Many children presenting as newborns, whereas others do not come to attention until later. Many can communicate, and although language is rare, there have been children who have near normal language for age. Craniofacial anomalies are similar to but less pronounced than in Zellweger syndrome. In some individuals a leukodystrophy develops, with degeneration of myelin, loss of previously acquired skills, and development of spasticity; this may stabilize, or progress and be fatal. Associated with p.Gly843Asp variant? Should this phenotype be included for P1000?

Heimler syndrome-1 (MIM #234580) represents the mildest end of the peroxisomal biogenesis disorder spectrum, characterized by sensorineural hearing loss, enamel hypoplasia of the secondary dentition, and nail abnormalities. Not severe enough to report for P1000. See PMID: 26387595.; to: Characterized clinically by severe neurologic dysfunction, craniofacial abnormalities, and liver dysfunction, and biochemically by the absence of peroxisomes. Most severely affected individuals with classic Zellweger syndrome phenotype die within the first year of life.
~98% of variants detectable by sequencing. The PEX1 variants c.2097_2098insT/p.Ile700YfsX42 and c.2528GRA/p.Gly843Asp are the most common.
Homozygosity for p.Ile700TyrfsTer42 is associated with a more severe phenotype. Homozygosity for p.Gly843Asp has to date been associated with a milder ZSD phenotype and sometimes with an intermediate phenotype.

Other phenotypes:
Peroxisome biogenesis disorder 1B (NALD/IRD), MIM #601539, characterised by overlapping phenotypes of neonatal adrenoleukodystrophy (NALD) and infantile Refsum disease (IRD), which represent the milder manifestations of the Zellweger syndrome spectrum. Many children presenting as newborns, whereas others do not come to attention until later. Many can communicate, and although language is rare, there have been children who have near normal language for age. Craniofacial anomalies are similar to but less pronounced than in Zellweger syndrome. In some individuals a leukodystrophy develops, with degeneration of myelin, loss of previously acquired skills, and development of spasticity; this may stabilize, or progress and be fatal. Associated with p.Gly843Asp variant?

Heimler syndrome-1 (MIM #234580) represents the mildest end of the peroxisomal biogenesis disorder spectrum, characterized by sensorineural hearing loss, enamel hypoplasia of the secondary dentition, and nail abnormalities. Not severe enough to report for P1000? See PMID: 26387595.
Prepair 1000+ v1.1568 DBR1 Andrew Coventry reviewed gene: DBR1: Rating: AMBER; Mode of pathogenicity: None; Publications: 37656279, 29474921, 38325642; Phenotypes: Xerosis and growth failure with immune and pulmonary dysfunction syndrome MIM#620510, Viral infections of the brainstem, Ichthyosis (MONDO#0019269); Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.1545 ISCA2 Zornitza Stark Phenotypes for gene: ISCA2 were changed from Multiple mitochondrial dysfunctions syndrome 4, 616370 (3) to Multiple mitochondrial dysfunctions syndrome 4, MIM #616370
Prepair 1000+ v1.1472 SLC19A3 Zornitza Stark Phenotypes for gene: SLC19A3 were changed from Thiamine metabolism dysfunction syndrome 2 (biotin- or thiamine-responsive encephalopathy type 2), 607483 (3) to Thiamine metabolism dysfunction syndrome 2 (biotin- or thiamine-responsive encephalopathy type 2), MIM# 607483
Prepair 1000+ v1.1460 SLC19A3 Cassandra Muller reviewed gene: SLC19A3: Rating: GREEN; Mode of pathogenicity: None; Publications: 15871139, 19387023, 20065143, 23423671; Phenotypes: Thiamine metabolism dysfunction syndrome 2 (biotin- or thiamine-responsive encephalopathy type 2), MIM# 607483; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.1456 ISCA2 Kate Scarff reviewed gene: ISCA2: Rating: GREEN; Mode of pathogenicity: None; Publications: 25539947, 29297947, 29122497, 29359243, 32424628, 39544370, 29470032; Phenotypes: Multiple mitochondrial dysfunctions syndrome 4, MIM #616370; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.1411 SFTPB Zornitza Stark Phenotypes for gene: SFTPB were changed from Surfactant metabolism dysfunction, pulmonary, 1, 265120 (3) to Surfactant metabolism dysfunction, pulmonary, 1, MIM# 265120
Prepair 1000+ v1.1397 SFTPB Lauren Rogers reviewed gene: SFTPB: Rating: GREEN; Mode of pathogenicity: None; Publications: 8163685, 8021783, 10378403, 10571948; Phenotypes: Surfactant metabolism dysfunction, pulmonary, 1, MIM# 265120; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.1127 NFU1 Zornitza Stark Phenotypes for gene: NFU1 were changed from Multiple mitochondrial dysfunctions syndrome 1, 605711 (3) to Multiple mitochondrial dysfunctions syndrome 1, MIM#605711
Prepair 1000+ v1.1019 SLC25A19 Zornitza Stark Phenotypes for gene: SLC25A19 were changed from Thiamine metabolism dysfunction syndrome 4 (progressive polyneuropathy type), 613710 (progressive polyneuropathy type), 613710 to Thiamine metabolism dysfunction syndrome 4 (progressive polyneuropathy type) (MIM#613710); Microcephaly, Amish type (MIM#607196)
Prepair 1000+ v1.992 SLC25A19 Ee Ming Wong reviewed gene: SLC25A19: Rating: GREEN; Mode of pathogenicity: None; Publications: 20301539, 31095747; Phenotypes: Thiamine metabolism dysfunction syndrome 4 (progressive polyneuropathy type) (MIM#613710), Microcephaly, Amish type (MIM#607196); Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Prepair 1000+ v1.992 ELP1 Clare Hunt changed review comment from: From OMIM; Hereditary sensory and autonomic neuropathy type III (HSAN3) is an autosomal recessive neurodegenerative disorder with onset soon after birth. Affected individuals show progressive symptoms resulting from depletion of sensory proprioceptive and autonomic neurons. Features include gastrointestinal dysfunction, gastroesophageal reflux, vomiting crises, recurrent pneumonia, seizures, gait abnormalities with loss of ambulation, kyphoscoliosis, postural hypotension, hypertension crises, absence of fungiform papillae on the tongue, decreased deep tendon reflexes, defective lacrimation, and impaired pain and temperature perception. The disorder is inevitably fatal, with only 50% of patients reaching 40 years of age.

HSAN3 has a high carrier frequency in the Ashkenazi Jewish population (summary by Morini et al., 2016).

Gene previously referred to as IKBKAP gene (ELP1; 603722) located on chromosome 9q31. Also previously referred to as Riley-Day syndrome.
From Mendeliome; AR dysautonomia: the condition is predominantly caused by homozygosity of c.2204+6T>C (major familial dysautonomia AJ haplotype - causes tissue-specific exon 20 skipping) in Ashkenazi Jewish individuals. Other variants have been reported in association with the disease.; to: From OMIM; Hereditary sensory and autonomic neuropathy type III (HSAN3) is an autosomal recessive neurodegenerative disorder with onset soon after birth. Affected individuals show progressive symptoms resulting from depletion of sensory proprioceptive and autonomic neurons. Features include gastrointestinal dysfunction, gastroesophageal reflux, vomiting crises, recurrent pneumonia, seizures, gait abnormalities with loss of ambulation, kyphoscoliosis, postural hypotension, hypertension crises, absence of fungiform papillae on the tongue, decreased deep tendon reflexes, defective lacrimation, and impaired pain and temperature perception. The disorder is inevitably fatal, with only 50% of patients reaching 40 years of age.

HSAN3 has a high carrier frequency in the Ashkenazi Jewish population (summary by Morini et al., 2016).

Gene previously referred to as IKBKAP gene (ELP1; 603722) located on chromosome 9q31.

From Mendeliome; AR dysautonomia: the condition is predominantly caused by homozygosity of c.2204+6T>C (major familial dysautonomia AJ haplotype - causes tissue-specific exon 20 skipping) in Ashkenazi Jewish individuals. Other variants have been reported in association with the disease.
Prepair 1000+ v1.992 ELP1 Clare Hunt changed review comment from: From OMIM; Hereditary sensory and autonomic neuropathy type III (HSAN3) is an autosomal recessive neurodegenerative disorder with onset soon after birth. Affected individuals show progressive symptoms resulting from depletion of sensory proprioceptive and autonomic neurons. Features include gastrointestinal dysfunction, gastroesophageal reflux, vomiting crises, recurrent pneumonia, seizures, gait abnormalities with loss of ambulation, kyphoscoliosis, postural hypotension, hypertension crises, absence of fungiform papillae on the tongue, decreased deep tendon reflexes, defective lacrimation, and impaired pain and temperature perception. The disorder is inevitably fatal, with only 50% of patients reaching 40 years of age. HSAN3 has a high carrier frequency in the Ashkenazi Jewish population (summary by Morini et al., 2016).

Gene previously referred to as IKBKAP gene (ELP1; 603722) located on chromosome 9q31. Also previously referred to as Riley-Day syndrome.; to: From OMIM; Hereditary sensory and autonomic neuropathy type III (HSAN3) is an autosomal recessive neurodegenerative disorder with onset soon after birth. Affected individuals show progressive symptoms resulting from depletion of sensory proprioceptive and autonomic neurons. Features include gastrointestinal dysfunction, gastroesophageal reflux, vomiting crises, recurrent pneumonia, seizures, gait abnormalities with loss of ambulation, kyphoscoliosis, postural hypotension, hypertension crises, absence of fungiform papillae on the tongue, decreased deep tendon reflexes, defective lacrimation, and impaired pain and temperature perception. The disorder is inevitably fatal, with only 50% of patients reaching 40 years of age.

HSAN3 has a high carrier frequency in the Ashkenazi Jewish population (summary by Morini et al., 2016).

Gene previously referred to as IKBKAP gene (ELP1; 603722) located on chromosome 9q31. Also previously referred to as Riley-Day syndrome.
From Mendeliome; AR dysautonomia: the condition is predominantly caused by homozygosity of c.2204+6T>C (major familial dysautonomia AJ haplotype - causes tissue-specific exon 20 skipping) in Ashkenazi Jewish individuals. Other variants have been reported in association with the disease.
Prepair 1000+ v1.992 ISCA1 Lauren Thomas changed review comment from: Multiple mitochondrial dysfunctions syndrome-5 (MMDS5) is an autosomal recessive disorder characterized mainly by progressive neurologic deterioration beginning in early infancy. Affected individuals have essentially no psychomotor development and have early-onset seizures with neurologic decline and spasticity. Brain imaging shows severe leukodystrophy with evidence of dys- or delayed myelination. Death usually occurs in early childhood.

HGNC approved symbol/name: ISCA1
Is the phenotype(s) severe and onset <18yo? Yes
Known technical challenges? No
Gene reported in 3 independent families: Yes; to: Multiple mitochondrial dysfunctions syndrome-5 (MMDS5) is an autosomal recessive disorder characterized mainly by progressive neurologic deterioration beginning in early infancy. Affected individuals have essentially no psychomotor development and have early-onset seizures with neurologic decline and spasticity. Brain imaging shows severe leukodystrophy with evidence of dys- or delayed myelination. Death usually occurs in early childhood.

HGNC approved symbol/name: ISCA1
Is the phenotype(s) severe and onset <18yo? Yes
Known technical challenges? No
Gene reported in 3 independent families: Yes

Most recent case report: PMID 32092383 (4th independent family)
Prepair 1000+ v1.992 ISCA1 Lauren Thomas changed review comment from: Multiple mitochondrial dysfunctions syndrome-5 (MMDS5) is an autosomal recessive disorder characterized mainly by progressive neurologic deterioration beginning in early infancy. Affected individuals have essentially no psychomotor development and have early-onset seizures with neurologic decline and spasticity. Brain imaging shows severe leukodystrophy with evidence of dys- or delayed myelination. Death usually occurs in early childhood.

HGNC approved symbol/name: ISCA1
Is the phenotype(s) severe and onset <18yo? Yes
Known technical challenges? No
Gene reported in 3 independent families: Yes; to: Multiple mitochondrial dysfunctions syndrome-5 (MMDS5) is an autosomal recessive disorder characterized mainly by progressive neurologic deterioration beginning in early infancy. Affected individuals have essentially no psychomotor development and have early-onset seizures with neurologic decline and spasticity. Brain imaging shows severe leukodystrophy with evidence of dys- or delayed myelination. Death usually occurs in early childhood.

HGNC approved symbol/name: ISCA1
Is the phenotype(s) severe and onset <18yo? Yes
Known technical challenges? No
Gene reported in 3 independent families: Yes
Prepair 1000+ v1.992 ISCA1 Lauren Thomas reviewed gene: ISCA1: Rating: GREEN; Mode of pathogenicity: None; Publications: 28356563, 29767723; Phenotypes: Multiple mitochondrial dysfunctions syndrome 5, MIM# 617613; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.992 NFU1 Ee Ming Wong reviewed gene: NFU1: Rating: GREEN; Mode of pathogenicity: None; Publications: 21944046, 22077971, 32747156, 29441221, 36256512; Phenotypes: Multiple mitochondrial dysfunctions syndrome 1 (MIM# 605711), Spastic paraplegia 93 (MIM# 620938); Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Prepair 1000+ v1.978 RBCK1 Kate Scarff changed review comment from: Characterized by onset in childhood of progressive proximal muscle weakness, resulting in difficulties in ambulation. Most patients also develop progressive dilated cardiomyopathy, which may necessitate cardiac transplant in severe cases. A small subset of patients present with severe immunodeficiency and a hyperinflammatory state in very early childhood.

A 32kb deletion which included the three last exons of TRIB3 and the first four exons of RBCK1 was identified in one family, also had a nonsense mutation (PMID: 23104095).

The nature and localization of the underlying mutation might predict the phenotype, with N-terminal mutations mainly causing immunological dysfunction. In contrast, variants in the middle- or C-terminal regions were presumed to predominantly cause cardiomyopathy and neuromuscular symptoms. Further, it was suggested that truncating variants might generally result in more severe phenotypes than missense mutations. Frameshift mutations beyond the N-terminus
of RBCK1 may lead to a combined phenotype including both myopathy and immunological dysfunction in single
families (PMID: 29260357).; to: Characterized by onset in childhood of progressive proximal muscle weakness, resulting in difficulties in ambulation. Most patients also develop progressive dilated cardiomyopathy, which may necessitate cardiac transplant in severe cases. A small subset of patients present with severe immunodeficiency and a hyperinflammatory state in very early childhood.

A 32kb deletion which included the three last exons of TRIB3 and the first four exons of RBCK1 was identified in one family, also had a nonsense mutation (PMID: 23104095).

The nature and localization of the underlying mutation might predict the phenotype, with N-terminal mutations mainly causing immunological dysfunction. In contrast, variants in the middle- or C-terminal regions were presumed to predominantly cause cardiomyopathy and neuromuscular symptoms. Further, it was suggested that truncating variants might generally result in more severe phenotypes than missense mutations. Frameshift mutations beyond the N-terminus of RBCK1 may lead to a combined phenotype including both myopathy and immunological dysfunction in single families (PMID: 29260357).
Prepair 1000+ v1.836 GUCY2D Kate Scarff changed review comment from: LCA1 is a congenital eye disorder that primarily affects the retina and causes vision loss, nystagmus, and severe retinal dysfunction. People with this disorder typically have severe visual impairment beginning at birth or shortly afterward. The visual impairment tends to be severe and may worsen over time.

Cone-rod dystrophy 6, MIM #601777 is a dominant condition due to heterozygous mutations in GUCY2D, not reportable for Prepair1000+.
Autosomal recessive GUCY2D mutations may cause congenital night blindness with normal acuity and refraction, and unique electroretinography. Progression to mild retinitis pigmentosa may occur. See PMID: 29559409. Not reportable for Prepair1000+ (severity).; to: LCA1 is a congenital eye disorder that primarily affects the retina and causes vision loss, nystagmus, and severe retinal dysfunction. People with this disorder typically have severe visual impairment beginning at birth or shortly afterward. The visual impairment tends to be severe and may worsen over time.

Cone-rod dystrophy 6, MIM #601777 is a dominant condition due to heterozygous mutations in GUCY2D, not reportable for Prepair1000+. See PMID: 35205358
Autosomal recessive GUCY2D mutations may cause congenital night blindness with normal acuity and refraction, and unique electroretinography. Progression to mild retinitis pigmentosa may occur. See PMID: 29559409. Not reportable for Prepair1000+ (severity).
Prepair 1000+ v1.531 BOLA3 Zornitza Stark Phenotypes for gene: BOLA3 were changed from Multiple mitochondrial dysfunctions syndrome 2, 614299 (3) to Multiple mitochondrial dysfunctions syndrome 2 with hyperglycinemia MIM#614299
Prepair 1000+ v1.486 BOLA3 Michelle Torres reviewed gene: BOLA3: Rating: GREEN; Mode of pathogenicity: None; Publications: 30302924, 29654549, 30302924; Phenotypes: Multiple mitochondrial dysfunctions syndrome 2 with hyperglycinemia MIM#614299; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.369 CYP27A1 Lilian Downie Added comment: Comment when marking as ready: Cerebrotendinous xanthomatosis (CTX) is a rare autosomal recessive lipid-storage disease characterized clinically by progressive neurologic dysfunction (cerebellar ataxia beginning after puberty, systemic spinal cord involvement and a pseudobulbar phase leading to death), premature atherosclerosis, and cataracts. Large deposits of cholesterol and cholestanol are found in virtually every tissue, particularly the Achilles tendons, brain, and lungs. Cholestanol, the 5-alpha-dihydro derivative of cholesterol, is enriched relative to cholesterol in all tissues. The diagnosis can be made by demonstrating cholestanol in abnormal amounts in the serum and tendon of persons suspected of being affected. Plasma cholesterol concentrations are low normal in CTX patients. (OMIM)
Prepair 1000+ v1.248 F2 Marta Cifuentes Ochoa changed review comment from: Prothrombin deficiency type I, known as true prothrombin deficiency or 'hypoprothrombinemia,' is defined as plasma levels of prothrombin being less than 10% of normal with a concomitant decrease in activity. These patients have severe bleeding from birth, including umbilical cord hemorrhage, hematomas, ecchymoses, hematuria, mucosal bleeding, hemarthroses, intracranial bleeding, gastrointestinal bleeding, and menorrhagia.

HGNC approved symbol/name: F2
Is the phenotype(s) severe and onset <18yo ? Y
Known technical challenges? N
Gene reported in >3 independent families

Type II deficiency, known as 'dysprothrombinemia,' is characterized by normal or low-normal synthesis of a dysfunctional protein; to: Prothrombin deficiency type I, known as true prothrombin deficiency or 'hypoprothrombinemia,' is defined as plasma levels of prothrombin being less than 10% of normal with a concomitant decrease in activity. These patients have severe bleeding from birth, including umbilical cord hemorrhage, hematomas, ecchymoses, hematuria, mucosal bleeding, hemarthroses, intracranial bleeding, gastrointestinal bleeding, and menorrhagia.

HGNC approved symbol/name: F2
Is the phenotype(s) severe and onset <18yo ? Y
Known technical challenges? N
Gene reported in >3 independent families

Type II deficiency, known as 'dysprothrombinemia,' is characterized by normal or low-normal synthesis of a dysfunctional protein

AD forms and multifactorial conditions described for this gene not reportable in screening context
Prepair 1000+ v1.236 DYSF Zornitza Stark Marked gene: DYSF as ready
Prepair 1000+ v1.236 DYSF Zornitza Stark Gene: dysf has been classified as Green List (High Evidence).
Prepair 1000+ v1.236 DYSF Zornitza Stark Phenotypes for gene: DYSF were changed from Muscular dystrophy, limb-girdle, type 2B, 253601 (3) to Miyoshi muscular dystrophy 1 MIM#254130; MONDO:0024545; Muscular dystrophy, limb-girdle, autosomal recessive 2 MIM#253601; MONDO:0009676; Myopathy, distal, with anterior tibial onset MIM#606768; MONDO:0011721
Prepair 1000+ v1.235 DYSF Zornitza Stark Publications for gene: DYSF were set to
Prepair 1000+ v1.234 DYSF Zornitza Stark reviewed gene: DYSF: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Miyoshi muscular dystrophy 1 MIM#254130, MONDO:0024545, Muscular dystrophy, limb-girdle, autosomal recessive 2 MIM#253601, MONDO:0009676, Myopathy, distal, with anterior tibial onset MIM#606768, MONDO:0011721; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.234 DYSF Marta Cifuentes Ochoa reviewed gene: DYSF: Rating: GREEN; Mode of pathogenicity: None; Publications: 37762951, 38540676, 36542547, 32400077; Phenotypes: Miyoshi muscular dystrophy 1 MIM#254130, MONDO:0024545, Muscular dystrophy, limb-girdle, autosomal recessive 2 MIM#253601, MONDO:0009676, Myopathy, distal, with anterior tibial onset MIM#606768, MONDO:0011721; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.234 DYSF Marta Cifuentes Ochoa Deleted their review
Prepair 1000+ v1.229 DYSF Marta Cifuentes Ochoa Deleted their comment
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+ v1.229 DYSF Marta Cifuentes Ochoa reviewed gene: DYSF: Rating: AMBER; Mode of pathogenicity: None; Publications: 37762951, 38540676, 36542547, 32400077; Phenotypes: Miyoshi muscular dystrophy 1 MIM#254130, MONDO:0024545, Muscular dystrophy, limb-girdle, autosomal recessive 2 MIM#253601, MONDO:0009676, Myopathy, distal, with anterior tibial onset MIM#606768, MONDO:0011721; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.82 ABCA3 Lisa Norbart reviewed gene: ABCA3: Rating: GREEN; Mode of pathogenicity: None; Publications: 15044640; Phenotypes: Surfactant metabolism dysfunction, pulmonary, 3, MIM#610921; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.65 TPK1 Lauren Rogers reviewed gene: TPK1: Rating: GREEN; Mode of pathogenicity: None; Publications: Thiamine metabolism dysfunction syndrome 5 (episodic encephalopathy type) MIM#614458; Phenotypes: 33086386, 32679198, 22152682, 33231275; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.43 COQ4 Lauren Rogers changed review comment from: At least 9 unrelated families reported.

Primary coenzyme Q10 deficiency-7 (COQ10D7) is an autosomal recessive disorder resulting from mitochondrial dysfunction. Most patients have onset of severe cardiac or neurologic symptoms soon after birth. IUGR reported.

Treatment: CoQ10 supplementation can limit disease progression and reverse some clinical manifestations.; to: At least 9 unrelated families reported.

Primary coenzyme Q10 deficiency-7 (COQ10D7) is an autosomal recessive disorder resulting from mitochondrial dysfunction. Most patients have onset of severe cardiac or neurologic symptoms soon after birth. IUGR reported.

Treatment: CoQ10 supplementation can limit disease progression and reverse some clinical manifestations.
Prepair 1000+ v1.43 COQ4 Lauren Rogers changed review comment from: At least 9 unrelated families reported.

Primary coenzyme Q10 deficiency-7 (COQ10D7) is an autosomal recessive disorder resulting from mitochondrial dysfunction. Most patients have onset of severe cardiac or neurologic symptoms soon after birth. IUGR reported.

Treatment: CoQ10 supplementation can limit disease progression and reverse some clinical manifestations.; to: At least 9 unrelated families reported.

Primary coenzyme Q10 deficiency-7 (COQ10D7) is an autosomal recessive disorder resulting from mitochondrial dysfunction. Most patients have onset of severe cardiac or neurologic symptoms soon after birth. IUGR reported.

Treatment: CoQ10 supplementation can limit disease progression and reverse some clinical manifestations.
Prepair 1000+ v1.3 SLC19A3 Seb Lunke Added phenotypes Thiamine metabolism dysfunction syndrome 2 (biotin- or thiamine-responsive encephalopathy type 2), 607483 (3) for gene: SLC19A3
Prepair 1000+ v1.3 DYSF Seb Lunke Added phenotypes Muscular dystrophy, limb-girdle, type 2B, 253601 (3) for gene: DYSF
Prepair 1000+ v1.3 ABCA3 Seb Lunke Added phenotypes Surfactant metabolism dysfunction, pulmonary, 3, 610921 (3) for gene: ABCA3
Prepair 1000+ v0.85 SLC26A4 Crystle Lee gene: SLC26A4 was added
gene: SLC26A4 was added to Reproductive Carrier Screen_VCGS. Sources: Literature
Mode of inheritance for gene: SLC26A4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SLC26A4 were set to 24599119
Phenotypes for gene: SLC26A4 were set to Deafness, autosomal recessive 4, with enlarged vestibular aqueduct (MIM#600791); Pendred syndrome (MIM#274600)
Review for gene: SLC26A4 was set to AMBER
Added comment: PDS and NSEVA are considered a disease spectrum and are distinguishable based on the presence of thyroid dysfunction in PDS (GeneReviews).

In relation to severity of hearing, there's no correlation between missense vs PTCs. There was great variation in hearing loss severity with the same mutations. Phenotype cannot be predicted from the genotype (PMID: 24599119)
Sources: Literature
Prepair 1000+ v0.0 ISCA1 Zornitza Stark gene: ISCA1 was added
gene: ISCA1 was added to Reproductive Carrier Screen_VCGS. Sources: Expert Review
Mode of inheritance for gene: ISCA1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ISCA1 were set to 32092383; 30113620; 30105122; 31016283; 28356563
Phenotypes for gene: ISCA1 were set to Multiple mitochondrial dysfunctions syndrome 5, MIM# 617613
Prepair 1000+ v0.0 XRCC4 Zornitza Stark gene: XRCC4 was added
gene: XRCC4 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: XRCC4 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: XRCC4 were set to Short stature, microcephaly, and endocrine dysfunction, 616541 (3), Autosomal recessive
Prepair 1000+ v0.0 VPS33B Zornitza Stark gene: VPS33B was added
gene: VPS33B was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: VPS33B was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: VPS33B were set to Arthrogryposis, renal dysfunction, and cholestasis 1, 208085 (3)
Prepair 1000+ v0.0 VIPAS39 Zornitza Stark gene: VIPAS39 was added
gene: VIPAS39 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: VIPAS39 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: VIPAS39 were set to Arthrogryposis, renal dysfunction, and cholestasis 2, 613404 (3)
Prepair 1000+ v0.0 TPK1 Zornitza Stark gene: TPK1 was added
gene: TPK1 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: TPK1 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: TPK1 were set to Thiamine metabolism dysfunction syndrome 5 (episodic encephalopathy type), 614458 (3)
Prepair 1000+ v0.0 SLC25A19 Zornitza Stark gene: SLC25A19 was added
gene: SLC25A19 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: SLC25A19 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: SLC25A19 were set to Thiamine metabolism dysfunction syndrome 4 (progressive polyneuropathy type), 613710 (progressive polyneuropathy type), 613710
Prepair 1000+ v0.0 SLC19A3 Zornitza Stark gene: SLC19A3 was added
gene: SLC19A3 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: SLC19A3 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: SLC19A3 were set to Thiamine metabolism dysfunction syndrome 2 (biotin- or thiamine-responsive encephalopathy type 2), 607483 (3)
Prepair 1000+ v0.0 SFTPB Zornitza Stark gene: SFTPB was added
gene: SFTPB was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: SFTPB was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: SFTPB were set to Surfactant metabolism dysfunction, pulmonary, 1, 265120 (3)
Prepair 1000+ v0.0 NFU1 Zornitza Stark gene: NFU1 was added
gene: NFU1 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: NFU1 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: NFU1 were set to Multiple mitochondrial dysfunctions syndrome 1, 605711 (3)
Prepair 1000+ v0.0 ISCA2 Zornitza Stark gene: ISCA2 was added
gene: ISCA2 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: ISCA2 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: ISCA2 were set to Multiple mitochondrial dysfunctions syndrome 4, 616370 (3)
Prepair 1000+ v0.0 IBA57 Zornitza Stark gene: IBA57 was added
gene: IBA57 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: IBA57 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: IBA57 were set to Multiple mitochondrial dysfunctions syndrome 3, 615330 (3), Autosomal recessive
Prepair 1000+ v0.0 DYSF Zornitza Stark gene: DYSF was added
gene: DYSF was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: DYSF was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: DYSF were set to Muscular dystrophy, limb-girdle, type 2B, 253601 (3)
Prepair 1000+ v0.0 BOLA3 Zornitza Stark gene: BOLA3 was added
gene: BOLA3 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: BOLA3 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: BOLA3 were set to Multiple mitochondrial dysfunctions syndrome 2, 614299 (3)
Prepair 1000+ v0.0 ABCA3 Zornitza Stark gene: ABCA3 was added
gene: ABCA3 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: ABCA3 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: ABCA3 were set to Surfactant metabolism dysfunction, pulmonary, 3, 610921 (3)