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| Fetal anomalies v3.156 | PLD1 |
Arina Puzriakova commented on gene: PLD1: Copied review from Paediatric or syndromic cardiomyopathy (749) v3.43 panel: Jesse Hayesmoore (Oxford Regional Genetics Laboratory) Red List (low evidence) "On the basis of functional data described in PMIDs: 27799408 and 33645542, PLD1 certainly seems to be a plausible functional candidate for causality of cardiac valvular defects. The main paper linking this gene with congenital heart disease / cardiomyopathy is Lahrouchi et al. (2021; PMID: 33645542; note this also includes the same 2 cases as described in Ta-Shma et al. 2017 PMID: 27799408). The paper presents 19 families with severe fetal- / neonatal-onset congenital heart (mainly valvular) defects and 2 with cardiomyopathy where affected babies were homozygous or compound heterozygous for PLD1 variants. The paper also provides some functional analysis of missense variants detected, showing that many but not all of them result significant loss of PLD1 function. Unfortunately, the paper does not include a LOD score, and there is very little cosegregation data presented for any of the variants. In addition, 4 of the 31 variants they promote as pathogenic for autosomal recessive disease are detected in multiple homozygous individuals on gnomAD, which I think provides significant evidence that they might not be pathogenic for a severe autosomal recessive condition. Most notably, 1 of the variants (i.e. I668F), which the authors promote as a pathogenic Ashkenazi Jewish founder variant (but which is also fairly frequent in non-Finnish Europeans) is detected in 7 homozygotes on gnomAD and was found to have ~80% loss of PLD1 function in their assay. This suggests that significant loss of function of this gene (i.e. down to 20%) might not be causative of a severe recessive condition (that is not to say that total or near total loss of function is not causative). Three other of the variants promoted as pathogenic in this article are also detected in homozygotes on gnomAD. I think one of the major pieces of missing information required to make a full assessment of this gene’s linkage to disease is that is unknown how frequent biallelic (apparently loss of function) variant genotypes are in the general population or in healthy control individuals. Although homozygosity for any one variant can be determined from gnomAD, compound heterozygosity (which is likely to represent the vast majority of biallelic genotypes) cannot be assessed on gnomAD, and I can find no record in the literature of this being assessed in a normal control cohort. Without this information, we cannot know whether biallelic PLD1 genotypes are specific to babies with this severe phenotype. Without knowing this, and in the absence of any significant cosegregation data for any variant, there is no reasonable basis upon which one can conclude that this is a valid autosomal recessive gene for the phenotype. Without such validation, PVS1 cannot be applied for any apparent loss of function variant. Given this, and the general lack of cosegregation data for any one variant, I do not believe there is any PLD1 variant reported in the literature that could be classified as anything but uncertain significance (if not benign or likely benign) on the basis of current variant classification guidelines. Also, there are only two cases of biallelic variants in neonates where the primary phenotype is cardiomyopathy, and of these only one was dilated cardiomyopathy (the other was histiocytoid cardiomyopathy). Hence, the evidence linking this gene to cardiomyopathy is even weaker than it is for valvular defects. I, therefore, do not feel there is sufficient evidence to justify this gene being tested as part of the R135 paediatric cardiomyopathy gene panel. Other papers (e.g. PMIDs: 33142350, 35380090, 36923242, 37770978) reporting a link between PLD1 genotypes and early onset cardiac disease (not cardiomyopathy) have been published. However, again, I do not think there is sufficient data in the articles to allow any of the variants detected to be confidently classified as anything but VUS according to current variant classification guidelines." Created: 31 Jan 2024, 12:04 p.m. | Last Modified: 31 Jan 2024, 12:17 p.m |
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| Fetal anomalies v3.155 | GRM1 | Arina Puzriakova Added comment: Comment on list classification: Demoted from Amber to Red inline with review by Zornitza Stark. Could not find any evidence of prenatal phenotypes in patients with GRM1 variants. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.142 | ROBO1 |
Arina Puzriakova Added comment: Comment on mode of inheritance: Should be updated from 'monoallelic' to 'both mono- and biallelic' at the next GMS panel update. Biallelic variants in the ROBO1 gene are associated with neurooculorenal syndrome (OMIM:620305). Clinical manifestations are generally highly variable and involve several organ systems. However, some cases do present in utero with renal agenesis and structural brain abnormalities (PMID: 29194579; 35227688) indicating that the phenotype is relevant to this panel. |
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| Fetal anomalies v3.141 | ROBO1 | Arina Puzriakova Phenotypes for gene: ROBO1 were changed from tetralogy of Fallot and septal defects to Tetralogy of Fallot and septal defects; Neurooculorenal syndrome, OMIM:620305 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.125 | CNBP | Sarah Leigh Tag currently-ngs-unreportable was removed from gene: CNBP. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.115 | FAM111A |
Sarah Leigh Added comment: Comment on mode of inheritance: PMID: 34382758 reports an autosomal recessive case of Kenny-Caffey Syndrome Type 2. The proband had inherited FAM111A variants from his healthy parents (paternal heterozygous missense variant c.976T>A (p.L326I) and maternal heterozygous in-frame deletion variant c.1714_1716del (p.Ile572del, rs779963813)). |
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| Fetal anomalies v3.109 | ESAM |
Julia Baptista gene: ESAM was added gene: ESAM was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: ESAM was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: ESAM were set to PMID: 36996813 Phenotypes for gene: ESAM were set to intracranial hemorrhage; cerebral anomalies Review for gene: ESAM was set to GREEN Added comment: Four fetuses from three unrelated families (different LOF biallelic variants) with fetal intracranial hemorrhage. Fetal brain tissue from one of the affected individuals at 31 weeks' gestational age showed lack of ESAM staining in the capillary endothelial cells, thus confirming loss of ESAM. Another individual had an abnormal prenatal ultrasound and the pregnancy was terminated at 32 weeks' gestation, but no DNA was available to test for the familial variant. Neurodevelopmental disorder with cerebral calcifications, hydrocephalus, focal white matter lesions, retina anomalies and dysmorphic features. Sources: Literature |
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| Fetal anomalies v3.103 | CLCNKB | Sarah Leigh Added comment: Comment on mode of inheritance: The mode of inheritance for CLCNKB should be BIALLELIC, autosomal or pseudoautosomal. Although digenic CLCNKB & CLCNKA variants are associated with Bartter syndrome, type 4b, digenic (OMIM:613090), the current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.92 | EN1 | Eleanor Williams commented on gene: EN1: This gene was copied from the Skeletal dysplasia panel to the Fetal anomalies panel. The Genomics England clinical team have agreed that Fetal anomalies is an appropriate panel for this gene and the rating should currently be amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.77 | WLS | Arina Puzriakova Added comment: Comment on list classification: There are sufficient unrelated cases with different homozygous variants in this gene and a consistent phenotype to support a gene-disease association. Some features such as microcephaly and digit malformations may plausibly be detected prenatally and therefore suggesting this gene is rated Green at the next GMS panel update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.73 | MYL9 | Arina Puzriakova commented on gene: MYL9: Third family reported by Billon et al. 2020 (PMID: 32621347) with the same homozygous exon 4 deletion of MYL9 as the one detected by Moreno et al. 2018 (PMID: 29453416) in an unrelated case. Family includes three sibs affected with megacystis, intestinal malrotation, small and thin colon, as well as some dysmorphic features. Fetopathological examination confirmed the diagnosis of MMIHS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.8 | ZMYM2 | Stephanie Allen reviewed gene: ZMYM2: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities, OMIM:619522; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.8 | AGTR1 | Stephanie Allen reviewed gene: AGTR1: Rating: GREEN; Mode of pathogenicity: ; Publications: 16116425, 22095942; Phenotypes: Renal tubular dysgenesis, OMIM:267430; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.7 | ZMYM2 |
Arina Puzriakova gene: ZMYM2 was added gene: ZMYM2 was added to Fetal anomalies. Sources: Expert Review Amber Mode of inheritance for gene: ZMYM2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene: ZMYM2 were set to Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities, OMIM:619522 |
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| Fetal anomalies v3.7 | AGTR1 |
Arina Puzriakova gene: AGTR1 was added gene: AGTR1 was added to Fetal anomalies. Sources: Expert Review Amber Mode of inheritance for gene: AGTR1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: AGTR1 were set to Renal tubular dysgenesis, OMIM:267430 |
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| Fetal anomalies v3.5 | CDX2 |
Arina Puzriakova Added comment: Comment on list classification: New gene added by Dmitrijs Rots (RadboudUMC). At least 8 unrelated families reported with de novo or inherited pathogenic variants in CDX2. Phenotypic findings comprise a broad spectrum of caudal abnormalities including defects of the uro‐recto‐genital tract, vertebrae, and the limbs. Cdx2 mutant mice show a variable phenotype that is comparable to that of patients (including imperforate anus, sirenomelia, posterior vertebral truncations, and bladder anomalies). Overall there is sufficient evidence to promote this gene to Green at the next GMS panel update. |
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| Fetal anomalies v2.14 | PLXND1 |
Achchuthan Shanmugasundram gene: PLXND1 was added gene: PLXND1 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: PLXND1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PLXND1 were set to 35396997 Phenotypes for gene: PLXND1 were set to Truncus arteriosus, HP:0001660 Review for gene: PLXND1 was set to GREEN Added comment: 10 individuals including four foetal cases from five unrelated families were identified with biallelic variants in PLXND1 gene and they presented with cardiac defects. The most frequent defect is common arterial trunk (CAT), which is also known as truncus arteriosus, a conotruncal malformation characterized by a single vessel exiting both ventricles. This gene has already been associated with PLXND1-related cardiac malformation syndrome with the confidence category of 'strong' in DD panel of Gene2Phenotype. However, no relevant phenotypes have been currently reported in OMIM. Sources: Literature |
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| Fetal anomalies v2.8 | KIF21A |
Hannah Robinson gene: KIF21A was added gene: KIF21A was added to Fetal anomalies. Sources: Literature,NHS GMS Mode of inheritance for gene: KIF21A was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: KIF21A were set to 34740919 Phenotypes for gene: KIF21A were set to Arthrogryposis; fetal akinesia Penetrance for gene: KIF21A were set to unknown Review for gene: KIF21A was set to GREEN gene: KIF21A was marked as current diagnostic Added comment: Falb et al 2023 (PMID: 34740919) describe two unrelated families in which biallelic loss of function variants segregated with a severe form of fetal akinesia characterised by arthrogryposis multiplex, pulmonary hypoplasia and variable facial dysmorphisms. Exeter Genomics Laboratory has identified an unrelated third case homozygous for a nonsense variant in KIF21A. The patient had an antenatal diagnosis of talipes, arthrogryposis, polyhydramnios and lack of fetal movements. At birth, all joints displayed fixed flexion deformities, no primitive reflexes, poor muscle bulk and care was re-oriented shortly after birth. Taken together, three unrelated cases including segregation evidence in the published families provides sufficient evidence for the gene-disease association. Sources: Literature, NHS GMS |
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| Fetal anomalies v1.988 | KDM5C |
Arina Puzriakova Added comment: Comment on mode of inheritance: A subset of female carriers have been shown to have impaired intellectual development and/or developmental delay (PMIDs: 10982473; 16538222; 18697827; 19826449; 21575681; 32279304) showing that females can be symptomatic. Therefore, the MOI should be updated from 'X-linked.. biallelic in females' to 'X-linked.. monoallelic in females may cause disease' at the next GMS panel update. This also reflects the current MOI on all other relevant panels. |
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| Fetal anomalies v1.980 | GNAS | Sarah Leigh Phenotypes for gene: GNAS were changed from Pseudohypoparathyroidism Ia, OMIM:103580; pseudohypoparathyroidism type 1A, MONDO:0007078; Pseudohypoparathyroidism Ib, OMIM:603233; pseudohypoparathyroidism type 1B, MONDO:0011301; Pseudohypoparathyroidism Ic, OMIM:612462; pseudohypoparathyroidism type 1C, MONDO:0012911; McCune-Albright syndrome, somatic, mosaic, OMIM:174800; panostotic fibrous dysplasia, MONDO:0043168; Osseous heteroplasia, progressive, OMIM:166350; ACTH-independent macronodular adrenal hyperplasia. OMIM:219080; ACTH-independent macronodular adrenal hyperplasia 1, MONDO:0020735; Pseudopseudohypoparathyroidism, OMIM:612463; pseudopseudohypoparathyroidism, MONDO:0012912 to Pseudohypoparathyroidism Ia, OMIM:103580; pseudohypoparathyroidism type 1A, MONDO:0007078; Pseudohypoparathyroidism Ib, OMIM:603233; pseudohypoparathyroidism type 1B, MONDO:0011301; Pseudohypoparathyroidism Ic, OMIM:612462; pseudohypoparathyroidism type 1C, MONDO:0012911; McCune-Albright syndrome, somatic, mosaic, OMIM:174800; panostotic fibrous dysplasia, MONDO:0043168; Osseous heteroplasia, progressive, OMIM:166350; progressive osseous heteroplasia, MONDO:0008153; ACTH-independent macronodular adrenal hyperplasia. OMIM:219080; ACTH-independent macronodular adrenal hyperplasia 1, MONDO:0020735; Pseudopseudohypoparathyroidism, OMIM:612463; pseudopseudohypoparathyroidism, MONDO:0012912 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.978 | GNAS | Sarah Leigh Phenotypes for gene: GNAS were changed from GNAS HYPERFUNCTION; ALBRIGHT HEREDITARY OSTEODYSTROPHY; ACTH-INDEPENDENT MACRONODULAR ADRENAL HYPERPLASIA; PSEUDOHYPOPARATHYROIDISM TYPE 1B to Pseudohypoparathyroidism Ia, OMIM:103580; pseudohypoparathyroidism type 1A, MONDO:0007078; Pseudohypoparathyroidism Ib, OMIM:603233; pseudohypoparathyroidism type 1B, MONDO:0011301; Pseudohypoparathyroidism Ic, OMIM:612462; pseudohypoparathyroidism type 1C, MONDO:0012911; McCune-Albright syndrome, somatic, mosaic, OMIM:174800; panostotic fibrous dysplasia, MONDO:0043168; Osseous heteroplasia, progressive, OMIM:166350; ACTH-independent macronodular adrenal hyperplasia. OMIM:219080; ACTH-independent macronodular adrenal hyperplasia 1, MONDO:0020735; Pseudopseudohypoparathyroidism, OMIM:612463; pseudopseudohypoparathyroidism, MONDO:0012912 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.909 | AGT | Arina Puzriakova Phenotypes for gene: AGT were changed from Renal dysgenesis to Renal tubular dysgenesis, OMIM:267430 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.905 | WNT7B |
Arina Puzriakova Added comment: Comment on list classification: New gene added by Julia Baptista. There is sufficient evidence to promote this gene to Green at the next GMS panel update. Three families reported with fetuses with multiple congenital anomalies (PMID: 35790350). Biallelic variants were identified in probands of two families and parents in third family were both heterozygous for a variant found in one of the other families. Although the fetus was not available for testing, the genotype can be inferred as homozygous for the variant given the consistent phenotype between cases. Supportive zebrafish model supports pathogenicity. |
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| Fetal anomalies v1.900 | RAB11A |
Eleanor Williams changed review comment from: PMID: 29100083 - Hamdan et al 2017 - performed WGS on 197 individuals with unexplained Developmental and epileptic encephalopathy and pharmaco-resistant seizures and in their unaffected parents. 2 patients reported with heterozygous missense variants in RAB11A, one of which had seizures (c.244C>T [p.Arg82Cys] variant) in addition to developing severe ID. 2 other individuals with missense variants in RAB11A and some phenotypic data from the DDD project are described. For 3 of the 4 individuals there are brain MRI data which indicate brain abnormalities including partial agenesis of the corpus callosum, or thin corpus collosum. PMID: 33875846 - Bertoli-Avella et al 2021 - in a large study of patients with no initial diagnostic variants identified by ES/GS, they identified two different heterozygous missense variants in RAB11A in two unrelated patients (NM_004663.4: c.375G>T, p. Lys125Asn and NM_004663.4: c.380A>G, p. Asp127Gly). Both are reported to have microcephaly (degree not stated) and brain anomalies (both with agenesis of corpus callosum, and one with additional abnormal cortical gyration, mylation abnormalites).; to: PMID: 29100083 - Hamdan et al 2017 - performed WGS on 197 individuals with unexplained Developmental and epileptic encephalopathy and pharmaco-resistant seizures and in their unaffected parents. 2 patients reported with heterozygous missense variants in RAB11A, one of which had seizures (c.244C>T [p.Arg82Cys] variant) in addition to developing severe ID. 2 other individuals with missense variants in RAB11A and some phenotypic data from the DDD project are described. For 3 of the 4 individuals there are brain MRI data which indicate brain abnormalities including partial agenesis of the corpus callosum, or thin corpus collosum. PMID: 33875846 - Bertoli-Avella et al 2021 - in a large study of patients with no initial diagnostic variants identified by ES/GS, they identified two different heterozygous missense variants in RAB11A in two unrelated patients (NM_004663.4: c.375G>T, p. Lys125Asn and NM_004663.4: c.380A>G, p. Asp127Gly). Both are reported to have microcephaly (degree not stated) and brain anomalies (both with agenesis of corpus callosum, and one with additional abnormal cortical gyration, myelination abnormalites). |
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| Fetal anomalies v1.900 | CHRM3 |
Rhiannon Mellis gene: CHRM3 was added gene: CHRM3 was added to Fetal anomalies. Sources: Expert Review,Literature Mode of inheritance for gene: CHRM3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: CHRM3 were set to PMID: 22077972; 31441039; 10944224 Phenotypes for gene: CHRM3 were set to Prune belly syndrome; Megacystis Review for gene: CHRM3 was set to AMBER Added comment: This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH). Outcome of review: May be fetally relevant but currently limited evidence, support adding to the Fetal anomalies panel as Amber gene. Details of review: Discussed as a potential cause of megacystis. Currently Red on Panelapp CAKUT panel (2016) because at that time there was only 1 reported family and a mouse model. The unpublished data mentioned in that panelapp review (from Adrian Woolf, Manchester) is now published so now 2 families PMID: 22077972; 31441039 plus a mouse model PMID: 10944224. However, prenatal findings (distended bladder and unilateral hydronephrosis) only documented for one individual. More evidence of prenatal phenotype would be helpful. Sources: Expert Review, Literature |
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| Fetal anomalies v1.900 | DEPDC5 |
Rhiannon Mellis commented on gene: DEPDC5: This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH). Outcome of review: May be fetally relevant but currently limited evidence, support adding to the Fetal anomalies panel as Amber gene. Currently rated Green on the following other PanelApp panel(s): Intellectual disability, Genetics epilepsies. Amber on cortical malformations panel. Details of review: Previously reviewed as Red because only associated with familial epilepsy without structural brain anomalies (AD - caused by het LOF variants) but data presented by Dr Lara Menzies at CGS Spring Meeting 2021 suggests that there may also be a biallelic phenotype with hypomorphic variants. 5 cases presented from 3 unrelated Irish traveller families with significant polymicrogyria and macrocephaly as well as seizures and severe dev delay. At least 2 of the cases had prenatal features: ventriculomegaly, macrocephaly and IUGR for one, polymicrogyria on MRI for another - fetal MRI done because of FHx of affected child. (Unpublished data) Liu et al 2020 (PMID: 32848577) report one case with homozygous missense variants in this gene, who had focal cortical dysplasia and seizures from 3yo |
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| Fetal anomalies v1.900 | ENG |
Rhiannon Mellis gene: ENG was added gene: ENG was added to Fetal anomalies. Sources: Expert Review,Literature Mode of inheritance for gene: ENG was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Phenotypes for gene: ENG were set to Telangiectasia, hereditary hemorrhagic, type 1 Review for gene: ENG was set to AMBER Added comment: This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH). Outcome of review: May be fetally relevant but currently limited evidence, support adding to the Fetal anomalies panel as Amber gene. Details of review: Consistency check because out of 4 known HHT genes EPHB4 and SMAD4 are on the fetal anomalies panel but ACVRL1 and ENG are not. No specific published reports of ENG variants detected prenatally but correlates with pulmonary AVMs which can present neonatally and can be detected on prenatal US (PMID: 17719943; PMID: 21988128). Sources: Expert Review, Literature |
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| Fetal anomalies v1.900 | PIGS |
Rhiannon Mellis gene: PIGS was added gene: PIGS was added to Fetal anomalies. Sources: Expert Review,Literature Mode of inheritance for gene: PIGS was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PIGS were set to PMID: 30269814 Phenotypes for gene: PIGS were set to Developmental and epileptic encephalopathy 95 Review for gene: PIGS was set to AMBER Added comment: This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH). Outcome of review: May be fetally relevant but currently limited evidence, support adding to the Fetal anomalies panel as Amber gene. Details of review: Currently red/amber on some other panels but reviewed on Congenital disorders of glycosylation panel as having sufficient evidence for green rating at next major review, in light of this same paper (PMID: 30269814). Three unrelated families reported. Severe neurological phenotype ranging from fetal akinesia to intellectual disability/epileptic encephalopathy. Fetal akinesia phenotype may be relevant for fetal anomalies panel. Sources: Expert Review, Literature |
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| Fetal anomalies v1.900 | MRPS16 |
Rhiannon Mellis gene: MRPS16 was added gene: MRPS16 was added to Fetal anomalies. Sources: Expert Review,Literature Mode of inheritance for gene: MRPS16 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: MRPS16 were set to PMID: 28749478 Phenotypes for gene: MRPS16 were set to Combined oxidative phosphorylation deficiency 2 Review for gene: MRPS16 was set to AMBER Added comment: This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH). Outcome of review: May be fetally relevant but currently limited evidence, support adding to the Fetal anomalies panel as Amber gene. Details of review: Amber on mitochondrial/inborn errors of metabolism etc. Not Green on any panel. One previous case reported with "agenesis of the corpus callosum, dysmorphism, and fatal neonatal lactic acidosis. The patient was small at birth, with dysmorphic facies, low-set ears, nonpitting edema of the limbs, brachydactyly, and redundant skin over the neck. She died of intractable metabolic acidosis at age 3 days." PMID:15505824 (2004). One further fetal case reported by Shamseldin et al. 2018 (PMID: 28749478) with hydrops, very short long bones, and partial ACC Sources: Expert Review, Literature |
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| Fetal anomalies v1.900 | THSD1 |
Rhiannon Mellis gene: THSD1 was added gene: THSD1 was added to Fetal anomalies. Sources: Expert Review,Literature Mode of inheritance for gene: THSD1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: THSD1 were set to PMID: 28749478; 26036949 Phenotypes for gene: THSD1 were set to Intracerebral aneurysms; ?Hydrops fetalis Review for gene: THSD1 was set to AMBER Added comment: This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH). Outcome of review: May be fetally relevant but currently limited evidence, support adding to the Fetal anomalies panel as Amber gene pending more evidence. Details of review: Not currently Green on any panels. Amber on Cerebral vascular malformations. (Heterozygous mutations identified in nine families with intracerebral aneurysms plus animal models but unclear on penetrance.) Shamseldin et al 2018 (PMID: 28749478) report a fetal case with hydrops and a HOMOZYGOUS likely pathogenic variant in THSD1. The same group previously identified this same founder mutation in THSD1 in another 3 families with hydrops/oedema (PMID: 26036949) Sources: Expert Review, Literature |
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| Fetal anomalies v1.900 | MYBPC3 |
Rhiannon Mellis gene: MYBPC3 was added gene: MYBPC3 was added to Fetal anomalies. Sources: Expert Review,Literature Mode of inheritance for gene: MYBPC3 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Publications for gene: MYBPC3 were set to PMID: 28749478; 19858127 Phenotypes for gene: MYBPC3 were set to Cardiomyopathy; ?Congenital myopathy Review for gene: MYBPC3 was set to AMBER Added comment: This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH). Outcome of review: May be fetally relevant but currently limited evidence, support adding to the Fetal anomalies panel as Amber gene pending more evidence. Currently rated Green on the following other PanelApp panel(s): Various cardiomyopathy panels. Amber on congenital myopathy panel. Details of review: Previously only one (AR) case with skeletal muscle phenotype, although is a known cardiomyopathy gene (PMID: 19858127). One fetal case reported by Shamseldin et al 2018 (PMID: 28749478) with hydrops. Sources: Expert Review, Literature |
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| Fetal anomalies v1.900 | CACNA1S |
Rhiannon Mellis gene: CACNA1S was added gene: CACNA1S was added to Fetal anomalies. Sources: Expert Review,Literature Mode of inheritance for gene: CACNA1S was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: CACNA1S were set to PMID: 33060286; 28012042 Phenotypes for gene: CACNA1S were set to Congenital myopathy; arthrogryposis Review for gene: CACNA1S was set to AMBER Added comment: This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH). Outcome of review: May be fetally relevant but currently limited evidence, support adding to the Fetal anomalies panel as Amber gene. Details of review: Previously only monoallelic variants reported associated with malignant hyperthermia and periodic paralysis but more recently biallelic variants have been associated with congenital myopathy. In Ravenscroft et al 2020 (PMID: 33060286) the reported biallelic variants were VUS but strong suspicion of causality: the proband had polyhydramnios, scalp oedema, bilateral wrist contractures, bilateral talipes and reduced fetal movements, ToP at 26/40. Mild facial dysmorphic features were noted on autopsy, including low anterior hairline, mild hypertelorism and moderate retrognathia. A previous pregnancy was affected with polyhydramnios and reduced fetal movements, delivered at 32/40 due to placental abruption and died at 10 days. On photos the baby had ptosis and broad nasal tip. The biallelic variants segregated within the family (parents and the 2 unaffected sibs all het). No cell lines available for functional studies. Another study (PMID: 28012042) reports 7 families with congenital myopathy and CACNA1S mutations (both recessive and dominant), of whom 3 had cases with antenatal onset (reduced fetal movements). Sources: Expert Review, Literature |
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| Fetal anomalies v1.900 | NDUFB10 |
Rhiannon Mellis gene: NDUFB10 was added gene: NDUFB10 was added to Fetal anomalies. Sources: Expert Review,Literature Mode of inheritance for gene: NDUFB10 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: NDUFB10 were set to PMID: 31130284; 28040730 Phenotypes for gene: NDUFB10 were set to Mitochondrial complex I deficiency Review for gene: NDUFB10 was set to AMBER Added comment: This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH). Outcome of review: May be fetally relevant but currently limited evidence, support adding to the Fetal anomalies panel as Amber gene. Details of review: Not Green on any other panels (Amber/Red because only 1 case reported, with functional studies). Causes Mitochondrial complex 1 deficiency. One fetal case reported by Monies et al 2019 (PMID: 31130284) with Non-immune hydrops fetalis and died after birth. The previous reported case on OMIM (from PMID: 28040730) was a female infant with IUGR, hydrops, lung hypoplasia and fetal cardiomyopathy - neonatal death with rapidly progressive lactic acidosis and PM found decreased complex 1 activity in skeletal muscle, heart, liver. Previous child of parents also had hydrops and died on day 1 of life. Sources: Expert Review, Literature |
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| Fetal anomalies v1.900 | FTO |
Rhiannon Mellis gene: FTO was added gene: FTO was added to Fetal anomalies. Sources: Expert Review,Literature Mode of inheritance for gene: FTO was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: FTO were set to PMID: 31130284; 19559399; 26378117 Phenotypes for gene: FTO were set to Growth retardation, developmental delay, facial dysmorphism Review for gene: FTO was set to AMBER Added comment: This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH). Outcome of review: May be fetally relevant but currently limited evidence, support adding to the Fetal anomalies panel as Amber gene. Details of review: Not Green on any panels (only 2 families reported to date). On OMIM: Growth retardation, developmental delay, facial dysmorphism. One fetal case reported by Monies et al 2019 (PMID: 31130284) with Dandy-Walker malformation, IUGR, and polyhydramnios. This fits with the phenotype reported in one consanguineous family with 9 affected individuals reported by Boissel 2009 PMID: 19559399. The other reported case is PMID: 26378117 - a homozygous missense variant in FTO was identified in a 21-month old girl who presented with growth retardation, failure to thrive, severely delayed development, Dysmorphic facial features, decreased brain parenchyma, delayed myelination, and a thin corpus callosum. Sources: Expert Review, Literature |
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| Fetal anomalies v1.900 | AGT |
Rhiannon Mellis gene: AGT was added gene: AGT was added to Fetal anomalies. Sources: Literature,Expert Review Mode of inheritance for gene: AGT was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: AGT were set to PMID: 28976722 Phenotypes for gene: AGT were set to Renal dysgenesis Review for gene: AGT was set to AMBER Added comment: This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH). Outcome of review: May be fetally relevant but currently limited evidence, support adding to the Fetal anomalies panel as Amber gene pending more evidence. Currently rated Green on the following other PanelApp panel(s): CAKUT and unexplained kidney failure in young people Details of review: Fu et al 2018 (PMID: 28976722) report one fetal case with Right multicystic dysplastic kidney Sources: Literature, Expert Review |
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| Fetal anomalies v1.900 | UNC13D |
Rhiannon Mellis gene: UNC13D was added gene: UNC13D was added to Fetal anomalies. Sources: Literature,Expert Review Mode of inheritance for gene: UNC13D was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: UNC13D were set to PMID: 33249554 Phenotypes for gene: UNC13D were set to Pancytopenia; ?Hydrops fetalis Review for gene: UNC13D was set to AMBER Added comment: This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH). Outcome of review: May be fetally relevant but currently limited evidence, support adding to the Fetal anomalies panel as Amber gene. Currently rated Green on the following other PanelApp panel(s): primary immunodeficiency Details of review: One fetal case reported in Diderich et al 2020 (PMID: 33249554) with hydrops, presumed secondary to fetal anaemia. Sources: Literature, Expert Review |
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| Fetal anomalies v1.900 | SERPINA11 |
Rhiannon Mellis gene: SERPINA11 was added gene: SERPINA11 was added to Fetal anomalies. Sources: Expert Review,Literature Mode of inheritance for gene: SERPINA11 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SERPINA11 were set to PMID: 31742715; 28749478 Phenotypes for gene: SERPINA11 were set to ?Hydrops fetalis Review for gene: SERPINA11 was set to AMBER Added comment: This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH). Outcome of review: May be fetally relevant but currently limited evidence, support adding to the Fetal anomalies panel as Amber gene to watch for further evidence. Not currently rated Green on any other PanelApp panel(s). Details of review: No OMIM disease association currently. Reported as a novel genotype-phenotype association in Aggarwal 2020 (PMID: 31742715) in a fetus with homozygous nonsense variant. Fetus presented with pericardial effusion and on post-mortem was found to have serous cavity effusions, and generalised blebs of gelatinous material on the visceral surfaces. Histopathology and stains showed derangement of ECM and collagen fibres. Consanguineous couple with one similarly affected previous pregnancy. This gene is also reported in Shamseldin et al 2018 (PMID: 28749478) as a candidate gene in a fetus with hydrops. Sources: Expert Review, Literature |
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| Fetal anomalies v1.900 | LOX |
Rhiannon Mellis gene: LOX was added gene: LOX was added to Fetal anomalies. Sources: Expert Review,Literature Mode of inheritance for gene: LOX was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: LOX were set to PMID: 31742715 Phenotypes for gene: LOX were set to Aortopathy Review for gene: LOX was set to AMBER Added comment: This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH). Outcome of review: May be fetally relevant but currently limited evidence, support adding to the Fetal anomalies panel as Amber gene. Currently rated Green on the following other PanelApp panel(s): familial thoracic aortic aneurysm Details of review: Reported as a novel genotype-phenotype association in Aggarwal et al 2020 (PMID: 31742715), in a fetus with homozygous missense variants. Heterozygous variants in this gene are known to cause thoracic aortic aneurysm. The fetus presented with unexplained IUD and on post-mortem had: Excessive skin folds, emphysematous bullae on lung surface, Facial dysmorphism, distal joint contractures, internal haemorrhages. Histopathology and special stains confirmed degradation of collagen and elastin in the aorta, pleura and skin. If we are going to add to panel suggest putting MOI as biallelic only (and accept that this would be an incidental finding for carrier parents that would lead to them needing monitoring for aortic aneurysm) Sources: Expert Review, Literature |
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| Fetal anomalies v1.880 | SPTA1 |
Rhiannon Mellis gene: SPTA1 was added gene: SPTA1 was added to Fetal anomalies. Sources: Literature,Expert Review Mode of inheritance for gene: SPTA1 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Publications for gene: SPTA1 were set to PMID: 34132406; PMID: 31333484 Phenotypes for gene: SPTA1 were set to Hydrops fetalis; Congenital anaemia Review for gene: SPTA1 was set to AMBER Added comment: This gene and phenotype were reviewed during a meeting on 21st July 2022 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rhiannon Mellis (North Thames GLH), and Stephanie Allen, Denise Williams, Esther Kinning and Anna de Burca (Central & South GLH). Outcome of review: Likely that the phenotype is fetally relevant, support adding to the Fetal anomalies panel as an Amber gene, pending further evidence and review of other congenital anaemia genes that may cause hydrops. Currently rated Green on the following other PanelApp panel(s): Congenital anaemias Details of review: The fetal case in Wagner et al 2021 (PMID: 34132406) had hydrops secondary to severe fetal anaemia at 28/40. Chonat et al 2019 (PMID: 31333484) also report 3 further unrelated cases with hydrops/fetal anaemia. Sources: Literature, Expert Review |
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| Fetal anomalies v1.880 | NEXN |
Rhiannon Mellis gene: NEXN was added gene: NEXN was added to Fetal anomalies. Sources: Literature,Expert Review Mode of inheritance for gene: NEXN was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: NEXN were set to PMID: 32058062; PMID: 33027564 Phenotypes for gene: NEXN were set to Cardiomyopathy Review for gene: NEXN was set to AMBER Added comment: This gene and phenotype were reviewed during a meeting on 21st July 2022 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rhiannon Mellis (North Thames GLH), and Stephanie Allen, Denise Williams, Esther Kinning and Anna de Burca (Central & South GLH). Outcome of review: Gene usually causes adult-onset AD cardiomyopathy. However, there may be a fetally relevant phenotype with biallelic variants. Support adding to the Fetal anomalies panel as an Amber gene, pending more evidence of fetal phenotype (only 2 reported unrelated cases to date). Currently rated Green on the following other PanelApp panel(s): Cardiomyopathy (dilated) Details of review: The fetal case in Sparks et al (PMID: 33027564) had pericardial effusion, ascites, cardiomegaly, dilation and hypertrophy of cardiac ventricles, hypoplastic and dysplastic aortic valve, diminished systolic function, fetal growth restriction, and was stillborn. 2 NEXN variants found in the fetus (1 mat inherited, 1 de novo) but unable to confirm phase. The fetal case in Rinaldi et al 2021 (PMID: 32058062) had Cardiomegaly, low contractility/outflow, fibroelastosis of right ventricle. The fetus was compound het for NEXN variants and parents were both unaffected het with normal echos. They'd had one previous pregnancy with same phenotype. Sources: Literature, Expert Review |
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| Fetal anomalies v1.873 | WNT7B |
Julia Baptista gene: WNT7B was added gene: WNT7B was added to Fetal anomalies. Sources: Expert Review Mode of inheritance for gene: WNT7B was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: WNT7B were set to 35790350 Phenotypes for gene: WNT7B were set to Pulmonary hypoplasia; Diaphragmatic anomalies; Anophthalmia/Microphthalmia; Cardiac defects Review for gene: WNT7B was set to GREEN Added comment: One homozygous nonsense variant identified in family 1. Compound heterozygous missense and nonsense variants identified in two affected fetuses in family 2. A third family with limited phenotypic information available, with parents heterozygous for the same nonsense variant, p. (Arg98Ter), identified in family 1, but no segregation studies in the affected. Animal studies in Danio rerio were supportive. Lung hypoplasia with tracheal, ocular, cardiac, and renal defects. Sources: Expert Review |
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| Fetal anomalies v1.873 | MTM1 | Arina Puzriakova Added comment: Comment on mode of inheritance: Rare manifesting females have been reported, including a heterozygous female with prenatal/neonatal onset (PMID: 12707446). MOI should therefore be updated form XLR to XLD at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.870 | SRY | Eleanor Williams commented on gene: SRY: Added Y chromosome tag to indicate this gene is encoded on the Y chromosome, which is currently not included in the Bioinformatics tiering pipeline. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.868 | CYP11B1 | Arina Puzriakova Added comment: Comment on mode of inheritance: Only biallelic MOI is relevant to this panel, causing Adrenal hyperplasia, congenital, due to 11-beta-hydroxylase deficiency, OMIM:202010, characterised by androgen excess, virilization, and hypertension (can be detected prenatally by increased levels of tetrahydro-11-deoxycortisol in the amniotic fluid). On the other hand, AD disease arises in the form of familial hyperaldosteronism/hypertension in childhood to early adulthood and therefore should be excluded from the fetal panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.867 | CYP11B1 | Arina Puzriakova Phenotypes for gene: CYP11B1 were changed from Aldosteronism, glucocorticoid-remediable 103900; Adrenal hyperplasia, congenital, due to 11-beta-hydroxylase deficiency 202010 to Adrenal hyperplasia, congenital, due to 11-beta-hydroxylase deficiency, OMIM:202010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.864 | ZFPM2 |
Anna de Burca gene: ZFPM2 was added gene: ZFPM2 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: ZFPM2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: ZFPM2 were set to 24702427 Phenotypes for gene: ZFPM2 were set to Congenital diaphragmatic hernia Penetrance for gene: ZFPM2 were set to Incomplete Review for gene: ZFPM2 was set to AMBER Added comment: Paper suggests that ZFPM2 variants may be associated with isolated congenital diaphragmatic hernia, but penetrance appears reduced. Given the apparently reduced penetrance and since isolated CDH is a relatively common congenital finding, the gene-disease association remains uncertain. Of note, variants in this gene have also been associated with 46,XY sex reversal and Tetralogy of Fallot. Sources: Literature |
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| Fetal anomalies v1.859 | DISP1 | Arina Puzriakova commented on gene: DISP1: Added 'watchlist' tag as inclusion of this gene on the R85 Holoprosencephaly panel is currently under GMS review (TBC_NHSE) and the final decision should also be reflected on this panel once determined. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.854 | LIFR |
Eleanor Williams changed review comment from: Heterozygous variants in LIFR are associated with a CAKUT phenotype, while homozygous variants are associated with skeletal Stuve-Wiedemann syndrome/Schwartz-Jampel type 2 syndromes. At the moment the mode of inheritance for this gene on the Fetal anomalies panel is biallelic only. GMS fetal group input is needed to decide whether the mode of inheritance for this gene should also include monoallelic cases as the renal phenotype might be detected antenatally e.g. hydronephrosis.; to: Heterozygous variants in LIFR are associated with a CAKUT phenotype, while homozygous variants are associated with skeletal Stuve-Wiedemann syndrome/Schwartz-Jampel type 2 syndromes. At the moment the mode of inheritance for this gene on the Fetal anomalies panel is biallelic only. GMS fetal group input is needed to decide whether the mode of inheritance for this gene should also include monoallelic cases as the renal phenotype might be detected antenatally e.g. hydronephrosis. The paper describing the CAKUT cases is PMID: 28334964 (Kosfeld et al 2017). |
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| Fetal anomalies v1.847 | PEX6 | Sarah Leigh edited their review of gene: PEX6: Added comment: For Peroxisome biogenesis disorder 4B (OMIM:614863), Falkenberg et al (PMID: 29220678) has identified Allelic Expression Imbalance (AEI) as a mechanism responsible for the condition. Affected patients (7 unrelated cases) were monoallelic for rs61753230 (c.2578C>T, p.Arg860Trp) and rs144286892 (c.∗442_445 delTAAA), with these variants being on the same chromosome (cis). It would appear that rs144286892 causes the over expression of the allele that it is on, resulting in over expression of rs61753230. The unaffected parents analysed were monoallelic for rs61753230 and biallelic for rs144286892, resulting in overexpression of both rs61753230 and wild type alleles (PMID: 29220678). Experimental evidence revealed that rs61753230 has a dominant-negative effect on the function of the PEX1- PEX6 complex in peroxisomal matrix protein import (PMID: 29220678).; Changed mode of pathogenicity: Other; Changed mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.845 | PEX6 | Sarah Leigh Added comment: Comment on mode of inheritance: The Q1_22_MOI tag has been added to this gene. The mode of inheritance for PEX6 should be set to: BOTH monoallelic and biallelic, autosomal or pseudoautosomal, in order to detect the dominant Peroxisome biogenesis disorder 4B (OMIM:614863). Incomplete penetrance has been noted, in order to highlight that unaffected parents may also carry rs61753230. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.827 | RAC3 |
Rhiannon Mellis gene: RAC3 was added gene: RAC3 was added to Fetal anomalies. Sources: Literature,Expert Review,NHS GMS Mode of inheritance for gene: RAC3 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: RAC3 were set to 30293988; 29276006 Phenotypes for gene: RAC3 were set to Abnormality of brain morphology; Abnormal muscle tone; Neurodevelopmental delay; Intellectual disability Mode of pathogenicity for gene: RAC3 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments Review for gene: RAC3 was set to GREEN Added comment: This gene already has sufficient evidence for Green rating on the ID panel (see below) and now adding evidence (from NHS GMS testing) for prenatal phenotype to support Green rating for the Fetal Anomalies panel also: A RAC3 likely pathogenic missense variant has been identified postnatally in a baby that presented prenatally with absent corpus callosum, bilateral ventriculomegaly, cerebellar and brainstem hypoplasia detected on fetal ultrasound and MRI. The variant is judged by the child's clinical team to be causative of the clinical and radiological features in the child. Copied from Green review on Intellectual Disability panel by Konstantinos Varvagiannis: PMID: 30293988 reports on 5 individuals (from 4 different families) with de novo missense variants in RAC3. All individuals demonstrated structural anomalies on brain MRI (notably agenesis/dysgenesis of the corpus callosum, variable degrees of polymicrogyria and ventricular anomalies) as well as shared non-specific neurological features including abnormal muscular tone, global developmental delay and severe to profound intellectual disability. Feeding difficulties were observed in 4/5 patients. All variants reported are missense and are presumed to result in constitutive protein activation, as suggested by previous observations either in RAC3 [eg. the p.(Gln61Leu) mutation] or the highly homologous RAC1 and RAC2. According to the authors this is further supported by the fact that Rac3 -/- mice do not show a severe phenotype while missense variants are underrepresented in the ExAC database (z=1.97) as opposed to loss-of-function variants (pLI=0.04 / probability of loss-of-function intolerance). Of the 3 SNVs reported, 2 variants were in adjacent amino-acid positions [p.(Gln61Leu) and p.(Glu62Lys)]. The latter variant was found in 2 half-sibs born to different fathers, due to suspected maternal gonadal mosaicism (variant absent in all sequencing reads in the maternal DNA sample). The specific variant was also found in a further affected individual from an unrelated family. Finally, as the authors point out a further individual with de novo RAC3 missense variant [p.(Ala59Gly)] was reported previously in an individual with thin corpus callosum and global developmental delay, although the phenotype was felt to be more reminiscent of Robinow syndrome (PMID: 29276006). Sources: Literature, Expert Review, NHS GMS |
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| Fetal anomalies v1.811 | CLPB | Arina Puzriakova Added comment: Comment on mode of inheritance: Association between biallelic variants and disease is well established, with more than 35 affected individuals reported. Recently, Wortmann et al. 2021 (PMID: 34140661) published six unrelated individuals with one of four different de novo monoallelic missense variants in CLPB. The phenotype strongly overlapped with that observed in the recessive disease. No prenatal findings were specifically mentioned but given the otherwise comparable clinical presentations, monoallelic inheritance may also be of relevance to this panel. Therefore, will flag this for further GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.803 | CNBP_CCTG | Arina Puzriakova Added comment: Comment on list classification: There is enough evidence to support the gene-disease association but setting rating to Red as currently the performance of the pipeline for this STR is very poor as it is located in a complex locus. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.802 | CNBP_CCTG |
Arina Puzriakova STR: CNBP_CCTG was added STR: CNBP_CCTG was added to Fetal anomalies. Sources: Expert Review STR, NGS Not Validated tags were added to STR: CNBP_CCTG. Mode of inheritance for STR: CNBP_CCTG was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Phenotypes for STR: CNBP_CCTG were set to Myotonic dystrophy 2, OMIM:602668 Added comment: The mutation is a CCTG repeat expansion in intron 1 of the CNBP (ZNF9) gene. The range of expanded allele sizes is 75 to 11,000 CCTG repeats, whereas normal is up to 30. The CCTG repeat tract in normal alleles typically contains one or more tetranucleotide interruptions. The sequence interruptions that are routinely found within the CCTG tracts of normal alleles are not found in sequenced pathogenic CCTG expansions of CNBP alleles. On transmission to the next generation, CNBP repeat length sometimes diminishes dramatically, without significant differences determined by the gender of the transmitting parent. ----- Copied from Rhiannon Mellis (GOSH) review of gene CNBP on Fetal anomalies panel: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Sources: Expert Review |
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| Fetal anomalies v1.801 | CNBP |
Arina Puzriakova Tag nucleotide-repeat-expansion tag was added to gene: CNBP. Tag currently-ngs-unreportable tag was added to gene: CNBP. |
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| Fetal anomalies v1.796 | MMP15 |
Ivone Leong Added comment: Comment on list classification: New gene added by Dmitrijs Rots (RadboudUMC). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. PMID: 33875846 describes 3 patients from 2 families with biallelic variants in MMP15 (one is Pro353fs and other is Gly231Arg). One family with 2 affected siblings presented with cholestasis, hepatomegaly, high hepatic transaminases, and congenital heart disease. The other unrelated case showed similar symptoms. As there are only 2 cases and currently there are no animal models that replicate the human phenotype this gene has been given an Amber rating until more evidence is available. |
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| Fetal anomalies v1.771 | GREB1L | Arina Puzriakova Phenotypes for gene: GREB1L were changed from Renal hypodysplasia/aplasia 3, 617805; renal agenesis to Renal hypodysplasia/aplasia 3, OMIM:617805; Renal agenesis, MONDO:0018470 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.749 | CSF1R |
Rhiannon Mellis gene: CSF1R was added gene: CSF1R was added to Fetal anomalies. Sources: Expert Review Mode of inheritance for gene: CSF1R was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: CSF1R were set to PMID: 30982608 Phenotypes for gene: CSF1R were set to Brain abnormalities, neurodegeneration, and dysosteosclerosis (BANDDOS) Review for gene: CSF1R was set to GREEN Added comment: This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH). Outcome of review: Confirmed that the phenotype is fetally relevant, support adding to the Fetal anomalies panel as a Green gene. Details of review: Homozygous variants cause Brain abnormalities, neurodegeneration, and dysosteosclerosis (BANDDOS). Skeletal phenotype is osteopetrosis, dysosteosclerosis, platyspondyly, widened metaphyses. Brain anomalies include ACC and Dandy walker. At least one reported case of prenatal presentation with multiple brain anomalies - PubMed: 30982608 NB Bilallelic LOF variants cause this condition with fetally relevant phenotype but Monoallelic variants with dominant-negative effect cause an adult-onset neurodegenerative disease. Only for fetal reporting in BIALLELIC form Sources: Expert Review |
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| Fetal anomalies v1.749 | PRIM1 |
Rhiannon Mellis gene: PRIM1 was added gene: PRIM1 was added to Fetal anomalies. Sources: Literature,Expert Review Mode of inheritance for gene: PRIM1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PRIM1 were set to PMID: 33060134 Phenotypes for gene: PRIM1 were set to Primordial dwarfism Review for gene: PRIM1 was set to GREEN Added comment: This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH). Outcome of review: Confirmed that the phenotype is fetally relevant, support adding to the Fetal anomalies panel as a Green gene. Details of review: Parry et al 2020 (PMID: 33060134) report this as a novel disease gene - biallelic LOF mutations in 5 patients (from 4 families) with primordial dwarfism phenotype, including prenatal features of IUGR and extreme microcephaly with simplified gyri. Sources: Literature, Expert Review |
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| Fetal anomalies v1.749 | CDK8 |
Rhiannon Mellis gene: CDK8 was added gene: CDK8 was added to Fetal anomalies. Sources: Literature,Expert Review Mode of inheritance for gene: CDK8 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: CDK8 were set to PMID: 31742715; 30905399 Phenotypes for gene: CDK8 were set to Syndromic developmental disorder with hypotonia and behavioural abnormalities Review for gene: CDK8 was set to GREEN Added comment: This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH). Outcome of review: Confirmed that the phenotype is fetally relevant, support adding to the Fetal anomalies panel as a Green gene. Already rated Green on the following other PanelApp panel(s): Intellectual disability; Severe paediatric disorders Details of review: Aggarwal et al 2020 report a heterozygous nonsense variant in a fetus with ventriculomegaly and Ebstein anomaly resulting in IUFD. Post-mortem found additionally congenital diaphragmatic hernia, common atrium and facial dysmorphism. This nonsense variant is at the same position as a hotspot for missense variants reported in a paediatric cohort (Calpena et al 2019, PMID: 30905399) with overlapping but milder phenotype: half of the 12 children in that cohort had cardiac defects, most had dysmorphic features - hence Aggarwal et al propose that this is a more severe (prenatal) presentation of the same multiple malformation syndrome, caused here by a nonsense rather than missense mutation. Sources: Literature, Expert Review |
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| Fetal anomalies v1.746 | CYP11A1 | Arina Puzriakova Phenotypes for gene: CYP11A1 were changed from Adrenal insufficiency, congenital, with 46XY sex reversal, partial or complete 613743 to Adrenal insufficiency, congenital, with 46XY sex reversal, partial or complete, OMIM:613743 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.727 | SCUBE3 | Sarah Leigh changed review comment from: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene. At least 5 variants reported in 5 unrelated cases, together with supportive functional and mouse model studies (PMID 33308444).; to: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene. PMID 33308444 reports eight SCUBE variants in nine unrelated families, including eighteen affected members. In vtro studies demonstrated a variable impact of disease-causing variants on transcript processing, protein secretion and function, resulting in dysregulation on bone morphogenetic protein (BMP) signaling and a Scube3−/− mouse showed shared phenotypic features with OMIM:619184. Prenatal growth retardation was evident in 8/11 relevant cases. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.727 | BMPR1B |
Arina Puzriakova changed review comment from: Comment on mode of inheritance: Biallelic variants lead to the Demirhan type of acromesomelic dysplasia (MIM# 609441) which is pertinent to this panel. Monoallelic variants cause brachydactyly (MIM# 616849 and MIM# 112600) with dysplasia of only a single or few phalanges which would be difficult to diagnose prenatally. For this reason the MOI should remain as biallelic only on this panel.; to: Comment on mode of inheritance: Biallelic variants lead to the Demirhan type of acromesomelic dysplasia (MIM# 609441) which is pertinent to this panel. Monoallelic variants cause brachydactyly (MIM# 616849 and MIM# 112600) with dysplasia of only a single or few phalanges which would be difficult to diagnose prenatally. For this reason the MOI should remain as biallelic only on this panel. ----- Confirmed with clinical team that this is the appropriate MOI for this panel. |
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| Fetal anomalies v1.720 | WLS |
Zornitza Stark gene: WLS was added gene: WLS was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: WLS was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: WLS were set to 34587386 Phenotypes for gene: WLS were set to structural congenital anomalies Review for gene: WLS was set to GREEN Added comment: - Homozygous variants in 10 affected persons from 5 unrelated families. - Affected individuals had multiorgan defects, including microcephaly, facial dysmorphism, foot syndactyly, renal agenesis, alopecia, iris coloboma, and heart defects. - The mutations affected WLS protein stability and Wnt signaling. Knock-in mice showed tissue and cell vulnerability consistent with Wnt-signaling intensity and individual and collective functions of Wnts in embryogenesis. Sources: Literature |
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| Fetal anomalies v1.720 | WNT9B |
Zornitza Stark gene: WNT9B was added gene: WNT9B was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: WNT9B was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: WNT9B were set to 34145744 Phenotypes for gene: WNT9B were set to Renal agenesis/hypoplasia/dysplasia Review for gene: WNT9B was set to AMBER Added comment: WNT9B plays a key role in the development of the mammalian urogenital system. It is essential for the induction of mesonephric and metanephric tubules, the regulation of renal tubule morphogenesis, and the regulation of renal progenitor cell expansion and differentiation. WNT9B−/− mice have renal agenesis/hypoplasia and reproductive tract abnormalities. Lemire et al. (2021) report 4 individuals from 2 unrelated consanguineous families with bilateral renal agenesis/hypoplasia/dysplasia and homozygous variants in WNT9B. The proband from Family 1 had bilateral renal cystic dysplasia and chronic kidney disease, with 2 deceased siblings with bilateral renal hypoplasia/agenesis. The 3 affected family members were homozygous for a Gly317Arg missense variant in WNT9B. Proband from Family 2 had renal hypoplasia/dysplasia, chronic kidney disease, and was homozygous for a Pro5Alafs*52 nonsense variant in WNT9B. The proband's unaffected brother is also homozygous for the nonsense variant in WNT9B, suggesting nonpenetrance. I wasn't sure which panel this is more pertinent to: we have added this gene to our CAKUT panel. Sources: Literature |
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| Fetal anomalies v1.717 | GREB1L | Rhiannon Mellis edited their review of gene: GREB1L: Added comment: A further prenatal case reported in PMID 31974414 (Vora et al 2020) - c.4881_4882del; [p.H1627fs] inherited from parent, 2 affected pregnancies with bilateral renal agenesis plus a living child with single kidney.; Changed rating: GREEN; Changed publications to: PMID: 31424080, 32378186, 31974414 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.705 | PRKD1 | Arina Puzriakova Added comment: Comment on mode of inheritance: MOI was reassessed following a recent review by Zornitza Stark highlighting the potential involvement of biallelic variants. Currently the evidence for biallelic inheritance only suffices for an Amber rating and so I have kept the MOI as monoallelic but with a 'watchlist_MOI' tag to monitor for additional evidence. The Genomics England pipeline would still pick up biallelic cases under the current MOI. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.696 | BMPR1B | Arina Puzriakova Added comment: Comment on mode of inheritance: Biallelic variants lead to the Demirhan type of acromesomelic dysplasia (MIM# 609441) which is pertinent to this panel. Monoallelic variants cause brachydactyly (MIM# 616849 and MIM# 112600) with dysplasia of only a single or few phalanges which would be difficult to diagnose prenatally. For this reason the MOI should remain as biallelic only on this panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.692 | MYOD1 | Ivone Leong changed review comment from: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM but not in Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.; to: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics) on Congenital myopathy panel. This gene is associated with a relevant phenotype in OMIM but not in Gene2Phenotype. There is currently not enough evidence to support a gene-disease association on this panel (Fetal anomalies). Therefore, this gene has been given an Amber rating. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.689 | DMPK_CTG |
Arina Puzriakova Added comment: Comment on list classification: The genetic defect is an amplified trinucleotide CTG repeat in the 3'UTR (normal range: 5–37; pathological: >50–>2000). Evidence level for this is high - it is a confirmed DD gene for DYSTROPHIA MYOTONICA TYPE 1. The DMPK gene was demoted and this STR was added to this panel to ensure that cases are appropriately detected. Only relevant prenatally if it is a large expansion. A small expansion has adult onset and would be an incidental finding. Therefore, this STR will be flagged for GMS expert review to determine the appropriate 'pathogenic number of repeats' relevant to this panel. |
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| Fetal anomalies v1.687 | DMPK |
Arina Puzriakova changed review comment from: Comment on list classification: This gene should be demoted from Green to Red at the next GMS review due to the disease-causing mechanism - genetic defect is an amplified trinucleotide CTG repeat in the 3'UTR (currently NGS unreportable), rather than SNVs within the gene. Evidence level for this is high - it is a confirmed DD gene for DYSTROPHIA MYOTONICA TYPE 1.; to: Comment on list classification: This gene should be demoted from Green to Red at the next GMS review due to the disease-causing mechanism - genetic defect is an amplified trinucleotide CTG repeat in the 3'UTR (currently NGS unreportable), rather than SNVs within the gene. Evidence level for this is high - it is a confirmed DD gene for DYSTROPHIA MYOTONICA TYPE 1. DMPK_CTG STR will be added to the panel to capture this entity and ensure that cases are detected. |
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| Fetal anomalies v1.687 | DMPK | Arina Puzriakova Added comment: Comment on list classification: This gene should be demoted from Green to Red at the next GMS review due to the disease-causing mechanism - genetic defect is an amplified trinucleotide CTG repeat in the 3'UTR (currently NGS unreportable), rather than SNVs within the gene. Evidence level for this is high - it is a confirmed DD gene for DYSTROPHIA MYOTONICA TYPE 1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.686 | DMPK |
Arina Puzriakova Tag nucleotide-repeat-expansion tag was added to gene: DMPK. Tag currently-ngs-unreportable tag was added to gene: DMPK. Tag Q3_21_rating tag was added to gene: DMPK. |
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| Fetal anomalies v1.686 | WBP11 | Ivone Leong Phenotypes for gene: WBP11 were changed from malformation syndrome affecting the cardiac, skeletal, gastrointestinal and renal systems to Vertebral, cardiac, tracheoesophageal, renal, and limb defects, OMIM:619227 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.680 | ACOX1 | Ivone Leong Phenotypes for gene: ACOX1 were changed from ADRENOLEUKODYSTROPHY PSEUDONEONATAL; Peroxisomal acyl-CoA oxidase deficiency, 264470 to ADRENOLEUKODYSTROPHY PSEUDONEONATAL; Peroxisomal acyl-CoA oxidase deficiency, OMIM:264470 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.671 | WDR91 |
Arina Puzriakova gene: WDR91 was added gene: WDR91 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: WDR91 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: WDR91 were set to 32732226 Phenotypes for gene: WDR91 were set to Hygroma; Hydrocephaly Review for gene: WDR91 was set to RED Added comment: Novel candidate gene identified in a fetus with hygroma and hydrocephaly detected by fetal ultrasound. Autopsy showed multiple congenital abnormalities including hygroma, macrocephaly, abnormal ears, unilateral simian crease, hydrocephaly, cerebellar hypoplasia, and interventricular communication. A homozygous truncating variant was found by exome sequencing with concordant segregation among 4 affected fetus, 2 healthy sibs and both parents Sources: Literature |
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| Fetal anomalies v1.665 | SMARCC1 |
Arina Puzriakova changed review comment from: Comment on list classification: There is sufficient evidence to rate this gene as Green at the next GMS panel update. At least 9 unrelated families with different heterozygous variants in the SMARCC1 gene (PMID: 29983323; 32732226; 33077954). Note there is reduced penetrance as 4 variants were transmitted from an unaffected parent (3 variants occurred de novo; 1 was unphased). All affected individuals presented congenital hydrocephalus and aqueductal stenosis. Other variable features include corpus callosum abnormalities, septal agenesis, developmental delay, along with cardiac and skeletal abnormalities.; to: Comment on list classification: There is sufficient evidence to rate this gene as Green at the next GMS panel update - sufficient cases (>3) of congenital hydrocephaly which may conceivably be detected prenatally. At least 9 unrelated families with different heterozygous variants in the SMARCC1 gene (PMID: 29983323; 32732226; 33077954). Note there is reduced penetrance as 4 variants were transmitted from an unaffected parent (3 variants occurred de novo; 1 was unphased). All affected individuals presented congenital hydrocephalus and aqueductal stenosis. Other variable features include corpus callosum abnormalities, septal agenesis, developmental delay, along with cardiac and skeletal abnormalities. |
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| Fetal anomalies v1.663 | DPH1 |
Arina Puzriakova gene: DPH1 was added gene: DPH1 was added to Fetal anomalies. Sources: Literature Q2_21_rating tags were added to gene: DPH1. Mode of inheritance for gene: DPH1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: DPH1 were set to 25558065; 29362492; 30877278; 32732226 Phenotypes for gene: DPH1 were set to Developmental delay with short stature, dysmorphic facial features, and sparse hair, OMIM:616901 Review for gene: DPH1 was set to GREEN Added comment: Biallelic variants in this gene cause a neurodevelopmental disorder characterised by ID/DD, short stature, dysmorphic features, craniofacial and ectodermal anomalies. Several reports note antenatal anomalies and multiple congenital abnormalities that may conceivably be detected prenatally. Fetal ultrasound phenotypes reported in literature include IUGR, polyhydramnios, craniostenosis, cardiac abnormalities, brain anomalies, and polydactyly (PMID: 25558065; 29362492; 30877278; 32732226) Sources: Literature |
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| Fetal anomalies v1.648 | OCRL | Eleanor Williams Phenotypes for gene: OCRL were changed from DENT DISEASE TYPE 2; LOWE OCULOCEREBRORENAL SYNDROME to Dent disease 2, OMIM:300555; Lowe syndrome, OMIM:309000 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.637 | PLD1 |
Suzanne Drury gene: PLD1 was added gene: PLD1 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: PLD1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PLD1 were set to 33645542 Phenotypes for gene: PLD1 were set to HP:0001654; HP:0001627; HP:0001638 Review for gene: PLD1 was set to GREEN Added comment: PMID 33645542 identified 30 patients from 21 unrelated families of different ancestries with biallelic PLD1 variants. All 30 patients were diagnosed with severe congenital heart disease or cardiomyopathy at the fetal or neonatal stage. PLD1 can also cause neonatal cardiomyopathy in the absence of congenital heart defects. Sources: Literature |
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| Fetal anomalies v1.630 | KIDINS220 |
Eleanor Williams changed review comment from: Associated with Spastic paraplegia, intellectual disability, nystagmus, and obesity #617296 in OMIM for monoallelic cases. 2 biallelic cases associated with cerebral ventriculomegaly and limb contractures, plus a mouse model that shows some phenotypic overlap: PMID: 33205811 - Jacquemin et al 2021 - report a consanguineous family of Pakistani origin in which 3 fetuses presented with brain ventriculomegaly and limb contractures. Autopsy of one fetus identifed bilateral club feet and club hands. They were found by WES to share a very rare homozygous variant of KIDINS220 (c.2327_2336del, Gln713_Leu715del). Parents and healthy siblings were heterozygous for this variant. Severe ventriculomegaly was diagnosed as early as 14 weeks. Binding of KIDINS220 to TrkA is decreased by the deletion mutation. PMID: 28934391 - Mero et al 2017 - report a consanguineous couple in which 4 fetuses presented with enlarged cerebral ventricles and limb contractures. Exome sequencing in two of the fetuses found a shared homozygous frameshift variant in exon 24 in KIDINS220 ((NM_020738:c.3394_3403del; p.Gln1132Serfs*30). Healthy family members were either carriers or homozygous for the wild-type allele. It is thought that the variant leads to NMD and complete loss of KIDINS220 protein. PMID: 28934391 - Cesca et al 2011 - report a Kidins220 mutant mouse. Kidins220 -/- mice die at late stages of gestation and show extensive neuronal cell death in the central and peripheral nervous systems, as well as heart malformations.; to: Associated with Spastic paraplegia, intellectual disability, nystagmus, and obesity #617296 in OMIM for monoallelic cases. 2 biallelic cases associated with cerebral ventriculomegaly and limb contractures, plus a mouse model that shows some phenotypic overlap: PMID: 33205811 - Jacquemin et al 2021 - report a consanguineous family of Pakistani origin in which 3 fetuses presented with brain ventriculomegaly and limb contractures. Autopsy of one fetus identifed bilateral club feet and club hands. They were found by WES to share a very rare homozygous variant of KIDINS220 (c.2327_2336del, Gln713_Leu715del). Parents and healthy siblings were heterozygous for this variant. Severe ventriculomegaly was diagnosed as early as 14 weeks. Binding of KIDINS220 to TrkA is decreased by the deletion mutation. PMID: 28934391 - Mero et al 2017 - report a consanguineous couple in which 4 fetuses presented with enlarged cerebral ventricles and limb contractures. Exome sequencing in two of the fetuses found a shared homozygous frameshift variant in exon 24 in KIDINS220 ((NM_020738:c.3394_3403del; p.Gln1132Serfs*30). Healthy family members were either carriers or homozygous for the wild-type allele. It is thought that the variant leads to NMD and complete loss of KIDINS220 protein. PMID: 22048169 - Cesca et al 2011 - report a Kidins220 mutant mouse. Kidins220 -/- mice die at late stages of gestation and show extensive neuronal cell death in the central and peripheral nervous systems, as well as heart malformations. |
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| Fetal anomalies v1.630 | KIDINS220 |
Eleanor Williams changed review comment from: Associated with Spastic paraplegia, intellectual disability, nystagmus, and obesity #617296 in OMIM for monoallelic cases. 2 biallelic cases associated with cerebral ventriculomegaly and limb contractures in the following two publications: PMID: 33205811 - Jacquemin et al 2021 - report a consanguineous family of Pakistani origin in which 3 fetuses presented with brain ventriculomegaly and limb contractures. Autopsy of one fetus identifed bilateral club feet and club hands. They were found by WES to share a very rare homozygous variant of KIDINS220 (c.2327_2336del, Gln713_Leu715del). Parents and healthy siblings were heterozygous for this variant. Severe ventriculomegaly was diagnosed as early as 14 weeks. Binding of KIDINS220 to TrkA is decreased by the deletion mutation. PMID: 28934391 - Mero et al 2017 - report a consanguineous couple in which 4 fetuses presented with enlarged cerebral ventricles and limb contractures. Exome sequencing in two of the fetuses found a shared homozygous frameshift variant in exon 24 in KIDINS220 ((NM_020738:c.3394_3403del; p.Gln1132Serfs*30). Healthy family members were either carriers or homozygous for the wild-type allele. It is thought that the variant leads to NMD and complete loss of KIDINS220 protein. PMID: 28934391 - Cesca et al 2011 - report a Kidins220 mutant mouse. Kidins220 -/- mice die at late stages of gestation and show extensive neuronal cell death in the central and peripheral nervous systems, as well as heart malformations.; to: Associated with Spastic paraplegia, intellectual disability, nystagmus, and obesity #617296 in OMIM for monoallelic cases. 2 biallelic cases associated with cerebral ventriculomegaly and limb contractures, plus a mouse model that shows some phenotypic overlap: PMID: 33205811 - Jacquemin et al 2021 - report a consanguineous family of Pakistani origin in which 3 fetuses presented with brain ventriculomegaly and limb contractures. Autopsy of one fetus identifed bilateral club feet and club hands. They were found by WES to share a very rare homozygous variant of KIDINS220 (c.2327_2336del, Gln713_Leu715del). Parents and healthy siblings were heterozygous for this variant. Severe ventriculomegaly was diagnosed as early as 14 weeks. Binding of KIDINS220 to TrkA is decreased by the deletion mutation. PMID: 28934391 - Mero et al 2017 - report a consanguineous couple in which 4 fetuses presented with enlarged cerebral ventricles and limb contractures. Exome sequencing in two of the fetuses found a shared homozygous frameshift variant in exon 24 in KIDINS220 ((NM_020738:c.3394_3403del; p.Gln1132Serfs*30). Healthy family members were either carriers or homozygous for the wild-type allele. It is thought that the variant leads to NMD and complete loss of KIDINS220 protein. PMID: 28934391 - Cesca et al 2011 - report a Kidins220 mutant mouse. Kidins220 -/- mice die at late stages of gestation and show extensive neuronal cell death in the central and peripheral nervous systems, as well as heart malformations. |
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| Fetal anomalies v1.627 | WBP11 |
Eleanor Williams gene: WBP11 was added gene: WBP11 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: WBP11 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: WBP11 were set to 33276377 Phenotypes for gene: WBP11 were set to malformation syndrome affecting the cardiac, skeletal, gastrointestinal and renal systems Review for gene: WBP11 was set to GREEN Added comment: PMID: 33276377 - Martin et al 2020 - report 13 affected individuals from 7 unrelated families identified through various different cohort analysis (vertebral malformation, renal hypodysplasia, syndromic esophageal atresia, multiple congenital anomalies) in whom a WBP11 heterozygous variant is considered the top causative candidate. 5 identified variants were predicted to be protein truncating whilst the 6th was a missense variant. All variants are absent from population databases. In family 1, the variant was inherited from the apparently unaffected mother, indicating reduced penetrance, and phenotypic variance within families was observed. Phenotypes covered cardiac, vertebral, renal, craniofacial and gastrointestinal systems. At least at least 5 of the patients affected had features in three component organs so can be considered a VACTERL association. Wbp11 heterozygous null mice had vertebral and renal anomalies. Sources: Literature |
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| Fetal anomalies v1.626 | OTUD5 | Arina Puzriakova Added comment: Comment on list classification: At least 8 families reported with a multiple congenital anomaly disorder and distinct hemizygous variants in this gene (PMIDs: 33131077 and 33523931). Phenotype may conceivably be detected prenatally and therefore this gene should be promoted to Green at the next GMS panel update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.625 | OTUD5 |
Arina Puzriakova gene: OTUD5 was added gene: OTUD5 was added to Fetal anomalies. Sources: Expert Review Q2_21_rating tags were added to gene: OTUD5. Mode of inheritance for gene: OTUD5 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: OTUD5 were set to 33131077; 33523931 Phenotypes for gene: OTUD5 were set to Multiple congenital anomalies-neurodevelopmental syndrome, X-linked, OMIM:301056 Review for gene: OTUD5 was set to GREEN Added comment: OTUD5 is associated with a relevant phenotype in OMIM but not yet in Gene2Phenotype. - PMID: 33131077 (2021) - 13 male patients from a single family with three generations affected. Patients presented prenatally or during the neonatal period with IUGR, ventriculomegaly, hydrocephalus, hypotonia, congenital heart defects, hypospadias, and severe neurodevelopmental delay. The disease is typically fatal during infancy, mainly due to sepsis (pneumonias). Female carriers are asymptomatic. WGS in four individuals identified a unique candidate variant in the OTUD5 gene (NM_017602.3:c.598G > A, p.Glu200Lys). The variant cosegregated with the disease in 10 tested individuals. - PMID: 33523931 (2021) - Another 10 individuals from 7 families reported. Key features include poor growth, global developmental delay with impaired intellectual development, and variable abnormalities of the cardiac, skeletal, and genitourinary systems. Most affected individuals also have hypotonia and dysmorphic craniofacial features. Brain imaging typically shows enlarged ventricles and thin corpus callosum; some have microcephaly, whereas others have hydrocephalus. The severity of the disorder is highly variable, ranging from death in early infancy to survival into the second or third decade. Sources: Expert Review |
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| Fetal anomalies v1.622 | SYNE1 | Arina Puzriakova Added comment: Comment on list classification: Upgraded from Red to Amber but there is sufficient evidence to promote to Green at the next GMS panel update - at least 3 unrelated cases with arthrogryposis multiplex congenita (AMC) which may be detected prenatally. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.620 | MYL9 |
Arina Puzriakova Added comment: Comment on list classification: Upgraded from Red to Amber as there are now two unrelated families presenting features of MMIHS, associated with different biallelic variants in the MYL9 gene (PMIDs: 29453416; 33031641). Additional cases/functional evidence required prior to inclusion as diagnostic-grade. |
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| Fetal anomalies v1.617 | SLC20A1 |
Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark. Rating Amber but there is sufficient evidence to promote to Green. At least three unrelated families with a BEEC phenotype (fetally-relevant) and different heterozygous variants in this gene (PMID: 32850778). In vitro assays and zebrafish model support pathogenicity. |
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| Fetal anomalies v1.612 | SUFU |
Arina Puzriakova changed review comment from: The patients described by Schroder et al 2020 (PMID: 33024317) display cerebellar abnormalities that were said to be within the milder range of the Joubert clinical spectrum. This gene will be flagged for review by the GMS team with regards to whether these features may conceivably be detected prenatally (added 'for-review' tag). Note that these individuals harboured heterozygous truncating variants, and monoallelic variants in this gene have also previously been associated with Basal cell nevus syndrome and Medulloblastoma.; to: SUFU was reassessed in line with the recent expert review by Rhiannon Mellis (GOSH). The patients described by Schroder et al 2020 (PMID: 33024317) display cerebellar abnormalities that were said to be within the milder range of the Joubert clinical spectrum. However, it is unclear whether these features may conceivably be detected prenatally and therefore this gene will be flagged for review by the GMS team with regards to phenotypic fit for this panel (added 'for-review' tag). Note that unlike the 2 Joubert syndrome families with biallelic variants reported by De Mori et al. (2017, PMID: 28965847), these individuals harboured heterozygous truncating variants in the SUFU gene. Monoallelic variants have previously been associated with basal cell nevus syndrome and medulloblastoma, and there was no evidence of tumours in any of the families described by Schroder et al. |
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| Fetal anomalies v1.541 | SOX18 | Arina Puzriakova Phenotypes for gene: SOX18 were changed from Hypotrichosis-lymphedema-telangiectasia-renal defect syndrome; Hypotrichosis-lymphedema-telangiectasia syndrome to Hypotrichosis-lymphedema-telangiectasia-renal defect syndrome, OMIM:137940; Hypotrichosis-lymphedema-telangiectasia-renal defect syndrome, MONDO:0019073; Hypotrichosis-lymphedema-telangiectasia syndrome, OMIM:607823; Hypotrichosis-lymphedema-telangiectasia syndrome, MONDO:0011914 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.480 | NEK8 | Arina Puzriakova Phenotypes for gene: NEK8 were changed from RENAL-HEPATIC-PANCREATIC DYSPLASIA 2; NEPHRONOPHTHISIS 9 to ?Nephronophthisis 9, OMIM:613824; Nephronophthisis 9, MONDO:0013444; Renal-hepatic-pancreatic dysplasia 2, OMIM:615415; Renal-hepatic-pancreatic dysplasia 2, MONDO:0014174 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.453 | NADSYN1 | Arina Puzriakova Phenotypes for gene: NADSYN1 were changed from Vertebral, cardiac, renal, and limb defects syndrome 3 to Vertebral, cardiac, renal, and limb defects syndrome 3, OMIM:618845; Vertebral, cardiac, renal, and limb defects syndrome 3, MONDO:0030077 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.431 | ITGA8 | Arina Puzriakova Phenotypes for gene: ITGA8 were changed from bilateral renal agenesis; anhydramnios; RENAL HYPODYSPLASIA/APLASIA 1; Renal hypodysplasia/aplasia 1, 191830 to Renal hypodysplasia/aplasia 1, OMIM:191830; Renal hypodysplasia/aplasia 1, MONDO:0024519 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.428 | ITGA8 |
Arina Puzriakova Added comment: Comment on list classification: Following curation and clinical review at GOSH it has been agreed that the associated phenotype is fetally-relevant. Therefore this gene should be promoted to Green at the next GMS panel update (added 'for-review' tag) ITGA8 is also Green on the 'Unexplained paediatric onset end-stage renal disease v.1.2' GMS panel |
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| Fetal anomalies v1.413 | GATA3 | Arina Puzriakova Phenotypes for gene: GATA3 were changed from Hypoparathyroidism, sensorineural deafness, and renal dysplasia to Hypoparathyroidism, sensorineural deafness, and renal dysplasia, OMIM:146255; Hypoparathyroidism-deafness-renal disease syndrome, MONDO:0007797 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.229 | ANKS6 |
Rhiannon Mellis gene: ANKS6 was added gene: ANKS6 was added to Fetal anomalies. Sources: Expert list Mode of inheritance for gene: ANKS6 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: ANKS6 were set to Nephronophthisis 16, 615382 Review for gene: ANKS6 was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Green on related panel(s): Cystic renal disease (super panel); Rare multisystem ciliopathy Super panel Sources: Expert list |
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| Fetal anomalies v1.229 | CENPF |
Rhiannon Mellis gene: CENPF was added gene: CENPF was added to Fetal anomalies. Sources: Expert list Mode of inheritance for gene: CENPF was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: CENPF were set to PMID: 26820108; 25564561 Phenotypes for gene: CENPF were set to Stromme syndrome, 243605 Review for gene: CENPF was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Green on related panel(s): Cystic renal disease (super panel); Hydrocephalus; Limb disorders; Rare multisystem ciliopathy Super panel; Severe microcephaly Additional comment: Fetal phenotype (ciliopathy) reported in PMID: 26820108 and PMID: 25564561 Sources: Expert list |
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| Fetal anomalies v1.229 | CEP55 | Rhiannon Mellis reviewed gene: CEP55: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Multinucleated neurons, anhydramnios, renal dysplasia, cerebellar hypoplasia, and hydranencephaly, 236500; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.228 | COLQ |
Rhiannon Mellis gene: COLQ was added gene: COLQ was added to Fetal anomalies. Sources: Expert list Mode of inheritance for gene: COLQ was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: COLQ were set to PMID: 9689136; 11865139 Phenotypes for gene: COLQ were set to Myasthenic syndrome, congenital, 5, 603034 Review for gene: COLQ was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Green on related panel(s): Arthrogryposis Additional comment: I can’t see any reported cases specifically with arthrogryposis, but some cases presented at birth with hypotonia/weakness/fatigability. PMID: 9689136; 11865139. Therefore included on basis of severe neonatal phenotype that may conceivably also present prenatally. Sources: Expert list |
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| Fetal anomalies v1.228 | CTU2 |
Rhiannon Mellis gene: CTU2 was added gene: CTU2 was added to Fetal anomalies. Sources: Expert list Mode of inheritance for gene: CTU2 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: CTU2 were set to Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome, 618142 Review for gene: CTU2 was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Green on related panel(s): CAKUT Sources: Expert list |
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| Fetal anomalies v1.225 | DNAJB11 |
Rhiannon Mellis gene: DNAJB11 was added gene: DNAJB11 was added to Fetal anomalies. Sources: Expert list Mode of inheritance for gene: DNAJB11 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene: DNAJB11 were set to Polycystic kidney disease 6 with or without polycystic liver disease, 618061 Review for gene: DNAJB11 was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Green on related panel(s): Cystic renal disease (super panel); Polycystic liver disease Sources: Expert list |
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| Fetal anomalies v1.215 | DNM2 |
Rhiannon Mellis gene: DNM2 was added gene: DNM2 was added to Fetal anomalies. Sources: Expert list Mode of inheritance for gene: DNM2 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Publications for gene: DNM2 were set to PMID: 30208955 Phenotypes for gene: DNM2 were set to Lethal congenital contracture syndrome 5, 615368 Review for gene: DNM2 was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Green on related panel(s): Arthrogryposis Additional comment: AR Phenotype = lethal congenital contracture syndrome – definite prenatal phenotype with arthrogryposis, decreased fetal movements, polyhydramnios. Mutations only identified in three siblings although supported by animal models --> Moderate evidence for arthrogryposis --> Made green on arthrogryposis panel after internal discussion (Jan 2017) NB in 2018 a further report of 3 unrelated cases with heterozygous DNM2 pathogenic variants with a more severe phenotype than usual for the AD disease (centronuclear myopathy) – all 3 had severe hypotonia and respiratory distress from birth. 1 had reduced fetal movements, polyhydramnios, distal contractures at birth (born at 29/40). 1 had micrognathia and clenched fists prenatally, multiple contractures at birth. All 3 were ventilator-dependent and died within first few months of life. (i.e. some overlap with the lethal congenital contracture phenotype despite heterozygous variants). PMID: 30208955 Sources: Expert list |
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| Fetal anomalies v1.215 | DZIP1L |
Rhiannon Mellis gene: DZIP1L was added gene: DZIP1L was added to Fetal anomalies. Sources: Expert list Mode of inheritance for gene: DZIP1L was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: DZIP1L were set to Polycystic kidney disease 5, 617610 Review for gene: DZIP1L was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Green on related panel(s): Cystic renal disease (super panel) Sources: Expert list |
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| Fetal anomalies v1.215 | GANAB |
Rhiannon Mellis gene: GANAB was added gene: GANAB was added to Fetal anomalies. Sources: Expert list Mode of inheritance for gene: GANAB was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene: GANAB were set to Polycystic kidney disease 3 Review for gene: GANAB was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Green on related panel(s): Cystic renal disease (super panel); Polycystic liver disease Sources: Expert list |
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| Fetal anomalies v1.215 | GATA3 |
Rhiannon Mellis gene: GATA3 was added gene: GATA3 was added to Fetal anomalies. Sources: Expert list Mode of inheritance for gene: GATA3 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene: GATA3 were set to Hypoparathyroidism, sensorineural deafness, and renal dysplasia Review for gene: GATA3 was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Green on related panel(s): CAKUT Sources: Expert list |
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| Fetal anomalies v1.215 | GFRA1 |
Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark. Two unrelated families with non-syndromic bilateral renal agenesis, detected during the prenatal period, and distinct homozygous LoF variants in GFRA1. Animal models support a role in renal morphogenesis (PMID:33020172). Rating Amber awaiting further cases/clinical evidence prior to inclusion as diagnositc-grade. |
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| Fetal anomalies v1.214 | GREB1L |
Rhiannon Mellis changed review comment from: Further cases of renal agenesis with GREBL1 pathogenic variants reported by Herlin et al, 2019 and Jacquinet et al 2020 (see below). However I note this gene has recently been changed from Green to Amber at NHSE request. PMID: 31424080: One family including a preterm infant with bilateral renal agenesis and Potters sequence. PMID: 32378186: Four families including fetuses with uterovaginal aplasia and bilateral renal agenesis.; to: Further cases of renal agenesis with GREBL1 pathogenic variants reported by Herlin et al, 2019 and Jacquinet et al 2020 (see below). PMID: 31424080: One family including a preterm infant with bilateral renal agenesis and Potters sequence. PMID: 32378186: Four families including fetuses with uterovaginal aplasia and bilateral renal agenesis. |
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| Fetal anomalies v1.214 | HADHB |
Rhiannon Mellis gene: HADHB was added gene: HADHB was added to Fetal anomalies. Sources: Expert list Mode of inheritance for gene: HADHB was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: HADHB were set to Trifunctional protein deficiency Review for gene: HADHB was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Green on related panel(s): Neuromuscular disorders Additional comment: Different clinical forms, including rapidly progressive neonatal onset with early death - associated with hydrops prenatally Sources: Expert list |
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| Fetal anomalies v1.214 | ICK |
Rhiannon Mellis gene: ICK was added gene: ICK was added to Fetal anomalies. Sources: Expert list Mode of inheritance for gene: ICK was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: ICK were set to Endocrine-cerebroosteodysplasia Review for gene: ICK was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Green on related panel(s): Clefting; Cystic renal disease (super panel); Rare multisystem ciliopathy Super panel; Skeletal dysplasia; Thoracic dystrophies Sources: Expert list |
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| Fetal anomalies v1.214 | ITGA8 | Rhiannon Mellis reviewed gene: ITGA8: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Renal hypodysplasia/aplasia 1; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.214 | KIAA0753 |
Rhiannon Mellis gene: KIAA0753 was added gene: KIAA0753 was added to Fetal anomalies. Sources: Expert list Mode of inheritance for gene: KIAA0753 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: KIAA0753 were set to ?Orofaciodigital syndrome XV Review for gene: KIAA0753 was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Green on related panel(s): Cystic renal disease (super panel); Rare multisystem ciliopathy Super panel; Skeletal dysplasia Sources: Expert list |
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| Fetal anomalies v1.214 | MYH2 |
Rhiannon Mellis gene: MYH2 was added gene: MYH2 was added to Fetal anomalies. Sources: Expert list Mode of inheritance for gene: MYH2 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: MYH2 were set to Proximal myopathy and ophthalmoplegia Review for gene: MYH2 was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Green on related panel(s): Arthrogryposis; Neuromuscular disorders Additional comments: Congenital contractures in some which improve with time - Contractures at birth are described (in some cases) so could be detected prenatally. Sources: Expert list |
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| Fetal anomalies v1.214 | MYH7 |
Rhiannon Mellis gene: MYH7 was added gene: MYH7 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: MYH7 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: MYH7 were set to PMID: 22859017; 25547560; 26337809 Phenotypes for gene: MYH7 were set to Cardiomyopathy, dilated, 1S; Cardiomyopathy, hypertrophic, 1; Laing distal myopathy; Left ventricular noncompaction 5 Review for gene: MYH7 was set to GREEN Added comment: Currently Green on arthrogryposis panel but no clear association with arthrogryposis in literature, it seems to be a more a slowly progressive myopathy phenotype. However, there are four reported cases of fetal cardiomyopathy related to MYH7, detectable on ultrasound. PMID: 22859017, PMID: 25547560, PMID: 26337809 Sources: Literature |
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| Fetal anomalies v1.214 | NADSYN1 |
Rhiannon Mellis gene: NADSYN1 was added gene: NADSYN1 was added to Fetal anomalies. Sources: Expert list Mode of inheritance for gene: NADSYN1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: NADSYN1 were set to Vertebral, cardiac, renal, and limb defects syndrome 3 Review for gene: NADSYN1 was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Green on related panel(s): CAKUT Sources: Expert list |
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| Fetal anomalies v1.214 | NEK8 | Rhiannon Mellis reviewed gene: NEK8: Rating: GREEN; Mode of pathogenicity: None; Publications: 18199800, 23418306, 26967905, 26697755, 26862157; Phenotypes: NEPHRONOPHTHISIS 9, RENAL-HEPATIC-PANCREATIC DYSPLASIA 2; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.205 | PLG |
Rhiannon Mellis gene: PLG was added gene: PLG was added to Fetal anomalies. Sources: Expert list Mode of inheritance for gene: PLG was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: PLG were set to Plasminogen deficiency, type I Review for gene: PLG was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Green on related panel(s): Hydrocephalus Additional comment: structural features detectable prenatally = -Occlusive hydrocephalus, congenital; Dandy-Walker malformation; Cerebellar hypoplasia Sources: Expert list |
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| Fetal anomalies v1.195 | SCLT1 |
Rhiannon Mellis gene: SCLT1 was added gene: SCLT1 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: SCLT1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: SCLT1 were set to No OMIM phenotype; Oro-facio-digital syndrome type IX; Senior-Løken Syndrome Review for gene: SCLT1 was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Green on related panel(s): Rare multisystem ciliopathy Super panel Copied from rare multisystem ciliopathies panel: PMID: 24285566 - Adly et al 2014 - 1 case with index patient with consanguineous Saudi parents and a severe ciliopathy phenotype. He had severe midline cleft lip and palate, microcephaly and choanal atresia. He also had significant eye involvement in the form of severe coloboma, and congenital heart disease (ASD and VSD). He had micropenis. Brain imaging revealed pachygyria and absent corpus callosum. He had abnormal inner ear structures. A splicing mutation was identified in SCLT1 (, NM_144643.2:exon5:c.290+2T>C). This mutation completely abolishes the consensus donor site of exon 5 as confirmed by RTPCR, which showed complete skipping of exon 5 resulting in a frameshift and introduction of a premature stop codon (p.Lys79Valfs*4), PMID: 28005958 - de Castro-Miró et al 2016 - A cohort of 33 pedigrees affected with a variety of retinal disorders was analysed by WES. 1 case with compound heterozygosity (one missense and one splicing altering mutations) in SCLT1 that segregates with the condition in the family (2 affected siblings). Proposed to be causative of early-onset Retinitis Pigmentosa. SCLT1 is a member of the centrosomal/ciliary protein family. PMID: 28486600 - Li et al 2017 - report a mouse model with mutated Sclt1 gene. The Sclt1-/- mice exhibit typical ciliopathy phenotypes, including cystic kidney, cleft palate and polydactyly. PMID: 30425282 - Katagiri et al 2018 - a patient with Senior Løken syndrome and her unaffected parents revealed that the patient had infantile-onset retinal dystrophy and juvenile-onset nephronophthisis. Other systemic abnormalities included hepatic dysfunction, megacystis, mild learning disability, autism, obesity, and hyperinsulinemia. Whole-exome sequencing identified compound heterozygous SCLT1 variants (c.1218 + 3insT and c.1631A > G) in the patient. The unaffected parents were heterozygous for each variant. Transcript analysis using reverse transcription PCR demonstrated that the c.1218 + 3insT variant leads to exon 14 skipping (p.V383_M406del), while the other variant (c.1631A > G) primarily leads to exon 17 skipping (p.D480EfsX11) as well as minor amounts of two transcripts. Immunohistochemical analysis demonstrated that the Sclt1 protein was localized to the distal appendage of the photoreceptor basal body, indicating a ciliary protein. = 3 cases plus a mouse model and functional evidence that the protein is a ciliary protein. Sources: Literature |
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| Fetal anomalies v1.187 | SOX18 |
Rhiannon Mellis gene: SOX18 was added gene: SOX18 was added to Fetal anomalies. Sources: Literature,Expert list Mode of inheritance for gene: SOX18 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal Phenotypes for gene: SOX18 were set to Hypotrichosis-lymphedema-telangiectasia-renal defect syndrome; Hypotrichosis-lymphedema-telangiectasia syndrome Review for gene: SOX18 was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Green on related panel(s): Primary lymphoedema Sources: Literature, Expert list |
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| Fetal anomalies v1.185 | TNNT3 |
Rhiannon Mellis gene: TNNT3 was added gene: TNNT3 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: TNNT3 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: TNNT3 were set to 32779773 Phenotypes for gene: TNNT3 were set to Arthrogryposis, distal, type 2B2 Mode of pathogenicity for gene: TNNT3 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments Review for gene: TNNT3 was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Additional comment: Clearly documented phenotype of distal arthrogryposis. Also, recent paper in Prenatal Diagnosis reporting a het pathogenic variant in TNNT3 in a fetus with FADS; that variant has previously only been described in a family with much milder distal arthrogryposis phenotype. PMID: 32779773 (copied from OMIM): In in vitro studies, Robinson et al. (2007) demonstrated that the TNNI2 R174Q (191043.0001) and R156X (191043.0002) mutations and the TNNT3 mutation R63H (600692.0001) resulted in a gain of function with increased ATPase activity in actin-activated myosin ATPase assays, reflecting increased calcium sensitivity and consistent with increased contractility. In patients, Robinson et al. (2007) concluded that the mutation would cause increased tension in developing muscles, thus resulting in contractures and limb deformities via an active process rather than a passive process. These findings implicated disturbed muscle function as the pathogenic mechanism underlying DA2B. Sources: Literature |
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| Fetal anomalies v1.185 | TOR1A |
Rhiannon Mellis gene: TOR1A was added gene: TOR1A was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: TOR1A was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TOR1A were set to 30244176; 29053766; 28516161 Phenotypes for gene: TOR1A were set to Arthrogryposis multiplex congenita 5 Review for gene: TOR1A was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Additional comment: documented phenotype of severe arthrogryposis multiplex congenital with prenatal onset Sources: Literature |
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| Fetal anomalies v1.185 | TRAF3IP1 |
Rhiannon Mellis gene: TRAF3IP1 was added gene: TRAF3IP1 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: TRAF3IP1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: TRAF3IP1 were set to Senior-Loken syndrome 9 Review for gene: TRAF3IP1 was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel (Cystic renal disease (super panel); Rare multisystem ciliopathy Super panel). Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Sources: Literature |
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| Fetal anomalies v1.185 | TXNDC15 |
Rhiannon Mellis gene: TXNDC15 was added gene: TXNDC15 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: TXNDC15 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: TXNDC15 were set to Meckel Gruber syndrome Review for gene: TXNDC15 was set to GREEN Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel (Cystic renal disease (super panel); Limb disorders; Rare multisystem ciliopathy Super panel). Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Comment from copied from skeletal ciliopathies panel: Shaheen et al. 2016 (PMID:27894351) report TXNDC15 variants in two consanguineous Saudi families that share the features of Meckel-Gruber syndrome (a ciliopathy phenotype). Phenotypes of both patients included polydactyly; one patients was still born, and one survived till 11 hours old. Furthermore, through an international collaboration, they were able to identify an additional Meckel-Gruber syndrome patient (Pakistani origin) with a homozygous truncating variant in this gene. The patient also had polydactyly, although a sibling presented similarly but with no polydactyl. Patient fibroblasts had aberrant ciliogenesis. Sources: Other Sources: Literature |
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| Fetal anomalies v1.185 | VAMP1 |
Rhiannon Mellis changed review comment from: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Sources: Literature; to: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene. Additional comment: Phenotype = congenital myasthenic syndrome. Reported patients present with severe hypotonia from birth, some have contractures, unclear if present at birth but decreased fetal movements reported so could present prenatally. PubMed: 28600779, 28253535, 28168212 Sources: Literature |
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| Fetal anomalies v1.183 | AMBRA1 |
Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark. Sufficient unrelated cases and supportive functional data. However, only a single publication linking this gene to human disease at present (PMID:32333458). Segregation data was not provided and penetrance remains unclear. AMBRA1 was investigated by targeted sequencing and so there also is a possibility of variants in other genes. Currently the evidence is insufficient for a Green rating, but this may be revised if further cases/clinical evidence arise (added 'watchlist' tag) |
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| Fetal anomalies v1.180 | CALCRL | Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark. Single family with recurrent hydrops fetalis (PMID:30115739), supported by in vitro and animal model data. Rating Red as additional cases required to corroborate this gene-disease association. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.179 | SHROOM4 | Arina Puzriakova Added comment: Comment on list classification: New gene added by Suzanne Drury. Rating Red as currently only a single case with a fetally-relevant phenotype (PMID: 32565546). Additional unrelated cases required to support this gene-disease association. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.176 | TMEM260 | Arina Puzriakova Phenotypes for gene: TMEM260 were changed from Neurodevelopmental, Cardiac, and Renal Syndrome to Structural heart defects and renal anomalies syndrome, OMIM:617478; Structural heart defects and renal anomalies syndrome, MONDO:0044321 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.174 | AGRN | Arina Puzriakova Added comment: Comment on list classification: Maintaining Red rating and currently only a single case (PMID: 31730230) has been reported with a relevant phenotype to this panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.170 | NONO | Arina Puzriakova Added comment: Comment on list classification: Currently there is not enough evidence to promote this gene to Green. Additional cases with a fetally-relevant phenotype are required prior to inclusion at diagnostic-grade. Maintaining Amber rating on this panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.168 | SNAP29 | Arina Puzriakova Added comment: Comment on list classification: Maintaining Amber rating as currently there is not enough evidence to promote to Green. Phenotypes do not appear to be fetally-relevant and gestation is typically uneventful. However, symptoms do arise during the first year of life. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.165 | NUP88 |
Arina Puzriakova Added comment: Comment on list classification: New gene added by Julia Baptista (Royal Devon and Exeter NHS Foundation Trust). Two unrelated families with lethal FADS and different biallelic variants in the NUP88 gene (PMID: 30543681). Zebrafish model recapitulated some human phenotypes such as locomotor and neuromuscular junction defects. NUP88 is associated with a relevant phenotype in OMIM but is not currently in Gene2Phenotype. Fetally-relevant phenotype but additional cases required prior to inclusion as diagnostic-grade. Added 'watchlist' tag. |
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| Fetal anomalies v1.162 | TRAPPC12 | Arina Puzriakova Added comment: Comment on list classification: Maintaining Amber rating as currently there are not enough unrelated cases with a fetally-relevant phenotype to promote to Green. Added 'watchlist' tag. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.158 | NEK9 |
Arina Puzriakova Added comment: Comment on list classification: There is now sufficient evidence to promote this gene to Green at the next GMS panel update (added 'for-review' tag). At least 3 unrelated families presenting a similar fetally-relevant phenotype in association with different biallelic variants in this gene. NEK9 is associated with relevant phenotypes in OMIM (MIM# 614262 and 617022) but currently is not in Gene2Phenotype. |
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| Fetal anomalies v1.155 | MN1 |
Arina Puzriakova Added comment: Comment on list classification: New gene added by Rhiannon Mellis (GOSH). Multiple unrelated individuals (>20) described with a complex developmental disorder and de novo truncating MN1 variants. This gene will be flagged for review to determine whether the phenotype is fetally-relevant and there is enough evidence to include as Green. Plausible that some features of the disorder, such as craniofacial abnormalities and structural brain anomalies may be detected prenatally. However based on published clinical descriptions, antenatal history was uneventful in most cases - but reports did include fetal brain anomalies (1), NICU admission (1) and IUGR (2). Similarly, neonatal problems were only reported in a few patients but included respiratory issues (3), abnormal ABR (1), congenital diaphragmatic hernia (1), perinatal hypoxia (1), congenital hypothyroidism (1), hearing impairment (1) and SCBU admission (1) (see Supplementary material in PMID: 31834374) |
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| Fetal anomalies v1.153 | ATP1A2 | Arina Puzriakova changed review comment from: Comment on list classification: There are now at least 4 unrelated families reported with a fetally-relevant phenotype and different homozygous truncating variants in the ATP1A2 gene (PMIDs: 30690204 and 316089320). Therefore this gene can now be promoted from Amber to Green at the next GMS panel update (added 'for-review' tag); to: Comment on list classification: There are now at least 4 unrelated families reported with a fetally-relevant phenotype and different homozygous truncating variants in the ATP1A2 gene (PMIDs: 30690204 and 31608932). Therefore this gene can now be promoted from Amber to Green at the next GMS panel update (added 'for-review' tag) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.153 | ATP1A2 | Arina Puzriakova Added comment: Comment on list classification: There are now at least 4 unrelated families reported with a fetally-relevant phenotype and different homozygous truncating variants in the ATP1A2 gene (PMIDs: 30690204 and 316089320). Therefore this gene can now be promoted from Amber to Green at the next GMS panel update (added 'for-review' tag) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.147 | TMEM107 |
Arina Puzriakova changed review comment from: Comment on list classification: New gene added by Rhiannon Mellis (GOSH). Associated with relevant phenotype in OMIM, but not in Gen2Phen at present. Biallelic variants identified in at least 5 unrelated families with a range of ciliopathic defects including oral-facial-digital syndrome (PMID: 26518474), Meckel-Gruber syndrome (PMID: 26123494), and Joubert syndrome (PMID: 26595381). Phenotype is fetally-relevant in the two apparently unrelated MKS-13 infants, although it should be noted that they were found to share a single haplotype (founder effect). However, it is unclear whether this panel is relevant to OFD case, which would be necessary to reach the threshold for inclusion of TMEM107 as Green. Therefore, rating Amber but will be flagged at the next GMS panel review to assess the phenotypic relevance in context of the panel scope (added 'for-review' tag); to: Comment on list classification: New gene added by Rhiannon Mellis (GOSH). Associated with relevant phenotype in OMIM, but not in Gen2Phen at present. Biallelic variants identified in at least 5 unrelated families with a range of ciliopathic defects including oral-facial-digital syndrome (PMID: 26518474 and 26595381), Meckel-Gruber syndrome (PMID: 26123494), and Joubert syndrome (PMID: 26595381). Phenotype is fetally-relevant in the two unrelated MKS-13 infants, although it should be noted that they were found to share a single haplotype (founder effect), as well as the OFD syndrome cases. Rating Amber but should be promoted to Green at the next GMS panel update (added 'for-review' tag) |
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| Fetal anomalies v1.147 | TMEM107 |
Arina Puzriakova changed review comment from: Comment on list classification: New gene added by Rhiannon Mellis (GOSH). Associated with relevant phenotype in OMIM, but not in Gen2Phen at present. Biallelic variants identified in at least 5 unrelated families with a range of ciliopathic defects including oral-facial-digital syndrome (PMID: 26518474), Meckel-Gruber syndrome (PMID: 26123494), and Joubert syndrome (PMID: 26595381). Phenotype is fetally-relevant in the two apparently unrelated MKS-13 infants, although it should be noted that they were found to share a single haplotype (founder effect). However, it is unclear whether this panel would be applicable in OFD case which would be necessary to reach the threshold for inclusion of TMEM107 as Green. Therefore, rating Amber but will be flagged at the next GMS panel review to assess the phenotypic relevance in context of the panel scope (added 'for-review' tag); to: Comment on list classification: New gene added by Rhiannon Mellis (GOSH). Associated with relevant phenotype in OMIM, but not in Gen2Phen at present. Biallelic variants identified in at least 5 unrelated families with a range of ciliopathic defects including oral-facial-digital syndrome (PMID: 26518474), Meckel-Gruber syndrome (PMID: 26123494), and Joubert syndrome (PMID: 26595381). Phenotype is fetally-relevant in the two apparently unrelated MKS-13 infants, although it should be noted that they were found to share a single haplotype (founder effect). However, it is unclear whether this panel is relevant to OFD case, which would be necessary to reach the threshold for inclusion of TMEM107 as Green. Therefore, rating Amber but will be flagged at the next GMS panel review to assess the phenotypic relevance in context of the panel scope (added 'for-review' tag) |
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| Fetal anomalies v1.147 | TMEM107 |
Arina Puzriakova Added comment: Comment on list classification: New gene added by Rhiannon Mellis (GOSH). Associated with relevant phenotype in OMIM, but not in Gen2Phen at present. Biallelic variants identified in at least 5 unrelated families with a range of ciliopathic defects including oral-facial-digital syndrome (PMID: 26518474), Meckel-Gruber syndrome (PMID: 26123494), and Joubert syndrome (PMID: 26595381). Phenotype is fetally-relevant in the two apparently unrelated MKS-13 infants, although it should be noted that they were found to share a single haplotype (founder effect). However, it is unclear whether this panel would be applicable in OFD case which would be necessary to reach the threshold for inclusion of TMEM107 as Green. Therefore, rating Amber but will be flagged at the next GMS panel review to assess the phenotypic relevance in context of the panel scope (added 'for-review' tag) |
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| Fetal anomalies v1.142 | KIF14 | Arina Puzriakova Phenotypes for gene: KIF14 were changed from ?Meckel syndrome 12; Microcephaly 20, primary to Microcephaly 20, primary, autosomal recessive, OMIM:617914; Microcephaly 20, primary, autosomal recessive, MONDO:0054761; Meckel syndrome 12, OMIM:616258; Lethal fetal cerebrorenogenitourinary agenesis/hypoplasia syndrome, MONDO:0014552 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.130 | TRIP4 | Arina Puzriakova Phenotypes for gene: TRIP4 were changed from Prenatal Spinal Muscular Atrophy and Congenital Bone Fractures to Spinal muscular atrophy with congenital bone fractures 1, OMIM:616866; Prenatal-onset spinal muscular atrophy with congenital bone fractures, MONDO:0000209; Spinal muscular atrophy with congenital bone fractures 1, MONDO:0014806; ?Muscular dystrophy, congenital, Davignon-Chauveau type, OMIM:617066; Congenital muscular dystrophy-respiratory failure-skin abnormalities-joint hyperlaxity syndrome, MONDO:0014896 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.119 | FKBP8 |
Eleanor Williams gene: FKBP8 was added gene: FKBP8 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: FKBP8 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: FKBP8 were set to 32969478 Phenotypes for gene: FKBP8 were set to spina bifida HP:0002414 Review for gene: FKBP8 was set to AMBER Added comment: Not associated with a phenotype in OMIM. PMID: 32969478 - Tian et al 2020 - performed Sanger sequencing of FKBP8 on DNA samples from 472 spina bifida (SB) affected fetuses and 565 unaffected controls. 5 different rare heterozygous variants (MAF ≤ 0.001) were identified among the SB patients, while no deleterious rare variants were identified in the controls. 4 of the variants are missense, the other is a stop-gain. 2 cases were in white-Hispanic patients while the other 3 were non-white Hispanic. Functional studies showed that p.Glu140* affected FKBP8 localization to the mitochondria and impaired its interaction with BCL2 ultimately leading to an increase in cellular apoptosis. p.Ser3Leu, p.Lys315Asn and p.Ala292Ser variants decreased FKBP8 protein level. Gene expression was studied in mouse Fkbp8-/- embryos and found to be abnormal. Previous mouse models have shown neural tube defects. Sufficient cases to rate green, but only the FKBP8 gene looked at so perhaps some caution required while further evidence is gathered. Sources: Literature |
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| Fetal anomalies v1.111 | MAPRE2 | Arina Puzriakova Phenotypes for gene: MAPRE2 were changed from Circumferential Skin Creases Kunze Type to Symmetric circumferential skin creases, congenital, 2, 616734 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.108 | GFRA1 |
Zornitza Stark gene: GFRA1 was added gene: GFRA1 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: GFRA1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GFRA1 were set to 33020172 Phenotypes for gene: GFRA1 were set to Renal agenesis Review for gene: GFRA1 was set to AMBER Added comment: Two unrelated families reported with bi-allelic LOF variants identified in individuals with bilateral renal agenesis. GFRA1 gene encodes a receptor on the Wolffian duct that regulates ureteric bud outgrowth in the development of a functional renal system. Also relevant to the CAKUT panel. Sources: Literature |
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| Fetal anomalies v1.107 | NEK9 |
Rhiannon Mellis edited their review of gene: NEK9: Added comment: Deden et al (2020) report a further family with two consecutive prenatal presentations with compound heterozygous NEK9 variants. Both fetuses had arthrogryposis. Both variants were reported as VUS when detected in the first fetus, which initially presented with 'short long bones, bowed femur, micrognathia, talipes and deviated hand' but re-evaluated after the phenotype progressed to arthrogryposis and then the next pregnancy showed the same ultrasound abnormalities and the same compound het variants. At this point the authors felt this represented a conclusive diagnosis.; Changed rating: GREEN; Changed publications: PMID: 26908619, 26633546, 32333414; Changed phenotypes: Arthrogryposis, short long bones |
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| Fetal anomalies v1.101 | TMEM260 | Rhiannon Mellis reviewed gene: TMEM260: Rating: AMBER; Mode of pathogenicity: None; Publications: PMID: 28318500; Phenotypes: STructural heart defects, Renal anomalies, Agenesis of corpus callosum; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.97 | NUAK2 |
Zornitza Stark gene: NUAK2 was added gene: NUAK2 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: NUAK2 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: NUAK2 were set to 32845958 Phenotypes for gene: NUAK2 were set to Anencephaly Review for gene: NUAK2 was set to AMBER Added comment: Novel gene described in single consanguineous family with three FDIU and extensive anencephaly. Hom inframe del affecting functional kinase domain, parents confirmed carriers. Good functional data showing loss of enzyme function and mouse model with 40% anencephaly after knock-out. Sources: Literature |
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| Fetal anomalies v1.97 | GREB1L | Rhiannon Mellis reviewed gene: GREB1L: Rating: AMBER; Mode of pathogenicity: None; Publications: PMID: 31424080, 32378186; Phenotypes: Renal agenesis; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.95 | B9D2 |
Rhiannon Mellis gene: B9D2 was added gene: B9D2 was added to Fetal anomalies. Sources: Literature,NHS GMS Mode of inheritance for gene: B9D2 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: B9D2 were set to PMID: 21763481; 26092869 Phenotypes for gene: B9D2 were set to Joubert syndrome; Meckel syndrome Review for gene: B9D2 was set to GREEN gene: B9D2 was marked as current diagnostic Added comment: 2 fetuses with MKS in one consanguineous family with homozygous B9D2 pathogenic variants. Functional studies of the variant confirmed loss of function. (PMID: 21763481) 2 unrelated patients with Joubert syndrome with different compound het B9D2 variants. (PMID: 26092869) NB: Currently Green in ciliopathies panels. We report variants in this gene on our postnatal ciliopathies panel at GOSH/NTGLH. Sources: Literature, NHS GMS |
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| Fetal anomalies v1.95 | TMEM107 |
Rhiannon Mellis gene: TMEM107 was added gene: TMEM107 was added to Fetal anomalies. Sources: Literature,NHS GMS Mode of inheritance for gene: TMEM107 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TMEM107 were set to PMID: 26123494; 26518474; 26595381 Phenotypes for gene: TMEM107 were set to ?Joubert syndrome 29; Meckel syndrome 13; Orofaciodigital syndrome XVI Review for gene: TMEM107 was set to GREEN gene: TMEM107 was marked as current diagnostic Added comment: 2 unrelated infants, born of consanguineous Saudi parents, with Meckel syndrome-13 (PMID: 26123494) 1 patient with oro-facio-digital syndrome, and a mouse model with ciliopathy phenotype (PMID: 26518474) 1 man with Jouberts syndrome and female twins (from an unrelated family) with orofaciodigital syndrome. Additional functional studies. (PMID: 26595381) NB: Currently Green on rare multisystem/renal/neurological ciliopathies panels. We report variants in this gene on our postnatal ciliopathies panel at GOSH/NTGLH Sources: Literature, NHS GMS |
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| Fetal anomalies v1.95 | TMEM216 | Rhiannon Mellis reviewed gene: TMEM216: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 20036350, 20512146; Phenotypes: Joubert syndrome, Meckel syndrome; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.95 | KIF14 |
Rhiannon Mellis gene: KIF14 was added gene: KIF14 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: KIF14 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: KIF14 were set to PMID: 24128419; 30388224; 28892560; 29343805 Phenotypes for gene: KIF14 were set to ?Meckel syndrome 12; Microcephaly 20, primary Review for gene: KIF14 was set to GREEN gene: KIF14 was marked as current diagnostic Added comment: Two fetuses in one family with complex multiple congenital anomalies consistent with ciliopathy phenotype. (PMID: 24128419) Four more families with fetuses with similar phenotype (microcephaly, brain malformations and renal agenesis or hypodysplasia). Also functional (zebrafish) studies. Authors conclude that LOF variants cause the above syndromic phenotype while hypomorphic variants cause microcephaly without kidney defects. (PMID: 30388224) Four unrelated families with AR primary microcephaly and biallelic KIF14 pathogenic variants (PMID: 28892560) Four more unrelated families with AR primary microcephaly and biallelic KIF14 pathogenic variants. Two sibs from one of the families were fetuses with severe microcephaly detected prenatally and leading to termination of pregnancy. (PMID: 29343805) Sources: Literature |
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| Fetal anomalies v1.95 | SLC20A1 |
Zornitza Stark gene: SLC20A1 was added gene: SLC20A1 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: SLC20A1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SLC20A1 were set to 32850778; 27013921 Phenotypes for gene: SLC20A1 were set to Bladder-Exstrophy-Epispadias Complex (BEEC) Review for gene: SLC20A1 was set to GREEN gene: SLC20A1 was marked as current diagnostic Added comment: Three individuals and animal model supporting role of this gene in urinary tract and urorectal development. We have included on our CAKUT panel. Sources: Literature |
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| Fetal anomalies v1.74 | AMBRA1 |
Zornitza Stark gene: AMBRA1 was added gene: AMBRA1 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: AMBRA1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: AMBRA1 were set to 17589504; 32333458 Phenotypes for gene: AMBRA1 were set to Neural tube defects Review for gene: AMBRA1 was set to GREEN gene: AMBRA1 was marked as current diagnostic Added comment: 5 rare missense variants were identified in 6 cases from a neural tube defect cohort, and 4 (p.Thr80Met, p.Leu274Phe, p.Ser743Phe, and p.Met884Val) of them were functionally validated to affect autophagy regulation in vitro or zebrafish embryo development in vivo. There is also null mouse model with neural tube defects. Sources: Literature |
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| Fetal anomalies v1.74 | CEP120 |
Rhiannon Mellis gene: CEP120 was added gene: CEP120 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: CEP120 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: CEP120 were set to PMID: 2720821; 25361962 Phenotypes for gene: CEP120 were set to Joubert syndrome 31; Short-rib thoracic dysplasia 13 with or without polydactyly Review for gene: CEP120 was set to GREEN Added comment: PMID: 27208211 identifies CEP120 variants in 6 unrelated families, segregating with disease within the families, including four children with milder Joubert phenotype and two fetuses with prenatal phenotypes of more severe ciliopathy. PMID: 25361962 describes 4 unrelated infants, 3 male and 1 female, with short-rib thoracic dysplasia and polydactyly (SRTD). CEP120 is rated Green on the following PanelApp panels: Thoracic dystrophies, Skeletal dysplasia, Skeletal ciliopathies, Rare multisystem ciliopathy disorders. Sources: Literature |
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| Fetal anomalies v1.73 | COL3A1 |
Rhiannon Mellis gene: COL3A1 was added gene: COL3A1 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: COL3A1 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal Publications for gene: COL3A1 were set to PMID: 28258187; 28742248; 25205403; 27168972; 24922459 Phenotypes for gene: COL3A1 were set to HP:0002126; HP:0001883; HP:0006496 Penetrance for gene: COL3A1 were set to Incomplete Review for gene: COL3A1 was set to GREEN Added comment: On OMIM COL3A1 has a polymicrogyria phenotype in the biallelic form, as well as talipes and other features (PMID: 28258187; PMID: 28742248; PMID: 25205403). No specifically prenatal reports of polymicrogyria in the literature but this feature would be detectable on fetal US and especially on fetal MRI. A monoallelic COL3A1 variant has been reported in one case in a prenatal exome series (PMID: 27168972), causing EDS IV with a prenatal phenotype of forearm hypoplasia and phalangeal defects. PMID: 24922459 evidences that limb hypoplasia/limb reduction is observed in a small subset of EDS IV patients (5 unrelated cases), as well as talipes in a larger number, and occasionally facial clefts – all of which would be prenatally detectable features. Sources: Literature |
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| Fetal anomalies v1.73 | ITGA8 | Rebecca Foulger Added comment: Comment on list classification: Kept rating as Amber awaiting GLH review. Additional phenotypes were reported in the fetuses and sibling (who died perinatally) from PMID:24439109 (clubbed feet, facial dysmorphism, pulmonary hypoplasia, bilateral cryptorchidism) although renal agenesis is the primary phenotype and only 2 families from one paper. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.72 | ITGA8 |
Rebecca Foulger changed review comment from: PMID:24439109, Humbert et al. (2014). In 3 fetuses of Roma Gypsy descent with bilateral renal hypodysplasia/aplasia-1, Humbert et al identified a homozygous T-to-C transition in intron 27 of the ITGA8 gene (c.2982+2T-C) leading to the skipping of exon 28 and an in-frame 34 amino acide deletion. 1 unaffected mother was heterozygous for the variant. All fetuses had bilateral renal agenesis and anhydramnios, resulting in death in utero. The authors also identified 2 siblings from West African with bilateral renal hypodysplasia/aplasia-1 and compound het variants in ITGA8 (Glu541AlafsTer12 and G407R). The missense variant was found once in the Exome Variant Server (1 in 13,005). One of the siblings was a fetus that aborted at gestational week 24 due to bilateral renal agenesis and anhydramnios. The second sibling died in the perinatal period.; to: PMID:24439109, Humbert et al. (2014). In 3 fetuses of Roma Gypsy descent with bilateral renal hypodysplasia/aplasia-1, Humbert et al identified a homozygous T-to-C transition in intron 27 of the ITGA8 gene (c.2982+2T-C) leading to the skipping of exon 28 and an in-frame 34 amino acide deletion. 1 unaffected mother was heterozygous for the variant. All fetuses had bilateral renal agenesis and anhydramnios, resulting in death in utero. The authors also identified 2 siblings from West African with bilateral renal hypodysplasia/aplasia-1 and compound het variants in ITGA8 (Glu541AlafsTer12 and G407R). The missense variant was found once in the Exome Variant Server (1 in 13,005). One of the siblings was a fetus that aborted at gestational week 24 due to bilateral renal agenesis and anhydramnios. The second sibling died in the perinatal period and presented with BRA and bilateral cryptorchidism. |
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| Fetal anomalies v1.72 | ITGA8 | Rebecca Foulger Phenotypes for gene: ITGA8 were changed from RENAL HYPODYSPLASIA/APLASIA 1; Renal hypodysplasia/aplasia 1, 191830 to bilateral renal agenesis; anhydramnios; RENAL HYPODYSPLASIA/APLASIA 1; Renal hypodysplasia/aplasia 1, 191830 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.71 | ITGA8 |
Rebecca Foulger changed review comment from: PMID:24439109, Humbert et al. (2014). In 3 fetuses of Roma Gypsy descent with bilateral renal hypodysplasia/aplasia-1, Humbert et al identified a homozygous T-to-C transition in intron 27 of the ITGA8 gene (c.2982+2T-C) leading to the skipping of exon 28 and an in-frame 34 amino acide deletion. 1 unaffected mother was heterozygous for the varinat. All fetuses had bilateral renal agenesis and anhydramnios, resulting in death in utero. The authors also identified 2 siblings from West African with bilateral renal hypodysplasia/aplasia-1 and compound het variants in ITGA8 (Glu541AlafsTer12 and G407R). The missense variant was found once in the Exome Variant Server (1 in 13,005). One of the siblings was a fetus that aborted at gestational week 24 due to bilateral renal agenesis and anhydramnios. The second sibling died in the perinatal period.; to: PMID:24439109, Humbert et al. (2014). In 3 fetuses of Roma Gypsy descent with bilateral renal hypodysplasia/aplasia-1, Humbert et al identified a homozygous T-to-C transition in intron 27 of the ITGA8 gene (c.2982+2T-C) leading to the skipping of exon 28 and an in-frame 34 amino acide deletion. 1 unaffected mother was heterozygous for the variant. All fetuses had bilateral renal agenesis and anhydramnios, resulting in death in utero. The authors also identified 2 siblings from West African with bilateral renal hypodysplasia/aplasia-1 and compound het variants in ITGA8 (Glu541AlafsTer12 and G407R). The missense variant was found once in the Exome Variant Server (1 in 13,005). One of the siblings was a fetus that aborted at gestational week 24 due to bilateral renal agenesis and anhydramnios. The second sibling died in the perinatal period. |
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| Fetal anomalies v1.71 | ITGA8 | Rebecca Foulger Added comment: Comment on list classification: Relevant phenotype (renal agenesis) but currently insufficient evidence (2 unrelated cases from PMID:24439109, and 'probable' rating in Gene2Phenotype) for diagnostic-grade rating. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.70 | ITGA8 | Rebecca Foulger Phenotypes for gene: ITGA8 were changed from RENAL HYPODYSPLASIA/APLASIA 1 to RENAL HYPODYSPLASIA/APLASIA 1; Renal hypodysplasia/aplasia 1, 191830 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.69 | ITGA8 |
Rebecca Foulger commented on gene: ITGA8: PMID:24439109, Humbert et al. (2014). In 3 fetuses of Roma Gypsy descent with bilateral renal hypodysplasia/aplasia-1, Humbert et al identified a homozygous T-to-C transition in intron 27 of the ITGA8 gene (c.2982+2T-C) leading to the skipping of exon 28 and an in-frame 34 amino acide deletion. 1 unaffected mother was heterozygous for the varinat. All fetuses had bilateral renal agenesis and anhydramnios, resulting in death in utero. The authors also identified 2 siblings from West African with bilateral renal hypodysplasia/aplasia-1 and compound het variants in ITGA8 (Glu541AlafsTer12 and G407R). The missense variant was found once in the Exome Variant Server (1 in 13,005). One of the siblings was a fetus that aborted at gestational week 24 due to bilateral renal agenesis and anhydramnios. The second sibling died in the perinatal period. |
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| Fetal anomalies v1.69 | REN | Rebecca Foulger Publications for gene: REN were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.68 | REN | Rebecca Foulger commented on gene: REN: PMID:31736371. He et al., performed a study to identify the potentially pathogenic gene variants that contribute to the AR renal tubular dysgenesis (RTD) in an aborted fetus. WES was performed on the fetus and his parents. Compound heterozygous variants (c.963T>A, p.Y321X and c.492+1G>A splicing site mutation) were identified in the fetus, one inherited from each parent. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.67 | GREB1L | Rebecca Foulger Added comment: Comment on list classification: Updated rating from Amber to Green following curation of PMID:29100091 which presents additional fetal cases of renal agenesis and GREB1L variants. Sufficient evidence for association of GREB1L with kidney agenesis, and phenotype can present fetally. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.65 | GREB1L | Rebecca Foulger Added comment: Comment on list classification: Added to panel and set rating to Amber. Not yet associated with a disorder in Gene2Phenotype, but 2 fetal cases presented in PMID:29261186. Renal agenesis phenotype is relevant to the panel. Therefore Amber awaiting further cases. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.64 | GREB1L |
Rebecca Foulger gene: GREB1L was added gene: GREB1L was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: GREB1L was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: GREB1L were set to 29261186 Phenotypes for gene: GREB1L were set to Renal hypodysplasia/aplasia 3, 617805; renal agenesis Added comment: Added to Fetal panel based on PMID:29261186 (Boissel et al., 2018) who performed WES in 101 fetuses or stillborns who presented prenatally with severe anomalies. In 2 cases presenting with renal agenesis, de novo variants in GREB1L were identified (p.A968V and p.S98X). Sources: Literature |
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| Fetal anomalies v1.60 | ACE | Rebecca Foulger commented on gene: ACE: PMID:30058238 (Bhowmik et al., 2018) report a 32-week old fetus with severe early onset oligohydramnios. A similarly affected sibling was reported from a previous pregnancy. Exome sequencing revealed a homozygous 3' splice-site variant in intron 17 of ACE gene, which confirmed AR renal tubular dysgenesis. It also facilitated prenatal diagnosis in a subsequent pregnancy. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.54 | PSAT1 | Rebecca Foulger commented on gene: PSAT1: PMID:25152457. Acuna-Hidalgo et al., 2014 report a rare AR disorder with severe malformations leading to prenatal or early postnatal lethality (Neu-Laxova syndrome). They identified variants in PHGDH, PSAT1 and PSPH in individuals with NLS, including 6 families with 3 different missense and frameshift PSAT1 variants which segregated with the disease. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.52 | ALG9 | Rebecca Foulger changed review comment from: Comment on list classification: ALG9 congenital disorder of glycosylation disorder has a broad phenotype and can include non-immune hydrops/NIHF (PMID:26453364 and 31420886). Although the NIHF phenotype is not consistent, even within families carrying the same variant, there are additional prenatal phenotypes reported in the literature for ALG9 cases: 3 fetally-lethal cases of skeletal dysplasia in PMID:25966638, and an individual with multiple malformations detected prenatally in PMID:28932688. Overall: fetally-relevant phenotype and sufficient cases for inclusion on panel and have therefore increased rating from Amber to Green.; to: Comment on list classification: ALG9 congenital disorder of glycosylation has a broad phenotype and can include non-immune hydrops/NIHF (PMID:26453364 and 31420886). Although the NIHF phenotype is not consistent, even within families carrying the same variant, there are additional prenatal phenotypes reported in the literature for ALG9 cases: 3 fetally-lethal cases of skeletal dysplasia in PMID:25966638, and an individual with multiple malformations detected prenatally in PMID:28932688. Overall: fetally-relevant phenotype and sufficient cases for inclusion on panel and have therefore increased rating from Amber to Green. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.52 | ALG9 | Rebecca Foulger Added comment: Comment on list classification: ALG9 congenital disorder of glycosylation disorder has a broad phenotype and can include non-immune hydrops/NIHF (PMID:26453364 and 31420886). Although the NIHF phenotype is not consistent, even within families carrying the same variant, there are additional prenatal phenotypes reported in the literature for ALG9 cases: 3 fetally-lethal cases of skeletal dysplasia in PMID:25966638, and an individual with multiple malformations detected prenatally in PMID:28932688. Overall: fetally-relevant phenotype and sufficient cases for inclusion on panel and have therefore increased rating from Amber to Green. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.49 | ALG9 |
Rebecca Foulger changed review comment from: PMID:28932688. Davis et al., 2017 review the literature for ALG9:CDG cases. They summarise 10 patients from 6 different families with one of four ALG9 variants. In addition to summarising the 3 patients from Tham et al (PMID:25966638) who died in utero , they report an additional patient with ALG9-CDH with a milder phenotype. Prenatally, dysmorphic features, renal cysts and cardiac malformations were detected. She had a homozygous variant in ALG9: p.Tyr287Cys.; to: PMID:28932688. Davis et al., 2017 review the literature for ALG9:CDG cases. They summarise 10 patients from 6 different families with one of four ALG9 variants. In addition to summarising the 3 patients from Tham et al (PMID:25966638) who died in utero, they report an additional patient with ALG9-CDH with a milder phenotype. Prenatally, dysmorphic features, renal cysts and cardiac malformations were detected. She had a homozygous variant in ALG9: p.Tyr287Cys. |
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| Fetal anomalies v1.49 | ALG9 |
Rebecca Foulger commented on gene: ALG9: PMID:28932688. Davis et al., 2017 review the literature for ALG9:CDG cases. They summarise 10 patients from 6 different families with one of four ALG9 variants. In addition to summarising the 3 patients from Tham et al (PMID:25966638) who died in utero , they report an additional patient with ALG9-CDH with a milder phenotype. Prenatally, dysmorphic features, renal cysts and cardiac malformations were detected. She had a homozygous variant in ALG9: p.Tyr287Cys. |
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| Fetal anomalies v1.45 | AHCY | Rebecca Foulger Added comment: Comment on list classification: Added to panel and rated Amber by Zornitza Stark. Two unrelated families with hydrops reported (PMID:30121674, 20852937). Note that previous reports of AHCY deficiency do not include hydrops (e.g. PMID:15024124). Overall, phenotype is relevant to the panel but currently insufficient evidence for Green rating. Rated Amber awaiting further evidence. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.41 | SMG9 | Rebecca Foulger commented on gene: SMG9: PMID:31390136. Lecoquierre et al., 2019 performed exome sequencing in a patient with syndromic DD and diverse malformations including cleft lip and palate, facial dysmorphia, brain abnormalities, herat defect, growth retardation and severe infections. She carried a homozygous SMG9 variant, p.(Gln393*). Her unaffected parents were both heterozygous. Phenotypes were first noted in-utero: polyhydamnios, lateral cleft lip and palate, and IUGR noted on ultrasound. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.41 | SMG9 | Rebecca Foulger commented on gene: SMG9: PMID:27018474. Shaheen et al, 2016 report 2 consanguineous families with different homozygous LOF variants in SMG9 and and a similar set of congenital anomalies including craniofacial dysmorphism, and major brain and heart malformations. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.32 | FGF20 |
Rebecca Foulger gene: FGF20 was added gene: FGF20 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: FGF20 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: FGF20 were set to 22698282; 23112089 Phenotypes for gene: FGF20 were set to ?Renal hypodysplasia/aplasia 2, 615721 Added comment: Added to Fetal panel based on literature search. PMID:22698282. Barak et al., 2012 identify a homozygous frameshift truncating variant (c.337delG) in FGF20, which segregated with the disorder in a consanguineous familly. Pregnancies showed anhydramnios and the fetuses had bilateral renal agenesis. All pregnancies were terminated. Mouse model shows loss of Fgf20 resulted in kidney agenesis. Additional papers report functional experiments (in mice) that confirm role of FGF20 in kidney development (e.g. PMID:23112089). Sources: Literature |
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| Fetal anomalies v1.28 | EXOC3L2 |
Rebecca Foulger gene: EXOC3L2 was added gene: EXOC3L2 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: EXOC3L2 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: EXOC3L2 were set to 30327448 Phenotypes for gene: EXOC3L2 were set to Dandy-Walker malformation Added comment: Added to panel based on PMID:30327448: Shalata et al., 2019 report 3 fetuses from a family with homozygous variants in EXOC3L2 (missense p.Leu41Gln) and severe forms of Dandy-Walker that were detectable by prenatal ultrasound. Sources: Literature |
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| Fetal anomalies v1.27 | DHCR7 | Rebecca Foulger commented on gene: DHCR7: PMID:31840946 (Schoner et al., 2020) performed autopsies and DHCR7 gene analyses in 8 fetuses suspected of having SLOS. 5/9 fetuses presented with classic SLOS features including 4 with atrial/atrioventricular septal defects and renal anomalies, and one with additional bilateral renal agenesis and a Dandy-Walker cyst. Two fetuses were mildly affected and two fetuses showed additional holoprosencephaly. DHCR7 variants were confirmed in cases 1-5 and 7. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.22 | POLE | Rebecca Foulger Phenotypes for gene: POLE were changed from IUGR; severe growth failure of prenatal onset to IUGR; severe growth failure of prenatal onset; FILS syndrome, 615139; facial dysmorphism, immunodeficiency, livedo, and short stature (FILS) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.20 | POLE |
Rebecca Foulger gene: POLE was added gene: POLE was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: POLE was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: POLE were set to 23230001 Phenotypes for gene: POLE were set to IUGR; severe growth failure of prenatal onset Added comment: Added to panel based on prenatal phenotype reported in PMID:30503519: (Logan et al., 2018) report biallelic variants in POLE in 15 indivs from 12 families (mix of countries). All subjects shared the same intronic variant (c.1686+32C>G) as part of a common haplotype, in combination with different loss-of-function variants in trans. Phenotypically, affected individuals all had IUGR and severe growth failure of prenatal onset. Sources: Literature |
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| Fetal anomalies v1.4 | CEP55 | Rebecca Foulger commented on gene: CEP55: PMID:28295209. Bondeson et al report a Swedish couple with 2 affected male fetuses homozygous for CEP55 p.Arg86*. Although the phenotype differed between fetuses, both exhibited kidney phenotypes (including renal dysplaisa). Segregation analysis supported the gene:disease association, and Haplotype analysis suggested a founder effect. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.4 | CEP55 | Rebecca Foulger commented on gene: CEP55: PMID:28264986: Frosk et al, 2017 report a Dutch-German Mennonite family with 3 affected fetuses homozygous for CEP55 nonsense variant p.Ser425* presenting with MIM:236500 including renal dysplasia. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.4 | CEP55 |
Rebecca Foulger gene: CEP55 was added gene: CEP55 was added to Fetal anomalies. Sources: Other Mode of inheritance for gene: CEP55 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: CEP55 were set to 28264986; 28295209 Phenotypes for gene: CEP55 were set to Multinucleated neurons, anhydramnios, renal dysplasia, cerebellar hypoplasia, and hydranencephaly, 236500; lethal CEP55-related syndromes Added comment: Added to Fetal anomalies panel on advice from Helen Brittain, Genomics England Clinical Team. MARCH phenotype is appropriate for this panel. Sources: Other |
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| Fetal anomalies v1.0 | AHCY |
Zornitza Stark gene: AHCY was added gene: AHCY was added to Fetal anomalies. Sources: Expert list Mode of inheritance for gene: AHCY was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: AHCY were set to 30121674; 20852937 Phenotypes for gene: AHCY were set to S-adenosylhomocysteine hydrolase deficiency Review for gene: AHCY was set to AMBER Added comment: Please note recent additional report of this condition presenting prenatally with hydrops. Sources: Expert list |
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| Fetal anomalies v1.0 | ALG9 | Zornitza Stark reviewed gene: ALG9: Rating: GREEN; Mode of pathogenicity: None; Publications: 26453364, 31420886; Phenotypes: Congenital disorder of glycosylation, type Il, MIM#608776; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.0 | ATP1A2 |
Zornitza Stark gene: ATP1A2 was added gene: ATP1A2 was added to Fetal anomalies. Sources: Expert list Mode of inheritance for gene: ATP1A2 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: ATP1A2 were set to 30690204 Phenotypes for gene: ATP1A2 were set to hydrops fetalis; microcephaly; arthrogryposis; extensive cortical malformations Review for gene: ATP1A2 was set to AMBER gene: ATP1A2 was marked as current diagnostic Added comment: Three individuals from two unrelated families reported with balleliic LoF variants in this gene and hydrops/congenital abnormalities. Mouse model is perinatal lethal. This is a distinct phenotype from the mono allelic variants associated with alternating hemiplegia. Sources: Expert list |
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| Fetal anomalies v1.0 | PSAT1 | Zornitza Stark reviewed gene: PSAT1: Rating: GREEN; Mode of pathogenicity: None; Publications: 25152457; Phenotypes: Neu-Laxova syndrome 2, MIM# 616038; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.355 | FBN1 | Rebecca Foulger Added comment: Comment on mode of inheritance: Changed MOI from 'Both AD + AR' to 'MONOALLELIC' only to match current DDG2P Allelic requirement of 'monoallelic' for all confirmed disorders (SHPRINTZEN-GOLDBERG CRANIOSYNOSTOSIS SYNDROME; MARFAN SYNDROME; MASS SYNDROME/OVERLAP CONNECTIVE TISSUE DISEASE). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.352 | SCO2 | Rebecca Foulger commented on gene: SCO2: PMID:18924171 (Verdijk et al, 2008) report the first prenatal diagnosis of a compound heterozygous SCO2 variant in the literature. The sibling died of fatal infantile cardioencephalomyopathy. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.349 | SIK3 |
Rebecca Foulger gene: SIK3 was added gene: SIK3 was added to Fetal anomalies. Sources: Other Mode of inheritance for gene: SIK3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SIK3 were set to 30232230; 22318228 Phenotypes for gene: SIK3 were set to ?Spondyloepimetaphyseal dysplasia, Krakow type, 618162 Added comment: Added to panel as suggested by Rhinannon Mellis. One pair of siblings with spondyloepimetaphyseal dysplasia reported in PMID:30232230 (Csukasi et al., 2018) plus one clinical case of suspected skeletal dysplasia prenatally. Sources: Other |
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| Fetal anomalies v0.346 | AMER1 | Rebecca Foulger Added comment: Comment on mode of inheritance: Changed MOI from Monoallelic to X-linked dominant to match other PanelApp panels. Although the Gene2Phenotype inheritance is currently listed as monoallelic, AMER1 is an X-linked gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.345 | FAM58A | Rebecca Foulger Added comment: Comment on mode of inheritance: Changed MOI from MONOALLELIC to X-linked dominant. Although monoallelic inheritance is currently listed in DDG2P for STAR SYNDROME, FAM58A (CCNQ) is an X-linked gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.344 | NMNAT2 | Rebecca Foulger Added comment: Comment on list classification: NMNAT2 was added to the Fetal anomalies panel and rated Green by Michael Coleman (University of Cambridge). Not yet associated with a disorder in OMIM or Gene2Phenotype. Currently 2 fetal siblings (1 case) in PMID:31136762 and a mouse model. Rated as Amber awaiting clinical feedback and further cases. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.338 | SLC35A2 | Rebecca Foulger Added comment: Comment on mode of inheritance: Gene2Phenotype currently records a 'monoallelic' MOI for SLC35A2 for 'CONGENITAL DISORDER OF GLYCOSYLATION'. Changed MOI from 'monoallelic' to 'XLD' because SLC35A2 is on the X-chromosome. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.337 | SASS6 | Rebecca Foulger Added comment: Comment on list classification: Updated rating from Red to Amber to match 'possible' Disease confidence rating in PAGE Additional genes list. Note that SASS6 is not currently associated with a disorder in Gene2Phenotype. Associated with OMIM disorder: ?Microcephaly 14, primary, autosomal recessive, 616402' based on 1 reported family. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.333 | VPS13B | Rebecca Foulger changed review comment from: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: As RM notes: Cerebellar hypoplasia has definitely been reported as a possible feature (PMID:20683995) and that could be detectable prenatally: keep on the Fetal anomalies panel as a Green gene.; to: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: RM notes that Cerebellar hypoplasia has definitely been reported as a possible feature (PMID:20683995) and that could be detectable prenatally: keep on the Fetal anomalies panel as a Green gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.333 | VPS13B | Rebecca Foulger changed review comment from: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Cerebellar hypoplasia has definitely been reported as a possible feature (PMID:20683995) and that could be detectable prenatally: keep on the Fetal anomalies panel as a Green gene.; to: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: As RM notes: Cerebellar hypoplasia has definitely been reported as a possible feature (PMID:20683995) and that could be detectable prenatally: keep on the Fetal anomalies panel as a Green gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.332 | VPS13B | Rebecca Foulger commented on gene: VPS13B: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Cerebellar hypoplasia has definitely been reported as a possible feature (PMID:20683995) and that could be detectable prenatally: keep on the Fetal anomalies panel as a Green gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.328 | SLC4A4 | Rebecca Foulger commented on gene: SLC4A4: SLC4A4 was re-reviewed by Anna de Burca (Genomics England clinical team) to determine if patients presented with cataracts. Anna notes that there aren’t very many published cases and not all had cataracts. Of those that did, PMID:16636648 cataracts were definitely not congenital and in PMID:11131345 they were only picked up at 4 years so probably not congenital either. Therefore appropriate to remain Red. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.326 | TRPV6 | Rebecca Foulger Added comment: Comment on list classification: Added to panel as Amber based on 'probable' Disease confidence in DDG2P for Transient Neonatal Hyperparathyroidism. Upgraded to Green on advice from Anna de Burca (Genomics England Clinical team) and Rhiannon Mellis (Great Ormond Street Hospital). They note that anomalies may be detected on third trimester scans but actually have a better prognosis in the long term so important diagnostically, and a differential diagnosis for Osteogenesis imperfecta. Plus Helen Brittain (Genomics England Clinical team) has reviewed on TRPV6 on the Skeletal dysplasia panel and notes: "6 unrelated children with skeletal abnormalities detected in the third trimester of pregnancy, who presented at birth with elevated serum PTH and alkaline phosphatase activity, with normal or low ionized calcium. Skeletal anomalies included generalized osteopenia, narrow chest, short ribs with multiple healing fractures, and bowing or fractures of long bones". Therefore sufficient cases and relevant phenotype for inclusion on the Fetal anomalies panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.317 | MYH10 | Rebecca Foulger Added comment: Comment on phenotypes: Added Prenatal imaging phenotype reported in Petrovski et al., 2018 (PMID:30712878) Table 1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | ABCC8 | Rebecca Foulger edited their review of gene: ABCC8: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team) and Karen Temple. Outcome of review: Growth restriction is less marked but queried whether hyperinsulinaemia might cause features that would be picked up on scan. Rate as Red.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | RAC1 | Rebecca Foulger edited their review of gene: RAC1: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team) and a Fetal Working Group call on July 19th 2019 with Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Rate Green because of finding in Petrovski et al., 2018 (PMID:30712878) plus additional case: Anna de Burca notes: Petrovski case had Dandy-Walker malformation and IUGR. 2 other reported cases: cerebellar anomalies and 2 different cases in same paper had signficant macrocephaly. Therefore 3 cases with structural brain anomalies if Petrovski included.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | ACTA1 | Rebecca Foulger edited their review of gene: ACTA1: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team) and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Rate Green because of finding in Normand et al., 2018 (PMID:30266093) plus additional case: Normand doesn't give any details of the clinical presentation. OMIM says the 'severe form' is associated with arthrogryposis. PMID:2724277 describes brothers with a heterozygous variant who presented antenatally with severe polyhydramnios and reduced fetal movements, postnatally were found to have arthrogryoposis. Parents were second cousins so might have been a missed second variant. PMID:11333380 reports 5 cases with heterozygous variants, some of which were born with severe hypotonia although the only antenatal feature was reduced fetal movements. Rate as Green for AD and AR as evident clinical variability.; Changed rating: GREEN; Changed publications: 2724277, 11333380 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | SBDS | Rebecca Foulger edited their review of gene: SBDS: Added comment: This gene was re-reviewed in a consistency check by Anna de Burca (Genomics England Clinical Team). Outcome of review: Shwachman-Diamond syndrome: skeletal defects usually develop within first 2 years but PMID:23254443 reports a case with prenatal onset of short limbs. Therefore Green rating is appropriate.; Changed rating: GREEN; Changed publications: 23254443 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | GAA | Rebecca Foulger edited their review of gene: GAA: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team) under the category of storage disorders. Outcome of review: Rate as Green-PMID:28657663 has prenatal onset of cardiomyopathy.; Changed rating: GREEN; Changed publications: 28657663 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | TTC19 | Rebecca Foulger edited their review of gene: TTC19: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | TMEM70 | Rebecca Foulger edited their review of gene: TMEM70: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED; Changed publications: 18953340 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | TMEM126B | Rebecca Foulger edited their review of gene: TMEM126B: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | TK2 | Rebecca Foulger edited their review of gene: TK2: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | SURF1 | Rebecca Foulger edited their review of gene: SURF1: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | SLC25A26 | Rebecca Foulger edited their review of gene: SLC25A26: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | SDHAF1 | Rebecca Foulger edited their review of gene: SDHAF1: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | SDHA | Rebecca Foulger edited their review of gene: SDHA: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | SCO1 | Rebecca Foulger edited their review of gene: SCO1: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | POLG | Rebecca Foulger edited their review of gene: POLG: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | PNPT1 | Rebecca Foulger edited their review of gene: PNPT1: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | PDSS2 | Rebecca Foulger edited their review of gene: PDSS2: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | PDHX | Rebecca Foulger edited their review of gene: PDHX: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | PC | Rebecca Foulger edited their review of gene: PC: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | NFU1 | Rebecca Foulger edited their review of gene: NFU1: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | NDUFV1 | Rebecca Foulger edited their review of gene: NDUFV1: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | NDUFS8 | Rebecca Foulger edited their review of gene: NDUFS8: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | NDUFS7 | Rebecca Foulger edited their review of gene: NDUFS7: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | NDUFS4 | Rebecca Foulger edited their review of gene: NDUFS4: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | NDUFS1 | Rebecca Foulger edited their review of gene: NDUFS1: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | NDUFA1 | Rebecca Foulger edited their review of gene: NDUFA1: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | MT-TP | Rebecca Foulger edited their review of gene: MT-TP: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | MPV17 | Rebecca Foulger edited their review of gene: MPV17: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | LRPPRC | Rebecca Foulger edited their review of gene: LRPPRC: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | FARS2 | Rebecca Foulger edited their review of gene: FARS2: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | DLD | Rebecca Foulger edited their review of gene: DLD: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | COX6B1 | Rebecca Foulger edited their review of gene: COX6B1: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | COX15 | Rebecca Foulger edited their review of gene: COX15: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | COX10 | Rebecca Foulger edited their review of gene: COX10: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | COQ8A | Rebecca Foulger edited their review of gene: COQ8A: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | COQ2 | Rebecca Foulger edited their review of gene: COQ2: Added comment: This gene was reviewed by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Presentation of mitochondrial disorders can be variable, and most aren't obvious at birth. Therefore exclude unless the gene has been directly associated with a fetal presentation.; Changed rating: RED; Changed publications: 23816342 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | NDP | Rebecca Foulger edited their review of gene: NDP: Added comment: This gene was re-reviewed in a consistency check by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Include on basis of PMID:30125416 (Prenatal diagnosis of Norrie disease based on ultrasound findings): Dubcus et al., 2018 describe a case of Norrie disease diagnosed based on ocular defects in the fetus on an ultrasound scan at 31+5 weeks gestation, and confirmed by identification of a de novo c.38T>C variant (p.Leu13Pro) in NDP. The authors say that this is the first case in which Norrie disease was diagnosed based on prenatal imaging only.; Changed rating: GREEN; Changed publications: 30125416 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.311 | FH | Rebecca Foulger edited their review of gene: FH: Added comment: This gene was re-reviewed in a consistency check by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Discussions and outcome of review: FH is biallelic for 'Fumarase deficiency', and monoallelic for 'Leiomyomatosis and renal cell cancer'. Fumarase deficiency can sometimes have prenatal onset: polyhydramnios & brain malformations. Include for biallelic inheritance only to avoid risk of incidental cancer finding. Therefore FH was upgraded from Red to Green.; Changed rating: GREEN; Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.304 | IARS | Rebecca Foulger Phenotypes for gene: IARS were changed from Growth Retardation with Prenatal Onset, Intellectual Disability, Muscular Hypotonia, and Infantile Hepatopathy to Growth retardation, impaired intellectual development, hypotonia, and hepatopathy, 617093 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.302 | IARS | Rebecca Foulger Added comment: Comment on list classification: Promoted IARS from Amber to Green on advice from Genomics England clinical team. Although the DD-G2P Disease confidence rating is 'probable' for 'Growth Retardation with Prenatal Onset, Intellectual Disability, Muscular Hypotonia, and Infantile Hepatopathy', there are sufficient cases from the literature to support Green rating. As reviewed by Louise Daugherty on the 'Intellectual disability' panel: Kopajtich et al., 2016 PMID:27426735 reported 3 unrelated patients with a multisystem disorder characterized by intrauterine and postnatal growth retardation, including small head circumference (-3 to -5 SD), hypotonia and delayed psychomotor development with variable severity of intellectual disability. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.284 | MYRF | Rebecca Foulger Added comment: Comment on list classification: Updated rating from Grey to Green. MYRF gene was added to the panel and reviewed by Julia Baptista. Sufficient cases to support MYRF variants causing Cardiac-urogenital syndrome (MIM:618280) from Pinz et al 2018 (PMID:29446546), Chitayat et al., (PMID:30070761), Qi et al.,2018 (PMID:30532227) and Rossetti et al., 2019 (PMID: 31069960). The phenotype is fetally-relevant (includes congenital diaphragmatic hernia/CDH, genital defects and cardiac defects) with multiple papers reporting detection in-utero: In both patients identified in Pinz et al 2018, anomalies were detected by ultrasound at 20 weeks gestation: mesocardia without other signs of heterotaxy (Patient 1), and a complex congenital heart defect with pericardial effusion (Patient 2). Chitayat et al., report a fetus with a novel de novo LOF variant in MYRF and a hypoplastic left heart and female external genitalia. In Rossetti et al., 2019, cardiac malformation and/or CDH was detected on a prenatal ultrasound. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.277 | PKD1 | Rebecca Foulger Added comment: Comment on mode of inheritance: Although not yet listed in DD-Gene2Phenotype, PKD1 is listed in OMIM with AD inheritance for Polycystic kidney disease 1, 173900. Monoallelic MOI was also listed in the original PAGE Additional gene list. However the external review and the two cited papers support both AD and AR inheritance for polycystic kidney disease (PKD). PMID:23624871 note that recessive polycystic kidney disease (ARPKD) frequently presents antenatally or in the neonatal period with severe renal involvement. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.276 | PKD1 | Rebecca Foulger commented on gene: PKD1: PMID:23624871 (Gilbert et al., 2013) was added as a publication by Julia Baptista. The authors describe a male fetus with renal enlargement and oligohydramnios diagnosed at 27 weeks of gestation. This presentation resembled autosomal recessive PKD (ARPKD). Genetic analysis revealed a heterozygous truncating variant (p.Ser2788fs) in PKD1 inherited from the mother, and three unreported PKD1 variants inherited from the father. Although the authors don't exclude the possibility of a pathogenic variant in an additional gene, the paternally-inherited alleles support biallelic PKD1 alleles causing the fetal kidney anomalies. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.249 | TRAF7 | Rebecca Foulger commented on gene: TRAF7: PMID:29961569 (Tokita et al, 2018 Table 1) list Prenatal ultrasound findings in five unrelated patients with the disorder 'Cardiac, facial, and digital anomalies with developmental delay' (MIM:618164) and TRAF7 missense variants. The prenatal findings include choroid plexus cyst, IUGR and cardiac defects. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.247 | CNOT1 | Rebecca Foulger commented on gene: CNOT1: De Franco et al., 2019 (PMID:31006513) investigated a cohort of 107 individuals with pancreatic agenesis and definite/possible holoprosencephaly, and identified a heterozygous missense variant in CNOT1 (NM_016284.4; c.1603C>T (p.Arg535Cys)) in three unrelated individuals. The variant was de novo in two individuals, and was not present in the DNA sample from the third individual's father (maternal sample was unavailable). Mice required a homozygous variant to display a phenotype: in homozygous mice embryos (embryonically lethal) morphological abnormalities were apparent upon dissection including edema, a smaller dorsal pancreas, and exencephaly. The DDD study identified de novo CNOT1 variants in three individuals with developmental delay but none had holoprosencephaly, diabetes or pancreatic or neurological structural malformations. The authors therefore suggest that a mutation-specific mechanism rather than LOF is responsible for the pancreatic and holoprosencephaly phenotype. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.244 | HNRNPK | Rebecca Foulger commented on gene: HNRNPK: Added HNRNPK to the Fetal anomalies panel as a Green gene based on the DDG2P Disease confidence rating of 'confirmed' for Au-Kline syndrome. There is sufficient evidence (>3 unrelated cases from PMIDs:26173930,26954065,28771707,29904177) supporting a link between HNRNPK and Au-Kline syndrome. Plus the phenotype includes structural anomalies and PMID:29904177 report a prenatal presentation. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.244 | HNRNPK | Rebecca Foulger commented on gene: HNRNPK: Au et al., 2018 (PMID:29904177) report prenatal presentation of Au-Kline syndrome: patient 9 presented prenatally with prune belly sequence, club feet, cystic kidneys associated with large cystic hygroma, pleural effusions and enlarged bladder. An additional 5 prenatal patients showed increased nuchal translucency and 5 patients had hydronephrosis. Congenital heart disease was reported for one patient prenatally. Agenesis of the corpus callosum was observed prenatally in one patient. Choroid plexus cysts, hyperechoic bowel, and ventriculomegaly have also been detected in ultrasound in single patients. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.244 | HNRNPK | Rebecca Foulger commented on gene: HNRNPK: Au-Kline syndrome is a multiple malformation syndrome associated with intellectual disability. Patients have facial dysmorphic features and frequently have skeletal and connective tissue anomalies, craniosynostosis, congenital heart malformations, and renal anomalies (PMID:29904177). Structural phenotypes reported in the literature include talipes and partial agenesis of corpus callosum. Au et al., 2018 (PMID:29904177) report prenatal presentation with 5 patients showing increased nuchal translucency and 5 patients had hydronephrosis. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.229 | ZNF423 | Rebecca Foulger Added comment: Comment when marking as ready: Marked ZNF423 as Ready on April 30th 2019: Fetally-relevant phenotype but currently insufficient evidence for inclusion. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.229 | SUFU | Rebecca Foulger Added comment: Comment when marking as ready: Marked SUFU as Ready on April 30th 2019: Fetally-relevant phenotype but currently insufficient evidence for inclusion. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.225 | WNT3 | Rebecca Foulger commented on gene: WNT3: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March and April 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is fetally-relevant but limited evidence: include on the Fetal anomalies panel as an Amber gene. Additional notes from clinical review: Currently insufficient evidence for fetally-relevant Tetra-Amelia syndrome. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.225 | SUZ12 | Rebecca Foulger edited their review of gene: SUZ12: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March and April 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: include on the Fetal anomalies panel as a Green gene. Additional notes from clinical review: Fetal relevance is borderline- PMIDs:28229514 and 30019515 report a set of features where it is unclear if they would be detected prenatally, including one case of increased head circumference at birth (but also one case with reduced head circumference at birth) some facial and limb features etc. Evidence wise, there are just enough cases from the literature (2 papers from the same group) to support inclusion: Imagawa et al., 2017 (PMID:28229514) identified a missense somatic mosaic mutation (c.1829A>T, p.Glu610Val) in SUZ12 in a patient with clinically suspected Weaver syndrome. Imagawa et al., 2018 (PMID:30019515) report two further Weaver syndrome-like patients with SUZ12 variants (a missense and a frameshift). On balance, it was decided that SUZ12 should be included on the Fetal anomalies panel.; Changed rating: GREEN; Changed publications: 28229514, 30019515 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.222 | TBX22 | Rebecca Foulger commented on gene: TBX22: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March and April 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is fetally-relevant but limited evidence: include on the Fetal anomalies panel as an Amber gene. Additional notes from clinical review: Amber for Abruzzo-Erickson syndrome (MIM: 302905) due to the limited evidence. The clefting phenotype has sufficient cases but is isolated cleft palate so unlikely to be seen prenatally (confirmed by Lyn Chitty, 26th April 2019). Therefore demote from Green to Amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.222 | KCNJ10 | Rebecca Foulger edited their review of gene: KCNJ10: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March and April 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is not fetally-relevant. Additional notes from clinical review: Digenic, and insufficient features that would be detected prenatally. Action taken: Demoted KCNJ10 gene rating from Green to Red.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.222 | ANOS1 | Rebecca Foulger edited their review of gene: ANOS1: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March and April 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: include on the Fetal anomalies panel as a Green gene. Additional notes from clinical review: Include on basis of renal agenesis.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.222 | LDB3 | Rebecca Foulger edited their review of gene: LDB3: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March and April 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Originally rated Amber based on DDG2P Disease confidence of 'both DD and IF' for at least one disorder. Outcome of review: Phenotype is not fetally-relevant. Additional notes from clinical review: Concluded that myopathy is unlikely to produce Fetal hydrops in this instance. Although PMID:17394203 report a proband with variants in both TAZ and LDB3, where the mother had five miscarriages (plus two sons who died in infancy and 2 surviving children) the LDB3 variant is paternally-inherited, and therefore the maternally-inherited TAZ allele is more relevant. Action taken: Demoted LDB3 gene rating from Amber to Red.; Changed rating: RED; Changed publications: 17394203 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.222 | ALAD | Rebecca Foulger edited their review of gene: ALAD: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March and April 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Originally rated Amber based on DDG2P Disease confidence of 'both DD and IF' for at least one disorder. Outcome of review: Phenotype is not fetally-relevant. Additional notes from clinical review: Postnatal phenotype, and no structural phenotype to detect prenatally. Action taken: Demoted ALAD gene rating from Amber to Red.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.218 | MYT1 | Rebecca Foulger commented on gene: MYT1: Berenguer et al 2017 (PMID:28612832) identified a third (de novo) MYT1 variant in a patient with OAVS: c.323C>T p.Ser108Leu from a cohort of 57 new patients with a typically heterogeneous OAVS. From functional studies, it's still unclear how these variants impact retinoic acid signaling and contribute to the phenotype. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.217 | MYT1 | Rebecca Foulger commented on gene: MYT1: MYT1 is not currently associated with a disorder in OMIM (April 2019). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.216 | EMG1 | Rebecca Foulger Added comment: Comment on list classification: Kept rating as Amber awaiting further published/clinical evidence. Phenotype is fetally-relevant (see review from Deirdre Cilliers) but current gene:disease evidence for Bowen-Conradi syndrome is limited to Hutterite families (PMID:19463982). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.215 | SUFU | Rebecca Foulger Added comment: Comment on list classification: Kept rating as Amber awaiting further published or clinical evidence. Joubert syndrome is fetally-relevant (see review by Dierdre Cilliers) but currently only 2 unrelated cases from one paper (PMID:28965847) and SUFU is Amber on the related 'Rare multisystem ciliopathy disorders' panel (for Joubert syndrome). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.210 | POMK | Rebecca Foulger commented on gene: POMK: Patient 3 in PMID:24925318 (Di Costanzo et al, 2014) was an Italian male presenting with the most severe form of dystroglycanopathy, Walker–Warburg syndrome (WWS) and compound het variants in POMK. Macrocephaly and hydrocephalus were diagnosed in utero upon prenatal ultrasound at 32 weeks of gestation. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.210 | POMK | Rebecca Foulger commented on gene: POMK: POMK was added to the fetal panel as Amber based on a 'probable' rating in the PAGE original Additional gene list. In the PAGE paper (Lord et al., 2019, PMID:30712880) POMK is listed as an Additional gene based on association with a prenatal phenotype reported in the literature (Supplementary Table 2). POMK is not currently associated with a disorder in DD-Gene2Phenotype but is associated with 'Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 12, 615249' in OMIM. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.210 | ZNF423 | Rebecca Foulger Added comment: Comment on list classification: Kept rating as Amber following review of literature evidence in PMID:22863007 and ZNF423 is currently Amber on the 'Rare multisystem ciliopathy disorders' panel. Fetally relevant phenotype but currently insufficient evidence for a Green gene rating. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.210 | ZNF423 | Rebecca Foulger Added comment: Comment on list classification: Kept rating as Amber following review of literature evidence in PMID:22863007 and ZNF423 is currently Amber on the 'Rare multisystem ciliopathy disorders' panel. Fetally relevant phenotype but currently insufficient evidence for a Green gene rating. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.208 | ZNF423 | Rebecca Foulger commented on gene: ZNF423: ZNF423 was added to the fetal panel as Amber based on a 'probable' rating in the PAGE original Additional gene list. In the PAGE paper (Lord et al., 2019, PMID:30712880) ZNF423 is listed as an Additional gene (Supplementary Table 2) based on association with a prenatal phenotype reported in the literature, with biallelic/monoallelic inheritance. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.207 | ROBO1 | Rebecca Foulger commented on gene: ROBO1: Evidence for inclusion on the PAGE Additional gene list comes from a single study in Kruszka et al. (2017, PMID:28592524) but 3 families of different ethnicities; each proband had a ventricular septal defect, and one proband had tetralogy of Fallot. Plus proband 1 had craniofacial findings, consistent with the mouse model. VSD can be detected prenatally (e.g. see PMID:24456562) so is relevant for the panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.207 | ROBO1 | Rebecca Foulger commented on gene: ROBO1: ROBO1 was added to the fetal panel as Amber based on a 'probable' rating in the PAGE original Additional gene list. In the PAGE paper (Lord et al., 2019, PMID:30712880), ROBO1 is listed as an Additional gene (Supplementary Table 2) based on association with a prenatal phenotype reported in the literature. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.205 | ARL13B | Rebecca Foulger Added comment: Comment on list classification: Updated rating from Amber to Green: ARL13B is on the Additional gene list in the PAGE paper (Lord et al., 2019, PMID:30712880) based on prenatal presentation of a phenotype in the literature. Sufficient (3 unrelated cases in OMIM (Pakistani, American, Tunisian) with homozygous or compound heterozygous variants in ARL13B in patients with a Joubert phenotype (from PMIDs 18674751 and 25138100). Plus functional evidence to support impairment of ARL13B protein function (PMID:29255182). Therefore sufficient evidence to support threshold for Green rating. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.204 | ARL13B |
Rebecca Foulger commented on gene: ARL13B: ARL13B was added to the fetal panel as Amber based on a 'probable' rating in the PAGE original Additional gene list. In the PAGE paper (Lord et al., 2019, PMID:30712880) ARL13B is listed as an Additional gene (Supplementary Table 2) based on association with a prenatal phenotype reported in the literature. ARL13B is not currently associated with a disorder in DD-Gene2Phenotype but in OMIM is linked to the biallelic disorder Joubert syndrome 8, 612291. |
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| Fetal anomalies v0.201 | ADAMTS17 | Rebecca Foulger Added comment: Comment on list classification: Updated rating from Amber to Green: ADAMTS17 is listed as an Additional gene in the PAGE paper (Lord et al., 2019, PMID:30712880) and therefore fetally-relevant (phenotype includes short stature). For evidence, there are sufficient cases in OMIM (5 variants from 5 different families (3 families from PMID:19836009 and one each from PMIDs:22486325 and 24940034) to support a Green (diagnostic-grade) rating. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.200 | ADAMTS17 |
Rebecca Foulger commented on gene: ADAMTS17: ADAMTS17 was added to the fetal panel as Amber based on a 'probable' rating in the PAGE original Additional gene list. In the PAGE paper (Lord et al., 2019, PMID:30712880) ADAMTS17 is listed as an Additional gene (Supplementary Table 2) based on association with a prenatal phenotype reported in the literature. ADAMTS17 is not currently associated with a disorder in DD-Gene2Phenotype but in OMIM is linked to the disorder 'Weill-Marchesani 4 syndrome, recessive, 613195). |
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| Fetal anomalies v0.199 | COG4 | Rebecca Foulger commented on gene: COG4: The evidence for Saul-Wilson syndrome (MIM:618150) comes from one 2018 paper (PMID:30290151): Ferreira et al. (PMID:30290151, 2018) identified 2 different de novo heterozygous vaiants in the COG4 gene in 14 individuals, c.1546G-A and c.1546G-C both of which give rise to an identical missense mutation (G516R). Functional analysis shows that a stable protein is produced and, despite Golgi collapse, glycosylation is relatively normal. Given the DD-G2P Disease confidence rating is 'probable' (March 2019), only a missense variant has been reported, and functional evidence doesn't yet show the effect of the protein alteration, I have kept the MOI for COG4 on the Fetal anomalies panel as biallelic (for the confirmed glycosylation disorder) and not included the monoallelic Saul-Wilson syndrome on the panel at this stage. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.199 | TTN |
Rebecca Foulger Added comment: Comment on list classification: Rated as Green following confirmation from Anna de Burca as the following papers demonstrate a fetal relevance: In PMID:29575618, six of the affecteds were diagnosed prenatally by fetal ultrasound. In PMID:28040389 a fetal ultrasound reported Clubfoot. In PMID:29691892 all 30 patients had prenatal or early onset hypotonia and/or congenital contractures. The authors state that: to date, 16 patients from 12 families with a recessive prenatal or infant onset form of titinopathy have been reported. |
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| Fetal anomalies v0.197 | FBXO11 | Rebecca Foulger commented on gene: FBXO11: Added watchlist tag to reflect multiple Disease confidence ratings in DD-G2P for different disorders: Rated confirmed for Variable Neurodevelopmental Disorder. Rated possible for FBXO11 related intellectual disability. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.197 | CACNA1E | Rebecca Foulger commented on gene: CACNA1E: Added watchlist tag to reflect multiple Disease confidence ratings in DD-G2P for different disorders: Rated confirmed for Developmental and Epileptic Encephalopathy with Contractures Macrocephaly and Dyskinesias. Rated probable for Epileptic Encephalopathy with Contractures, Macrocephaly, and Dyskinesia. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.196 | SPTBN2 | Rebecca Foulger Added comment: Comment on mode of inheritance: Two new disorders added to DD-G2P in March 2019, with different modes of inheritance: biallelic for SCA14, and monoallelic for Infantile ataxia with oculomotor and pyramidal signs. Set inheritance to 'biallelic' only because biallelic 'SCA14' disorder is confirmed, and monoallelic 'Infantile ataxia with oculomotor and pyramidal signs' disorder is probable. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.188 | PCGF2 | Rebecca Foulger commented on gene: PCGF2: Added 'watchlist' tag to reflect multiple Disease confidence ratings for different disorders in Gene2Phenotype: Rated probable for INTELLECTUAL DUSBILITY. Rated confirmed for Craniofacial Neurological Cardiovascular and Skeletal. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.184 | P3H1 | Rebecca Foulger edited their review of gene: P3H1: Added comment: Additional evidence from PMID:29595812:AR Bi-parental-inherited variant identified in P3H1 from fetal exome sequencing in Chandler et al., 2018 (Rapid diagnosis of fetal skeletal dysplasia using targeted exome sequencing, PMID:29595812).; Changed publications: 29595812 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.184 | OBSL1 | Rebecca Foulger edited their review of gene: OBSL1: Added comment: Additional evidence from PMID:29595812:AR Biparental-inherited variant identified in OBSL1 from fetal exome sequencing in Chandler et al., 2018 (Rapid diagnosis of fetal skeletal dysplasia using targeted exome sequencing, PMID:29595812).; Changed publications: 29595812 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.166 | TPP1 | Rebecca Foulger edited their review of gene: TPP1: Added comment: This gene and phenotype were discussed during review of borderline cases in April 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is not fetally-relevant. Additional notes from clinical review: Probably won't present prenatally. Action taken: Demoted gene rating from Green to Red.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.166 | DSP | Rebecca Foulger edited their review of gene: DSP: Added comment: This gene and phenotype were discussed during review of borderline cases in April 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: keep on the Fetal anomalies panel as Green. Additional notes from clinical review: Include because tooth agenesis can be detected prenatally.; Changed rating: GREEN; Changed publications: 30993396 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.166 | OTULIN | Rebecca Foulger edited their review of gene: OTULIN: Added comment: This gene and phenotype were discussed during review of borderline cases in April 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is not fetally-relevant. Additional notes from clinical review: Lipodystrophy. Early treatment could be helpful but no obvious detectable prenatal phenotype. Action taken: Demoted gene rating from Green to Red.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.161 | WDR45 | Rebecca Foulger edited their review of gene: WDR45: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is not fetally-relevant. Additional notes from clinical review: Iron deposition, doesn't seem to present prenatally. Action taken: Demoted WDR45 gene rating from Green to Red.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.161 | SUCLG1 | Rebecca Foulger edited their review of gene: SUCLG1: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: keep on the Fetal anomalies panel as a Green gene. Additional notes from clinical review: Has presented prenatally (PMID:21093335); Changed rating: GREEN; Changed publications: 21093335 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.161 | SPEG | Rebecca Foulger edited their review of gene: SPEG: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: keep on the Fetal anomalies panel as a Green gene. Additional notes from clinical review: Severe phenotype with onset in infancy so assume contractures etc could present prenatally.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.153 | QRICH1 | Rebecca Foulger edited their review of gene: QRICH1: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: keep on the Fetal anomalies panel as a Green gene. Additional notes from clinical review: Only 5 cases reported so far so phenotype is not that well-characterised yet. Some dysmorphic features may be detectable prenatally- one case had IUGR, and another had severe microcephaly.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.153 | PSPH | Rebecca Foulger edited their review of gene: PSPH: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: keep on the Fetal anomalies panel as a Green gene. Additional notes from clinical review: Neu-Laxova syndrome would present prenatally, but probably not the milder Phosphoserine phosphatase deficiency.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.153 | OTOGL | Rebecca Foulger edited their review of gene: OTOGL: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is not fetally-relevant. Additional notes from clinical review: Phenotypes aren't structural (Nonsyndromic sensorineural deafness). Action taken: Demoted OTOGL gene rating from Green to Red.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.148 | POLD1 | Rebecca Foulger edited their review of gene: POLD1: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is not fetally-relevant. Additional notes from clinical review: Disease confidence in DD-G2P is 'both DD and IF'. Does not seem to have evidence for prenatal presentation, and risk of cancer predisposition as an incidental finding. Action taken: Demoted POLD1 gene rating from Amber to Red.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.148 | KRIT1 | Rebecca Foulger edited their review of gene: KRIT1: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant. Additional notes from clinical review: Disease confidence in DD-G2P is 'both DD and IF'. One case has been reported for a Biallelic variant in this gene prenatally, for a different phenotype (PMID: 28749478). Action taken: Promoted KRIT1 gene rating from Amber to Green.; Changed rating: GREEN; Changed publications: 28749478 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.141 | ACOX1 | Rebecca Foulger Added comment: Comment on phenotypes: 'Peroxisomal acyl-CoA oxidase deficiency, 264470' phenotype was added from OMIM, following clinical review. The 'ADRENOLEUKODYSTROPHY PSEUDONEONATAL' phenotype came from the original PAGE file and DD-Gene2Phenotype. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.141 | ACOX1 | Rebecca Foulger Phenotypes for gene: ACOX1 were changed from ADRENOLEUKODYSTROPHY PSEUDONEONATAL; Peroxisomal acyl-CoA oxidase deficiency, 264470 to ADRENOLEUKODYSTROPHY PSEUDONEONATAL; Peroxisomal acyl-CoA oxidase deficiency, 264470 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.135 | ACOX1 | Rebecca Foulger Added phenotypes ADRENOLEUKODYSTROPHY PSEUDONEONATAL; Peroxisomal acyl-CoA oxidase deficiency, 264470 for gene: ACOX1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | GJB2 | Rebecca Foulger edited their review of gene: GJB2: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: keep on the Fetal anomalies panel as Green. Additional notes from clinical review: Include on panel on basis of possible congenital digit constrictions and no harm done. Change MOI to monoallelic only: Recessive inheritance is attributed to the deafness phenotype, which would not be detected prenatally. Action taken: Changed mode of inheritance from 'both biallelic and monoallelic' to 'monoallelic' only.; Changed rating: GREEN; Changed mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | GHR | Rebecca Foulger edited their review of gene: GHR: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is not fetally-relevant. Additional notes from clinical review: Baby is normal size at birth and fails to grow afterwards, so not detectable prenatally. Action taken: Demoted GHR gene rating from Green to Red. ; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | GAMT | Rebecca Foulger edited their review of gene: GAMT: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is not fetally-relevant. Additional notes from clinical review: Nothing detectable prenatally, though it would be informative as clinically actionable at birth. Action taken: Demoted GAMT gene rating from Green to Red. ; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | GALT | Rebecca Foulger edited their review of gene: GALT: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is not fetally-relevant. Additional notes from clinical review: Nothing detectable prenatally, though it would be informative as clinically actionable at birth. Action taken: Demoted GALT gene rating from Green to Red. ; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | GALK1 | Rebecca Foulger edited their review of gene: GALK1: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is not fetally-relevant. Additional notes from clinical review: Just cataracts, preventable with early dietary management so not detectable prentally. Action taken: Demoted GALK1 gene rating from Green to Red. ; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | FLAD1 | Rebecca Foulger edited their review of gene: FLAD1: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is not fetally-relevant. Additional notes from clinical review: Not detectable prenatally. Action taken: Demoted FLAD1 gene rating from Green to Red. ; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | DMPK | Rebecca Foulger edited their review of gene: DMPK: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: keep on the Fetal anomalies panel as Green. Additional notes from clinical review: Note of caution that repeat expansion is clinically-relevant and not detectable on exome. Only relevant prenatally if it is a large expansion. A small expansion has adult onset and would be an incidental finding.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | DHCR7 | Rebecca Foulger edited their review of gene: DHCR7: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: keep on the Fetal anomalies panel as Green. Additional notes from clinical review: Lots of phenotypes that would present prenatally including ambiguous genitalia.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | DEPDC5 | Rebecca Foulger edited their review of gene: DEPDC5: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is not fetally-relevant. Additional notes from clinical review: Epilepsy but no structural brain defects, so probably not detectable prenatally. Action taken: Demoted DEPDC5 gene rating from Green to Red.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | CLPB | Rebecca Foulger edited their review of gene: CLPB: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: keep on the Fetal anomalies panel as Green. Additional notes from clinical review: Presentation at birth/prenatal in severe forms.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | CLDN19 | Rebecca Foulger edited their review of gene: CLDN19: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is not fetally-relevant. Additional notes from clinical review: Phenotypes are not detectable prenatally (unlikely to see coloboma). Action taken: Demoted CLDN19 gene rating from Green to Red. ; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | CIB2 | Rebecca Foulger edited their review of gene: CIB2: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is not fetally-relevant. Additional notes from clinical review: The phenotypes of deafness and Retinitis pigmentosa (part of Usher syndrome, type IJ) would not present prenatally. Action taken: Demoted CIB2 gene rating from Green to Red. ; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | CDKN1C | Rebecca Foulger edited their review of gene: CDKN1C: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: keep on the Fetal anomalies panel as Green. Additional notes from clinical review: Point mutations in CDKN1C can cause phenotypes, and be picked up by this panel. OMIM confirms that CDKN1C is paternally-imprinted with preferential expression of the maternal allele.; Changed rating: GREEN; Changed mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, paternally imprinted (maternal allele expressed) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | ALDH7A1 | Rebecca Foulger edited their review of gene: ALDH7A1: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: keep on the Fetal anomalies panel as Green. Additional notes from clinical review: Phenotype has prenatal or neonatal onset and includes in utero convulsions. Treatable.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | AGK | Rebecca Foulger edited their review of gene: AGK: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: keep on the Fetal anomalies panel as Green. Additional notes from clinical review: Bilateral cataracts in first week of life which can be picked up prenatally. 3/12 died in neonatal period.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | ACOX1 | Rebecca Foulger edited their review of gene: ACOX1: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: keep on the Fetal anomalies panel as Green. Additional notes from clinical review: Brain malformations may be picked up in a late MRI scan.; Changed rating: GREEN; Changed phenotypes: ADRENOLEUKODYSTROPHY PSEUDONEONATAL, Peroxisomal acyl-CoA oxidase deficiency, 264470 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | REN | Rebecca Foulger edited their review of gene: REN: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: keep on the Fetal anomalies panel as Green. Additional notes from clinical review: Include with biallelic inheritance.; Changed rating: GREEN; Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | MLH1 | Rebecca Foulger edited their review of gene: MLH1: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: keep on the Fetal anomalies panel as Green. Additional notes from clinical review: Include with biallelic inheritance only- phenotype presents in childhood, but very rarely there is a chance of tumours presenting very early as fetal adrenal/renal masses. Action taken: Changed Mode of inheritance from 'both monoallelic and biallelic' to 'biallelic' only.; Changed rating: GREEN; Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | ITGB4 | Rebecca Foulger edited their review of gene: ITGB4: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: keep on the Fetal anomalies panel as Green. Additional notes from clinical review: Prenatally relevant. ITGB4 is rated Green on the V1.6 'Epidermolysis bullosa' panel.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | ITGA6 | Rebecca Foulger edited their review of gene: ITGA6: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: keep on the Fetal anomalies panel as Green. Additional notes from clinical review: Prenatally relevant. Although there is only one reported case in OMIM, ITGA6 is rated Green on the V1.6 'Epidermolysis bullosa' panel due to expert review and recent additional publications.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | AGRN | Rebecca Foulger edited their review of gene: AGRN: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is not fetally-relevant. Additional notes from clinical review: Unlikely to detect congenital myasthenia prenatally. Action taken: Demoted AGRN gene rating from Green to Red. ; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.134 | COL1A1 | Rebecca Foulger edited their review of gene: COL1A1: Added comment: This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: keep on the Fetal anomalies panel as a Green gene. Additional notes from clinical review: Need caution when reviewing variants in COL1A1, because different variants are associated with different phenotypes. Gain of function variants cause a more severe phenotype than LOF variants, which cause a mild phenotype.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.132 | ASCC1 |
Julia Baptista gene: ASCC1 was added gene: ASCC1 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: ASCC1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: ASCC1 were set to PMID: 26924529; 30327447; 28749478 Phenotypes for gene: ASCC1 were set to spinal muscular atrophy; arthrogryposis; fetal akinesia; hypotonia; contractures Review for gene: ASCC1 was set to GREEN gene: ASCC1 was marked as current diagnostic Added comment: Homozygous frameshift variant reported in two siblings from a Turkish family and one child from a Portuguese family affected with fetal akinesia, arthrogryposis, hypotonia, muscle weakness and congenital bone fractures. One further family reported with fetal akinesia and a homozygous splicing variant. Sources: Literature |
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| Fetal anomalies v0.120 | MYT1 | Rebecca Foulger commented on gene: MYT1: MYT1 was added to the panel as Amber based on a 'Probable' rating in the Additional Gene list supplied by the PAGE group. Note that 'OAVS/Goldenhar syndrome' currently has a 'possible' rating in DD-G2P. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.115 | SAMD9 |
Rebecca Foulger gene: SAMD9 was added gene: SAMD9 was added to Fetal anomalies. Sources: DD-Gene2Phenotype,Expert Review Green Mode of inheritance for gene: SAMD9 was set to Publications for gene: SAMD9 were set to 27182967; 28346228 Phenotypes for gene: SAMD9 were set to MIRAGE - myelodysplasia, infection, restriction of growth, adrenal hypoplasia, genital phenotypes, enteropathy |
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| Fetal anomalies v0.114 | AAAS | Rebecca Foulger commented on gene: AAAS: AAAS Gene and phenotype discussed at meeting with Lynn Chitty, Richard Scott and Anna De Burca (meeting at Great Ormond Street, February 27th 2019). Although microcephaly may or may not show in a prenatal setting, the advice is to leave AAAS on the fetal panel as Green. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.110 | SLC4A1 | Rebecca Foulger commented on gene: SLC4A1: Changed rating to Amber to reflect DDG2P Disease confidence of 'DD and IF' for RENAL TUBULAR ACIDOSIS, DISTAL, AD; RENAL TUBULAR ACIDOSIS, DISTAL, AR. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.110 | RET | Rebecca Foulger commented on gene: RET: Changed rating to Amber to reflect DDG2P Disease confidence of 'DD and IF' for RENAL AGENESIS; MULTIPLE ENDOCRINE NEOPLASIA IIB. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.110 | COL4A2 | Rebecca Foulger commented on gene: COL4A2: Changed rating to Amber to reflect DDG2P Disease confidence of 'DD and IF' for PORENCEPHALY 2. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.110 | COL4A1 | Rebecca Foulger commented on gene: COL4A1: Changed rating to Amber to reflect DDG2P Disease confidence of 'DD and IF' for PORENCEPHALY 1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.110 | ABCD1 | Rebecca Foulger commented on gene: ABCD1: Changed rating to Amber to reflect DDG2P Disease confidence of 'DD and IF' for ADRENOLEUKODYSTROPHY, X-LINKED. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.103 | TWIST2 | Rebecca Foulger Added comment: Comment on list classification: Updated rating from Amber to Green following comment from Deirdre Cilliers (OUH). Originally rated Amber based on multiple ratings for different disorders, but as Deirdre notes: Setleis would not present prenatally. Sufficient cases (>3) of Barber-Say and ablepharon-macrostomia syndrome to support causation. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.102 | TWIST2 | Rebecca Foulger Added comment: Comment on mode of pathogenicity: Changed MOP to 'Other' based on comment by Deirdre Cilliers: gain of function for Barber-Say and ablepharon-macrostomia syndrome, which are relevant to this fetal panel. As noted in original upload, DD-G2P record a 'loss of function' mechanism for SETLEIS SYNDROME, but this wouldn't present prenatally (see comment from Deirdre Cilliers). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.101 | TWIST2 | Rebecca Foulger commented on gene: TWIST2: Communication from Deirdre Cilliers, Oxford University Hospitals (via email, February 2019) to support Green rating: Yes [TWIST2 should be on the Fetal anomalies panel]. Very particular mutations which improve the chance of variant interpretation - gain of function for Barber-Say and ablepharon-macrostomia syndrome. May present with ambiguous genitalia (microarray may identify a male karyotype when thought that female genitalia were seen on scan) or talipes which may be identified, but other features not clear on scan (loss of lateral lower lip). Setleis type of focal facial dermal dysplasia would not present prenatally, although there is a small chance of an incidental finding if this gene is on the panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.100 | TBCE | Rebecca Foulger commented on gene: TBCE: Communication from Deirdre Cilliers, Oxford University Hospitals (via email, February 2019) to support Green rating: No [TBCE should not be on the Fetal anomalies panel]. Would not usually present prenatally. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.98 | SUFU | Rebecca Foulger commented on gene: SUFU: In 4 children from 2 unrelated consanguineous families (Egyptian and Italian) with Joubert syndrome-32 (JBTS32; 617757), De Mori et al. (2017, PMID:28965847) identified 2 different homozygous missense mutations in the SUFU gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.96 | SUFU | Rebecca Foulger commented on gene: SUFU: Communication from Deirdre Cilliers, Oxford University Hospitals (via email, February 2019): Yes [SUFU should be on the Fetal anomalies panel]. Joubert syndrome would present prenatally with the cerebellar vermis hypoplasia and/or polydactyly. If the test incidentally identifies the predisposition to cancer, screening would be offered early in childhood in any case, although this would be difficult news to hear in the prenatal setting. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.96 | MITF | Rebecca Foulger Added comment: Comment on mode of inheritance: Changed MOI from 'both biallelic and monoallelic' to 'biallelic' as COMMAD phenotype has recessive inheritance, and COMMAD phenotype would present prenatally (see comment from Deirdre Cilliers). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.95 | MITF | Rebecca Foulger commented on gene: MITF: In 2 unrelated children with coloboma, osteopetrosis, microphthalmia, macrocephaly, albinism, and deafness (COMMAD; 617306), whose parents exihibited features of WS2A, George et al. (2016, PMID:27889061) identified compound heterozygosity for variants in the MITF gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.92 | MITF | Rebecca Foulger commented on gene: MITF: Communication from Deirdre Cilliers, Oxford University Hospitals (via email, February 2019): Yes [CFC1 should be on the Fetal anomalies panel]. COMMAD would present prenatally as microphalmia and congenital cataracts would be seen on ultrasound scan as may be the macrocephaly and frontal bossing. The parents would likely exhibit the Tietz albinism deafness/Waardenburg phenotypes so would be able to interpret variants for this condition. However, some fetusses may incidentally be identified to have Tietz albinism deafness/Waardenburg phenotypes, but this may also be informative to parents, although more difficult information for them to receive. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.89 | MAGEL2 | Rebecca Foulger commented on gene: MAGEL2: Communication from Deirdre Cilliers, Oxford University Hospitals (via email, February 2019): Yes [MAGEL2 should be on the Fetal anomalies panel]. The phenotype would be clear on scan and the test likely requested because of the scan findings of akinesia. Even if incidentally identified, it will be useful information for the parents, e.g. expectation of learning difficulties, if positive. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.89 | MAFB | Rebecca Foulger Added comment: Comment on list classification: Originally rated as Amber based on different DDG2P/PAGE ratings for different disorders. Kept rating as Amber following comment from Deidre Cilliers that phenotype is not fetally-relevant. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.89 | MAFB | Rebecca Foulger Added comment: Comment on list classification: Originally rated as Amber based on different DDG2P/PAGE ratings for different disorders. Kept rating as Amber following comment from Deidre Cilliers that phenotype is not fetally-relevant. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.89 | MAFB | Rebecca Foulger Added comment: Comment on list classification: Originally rated as Amber based on different DDG2P/PAGE ratings for different disorders. Kept rating as Amber following comment from Deidre Cilliers that phenotype is not fetally-relevant. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.88 | MAFB | Rebecca Foulger commented on gene: MAFB: Communication from Deirdre Cilliers, Oxford University Hospitals (via email, February 2019): No [Would not include MAFB on the Fetal anomalies panel]: Not usually manifesting in the prenatal setting. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.85 | EMG1 | Rebecca Foulger commented on gene: EMG1: Bowen-Conradi syndrome includes marked prenatal and postnatal growth retardation, microcephaly, a prominent nose with an absent glabellar angle, micrognathia, joint abnormalities including flexion contractures, camptodactyly, rocker-bottom feet, and severe psychomotor delay (PMID:19463982). So far, one EMG1 variant (D86G) recorded for Bowen-Conradi Syndrome, with virtually all affected babies born into Hutterite families. PMID:19463982 does however report that there are at least 4 published (Russian, German, Turkish and two Indian babies) and four unpublished reports of non-Hutterite babies with BCS-compatible features. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.84 | EMG1 | Rebecca Foulger commented on gene: EMG1: Communication from Deirdre Cilliers, Oxford University Hospitals (via email, February 2019): Yes [EMG1 should be on the Fetal anomalies panel]. There are structural findings that will be identified on ultrasound scan, namely IUGR, microcephaly, cleft lip and hypospadias (even rocker bottom feet can sometimes be identified on ultrasound scan, although testing would not be offered for this in isolation). These findings are less frequent in the condition, but will be ascertained prenatally. Poor outcome also and this would be useful information for parents to consider in pregnancy – although it is a rare condition. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.84 | DNAH5 | Rebecca Foulger Added comment: Comment on list classification: Updated rating from Amber to Green following advice from Fetal expert, Deidre Cilliers that heterotaxy phenotype is prenatally-relevant. Originally rated Amber on the panel based on different PAGE/DDG2P ratings for different disorders. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.83 | DNAH5 | Rebecca Foulger commented on gene: DNAH5: Communication from Deirdre Cilliers, Oxford University Hospitals (via email, February 2019) to support Green rating: Yes [DNAH5 should be on the Fetal anomalies panel]. The prenatal phenotype would be heterotaxy and often seen on ultrasound scan and about half of affected pregnancies with this mutation would have this phenotype. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.82 | DEAF1 | Rebecca Foulger Added comment: Comment on list classification: Originally rated as Amber based on multiple DDG2P/PAGE ratings for different disorders. Have kept rating as Amber following advice from fetal expert, Deidre Cilliers (see review for details). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.81 | DEAF1 | Rebecca Foulger commented on gene: DEAF1: Communication from Deirdre Cilliers, Oxford University Hospitals (via email, February 2019): Probably not [include DEAF1 on the Fetal anomalies panel] if the panel was requested only for fetal structural anomalies. Difficult to decide as one would like to make this diagnosis prenatally. However, no structural features on ultrasound scan and this would make variant interpretation difficult – especially as some of the mutations have been missense mutations. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.76 | IFIH1 | Rebecca Foulger Added comment: Comment on publications: PMID:25542954 describes a prenatal diagnosis of Aicardi-Goutières syndrome. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.75 | IFIH1 | Rebecca Foulger Added comment: Comment on mode of inheritance: Changed MOI from 'monoallelic' to 'biallelic' after discussion with Genomics England clinical fellows: monoallelic form is associated with cardiovascular features so risk of incidental findings with monoallelic recorded inheritance. Further advice came from Deidre Cilliers Oxford University Hospitals who notes: I would report biallelic inheritance in the known genes with an AR inheritance pattern as there is a high recurrence risk for the family, e.g. AGS caused by TREX1 and there is a clear prenatal phenotype. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.74 | IFIH1 | Rebecca Foulger commented on gene: IFIH1: Communication from Deirdre Cilliers, Oxford University Hospitals (via email, February 2019) to support Green rating: Yes [IFIH1 should be on the Fetal anomalies panel]. Aicardi-Goutieres is often missed in the prenatal period as it is assumed that there is congenital infection present (even if testing negative). When reading through the cases in the literature, I think that later ultrasound scans in pregnancy might have identified some of the IFIH1 mutations in addition to the more commonly found TREX1. I have had two families in the past 2 years where I suggested the diagnosis in the prenatal period, although in one family with two affected pregnancies we never found the mutations. However, the phenotype is also clear on ultrasound scan as it looks like infection and the screen for this is negative. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.72 | ARCN1 | Rebecca Foulger commented on gene: ARCN1: Communication from Deirdre Cilliers, Oxford University Hospitals (via email, February 2019) to support Green rating: Yes [ARCN1 should be on the Fetal anomalies panel]. All [patients from PMID:27476655] have a degree of developmental delay, although most were mildy affected (useful for parents to have this information). Microcephaly and IUGR will be seen on ultrasound scan as well as structural anomalies, e.g. diaphragmatic hernia, VSD and severe micrognathia (some of these patients may need a paediatrician at birth for airway management as some have required tracheostomies). Cleft palate would likely be missed in most cases on ultrasound scan. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.66 | CFC1 | Rebecca Foulger commented on gene: CFC1: Communication from Deirdre Cilliers, Oxford University Hospitals (via email, February 2019) to support Green rating: Yes [CFC1 should be on the Fetal anomalies panel]. The phenotype would easily be seen on ultrasound scan and such a result would give the parents good information about the pregnancy and also help allow variant interpretation. It would let them know that the intellect is likely normal and they can then concentrate on the particular cardiac problem only. If incidentally identified, ultrasound scans can be offered in pregnancy. Also, one of the patients [in PMID:11062482] had an absent corpus callosum, although it may have been an incidental finding. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.66 | CFC1 | Rebecca Foulger commented on gene: CFC1: Further information on evidence for Green rating: Reviewed as Green on the 'Familial non syndromic congenital heart disease' panel in relation to heterotaxy phenotype. 3 cases in OMIM cases to support causation of 'Heterotaxy, visceral, 2, autosomal, 605376' although incomplete penetrance (with phenotypically-normal parent carrying the variant) seen in two cases. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.63 | TBX18 | Rebecca Foulger edited their review of gene: TBX18: Added comment: Additional details for change of rating from Amber ('probable' PAGE rating) to Green: Phenotype is fetally-relevant, and rated green on the 'CAKUT' panel with the phenotype 'Congenital anomalies of kidney and urinary tract 2'. Sufficient cases to support association from one paper:PMID:26235987 (2015) shows variants in 3 unrelated families with a variety of renal malformations.; Changed rating: GREEN; Changed publications: 26235987; Changed phenotypes: Congenital anomalies of kidney and urinary tract 2, 143400 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.60 | SIL1 | Louise Daugherty Phenotypes for gene: SIL1 were changed from MARINESCO-SJOEGREN SYNDROME to Marinesco-Sjogren syndrome, 248800 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.54 | ATAD3A | Rebecca Foulger Added comment: Comment on mode of inheritance: Changed MOI from 'Both monoallelic and biallelic' to only monoallelic, based on Anna's review: Green rating is appropriate for monoallelic inheritance only as there is currently insufficient evidence for biallelic disorder. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.53 | ATAD3A | Rebecca Foulger Added comment: Comment on list classification: Updated rating from Amber to Green following review from Anna de Burca. Originally assigned an Amber rating because of different PAGE/DDG2P ratings for different disorders. Green rating is appropriate for monoallelic inheritance only, as stated in Anna's review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.49 | BGN | Rebecca Foulger Added comment: Comment on list classification: Originally assigned an Amber rating because of different PAGE/DDG2P ratings for different disorders. Kept rating as Amber based on Anna's review: sufficient evidence for TAAD causation but phenotype presents later. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.45 | ITPR1 | Rebecca Foulger Added comment: Comment on list classification: Kept rating as Amber following email correspondance from Anna de Burca who notes that SCA15 is an adult onset condition and that ITPR1 is also associated with Gillespie syndrome which might possibly present prenatally with cerebellar hypoplasia but on balance it would be better to exclude. Therefore although there is sufficient evidence (>3 cases) for association with Gillespie syndrome, the phenotype is not appropriate for this Fetal panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.44 | ACTB | Rebecca Foulger Added comment: Comment on list classification: Updated rating from Amber to Green following review and email correspondance from Anna de Burca. Originally assigned an Amber rating because of different PAGE/DDG2P ratings for different disorders. As summarised by Anna there is good evidence for GOF variants causing Baraitser-Winter syndrome plus some evidence for LOF variants associated (in some cases) with structural anomalies. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.43 | ACTB | Rebecca Foulger Added comment: Comment on mode of pathogenicity: Anna notes that there is good evidence for GOF variants causing Baraitser-Winter syndrome but there is also a paper from DDD (PMID:29220674) reporting LOF variants associated predominantly with developmental delay but in some cases structural anomalies including congenital heart defects and/or CAKUT- this may not be a severe enough prenatal phenotype for inclusion in a fetal panel but overall Anna notes that it is probably reasonable to report any variants in this gene, whether GOF or LOF. Therefore no exception to LOF was added to the MOP section. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.39 | ERCC4 | Rebecca Foulger Added comment: Comment on list classification: Updated rating from Amber to Green following email correspondance from Anna de Burca. Originally assigned an Amber rating because of different PAGE/DDG2P ratings for different disorders. Anna notes that ERCC4 is green on congenital anaemias panel for XP/progeroid syndrome and therefore Green rating is probably appropriate for Fetal anomalies panel also. Confirmed DD-G2P rating for XERODERMA PIGMENTOSUM, GROUP F. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.38 | TCTN1 | Rebecca Foulger Added comment: Comment on list classification: Updated rating from Amber to Green following email correspondance from Anna de Burca. Originally assigned an Amber rating because of different PAGE/DDG2P ratings for different disorders. Anna notes that TCTN1 is Green on the 'Rare multisystem ciliopathy disorders' panel with Joubert syndrome phenotype, and therefore Green rating is appropriate for this Fetal anomalies panel. 3 cases from the literature to support Green rating: Two Bangladeshi sisters in PMID:21725307 with homozgyous variant in TCTN1. A compound het variant from PMID:26477546 in a male fetus, and PMID:26489806 report an additional compound het case. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.35 | IL11RA | Rebecca Foulger Added comment: Comment on list classification: Updated rating from Amber to Green following email correspondance from Anna de Burca. Originally assigned an Amber rating because of different PAGE/DDG2P ratings for different disorders. Rated as 'Confirmed' for AR Craniosynostosis. As noted by Anna, IL11RA is Green on the Craniosynostosis panel, so Green rating also appropriate for Fetal Anomalies panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.34 | ATAD3A | Anna de Burca commented on gene: ATAD3A: PMID: 27640307 reports a recurrent de novo variant in ATAD3A in five unrelated individuals with developmental delay and hypotonia. Some individuals had peripheral neuropathy, optic atrophy and hypertrophic cardiomyopathy. A toxic gain of function mechanism was postulated. PMID: 28327206 reports an additional case with the same de novo variant. This individual had delayed motor development and hypotonia. PMID: 27640307 also reports a biallelic missense variant in siblings of distantly related parents with motor and speech delay, hypotonia, cerebellar atrophy, ataxia, seizures, muscle weakness, cataracts and optic nerve hypoplasia. There is insufficient evidence for this association at present. Therefore, this gene should be classified green with regard to monoallelic gain of function only. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.32 | TRIP4 | Rebecca Foulger Added comment: Comment on list classification: Updated rating from Amber to Green: Rated Green on relevant V1 panel(s) PLUS phenotype (Prenatal Spinal Muscular Atrophy and Congenital Bone Fractures) appropriate for fetal panel, as noted by Helen Brittain and Anna de Burca (Genomics England Clinical team). Rated Green on 'Paediatric motor neuronopathies' panel based on sufficient cases, zebrafish model and Green review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.23 | KYNU | Rebecca Foulger Added comment: Comment on list classification: Updated rating from Amber to Green: Rated Green on relevant V1 panel(s) PLUS phenotype (MIM:617661) appropriate for fetal panel, as noted by Helen Brittain and Anna de Burca (Genomics England Clinical team). The literature evidence amounts to 2 unrelated patients with vertebral, cardiac, renal, and limb defects syndrome-2 (MIM:617661) and variants in HAAO (Shi et al. 2017, PMID:28792876) plus mouse model of embryonic defects from the same paper. However, the comment on the 'VACTERL-like phenotypes' and 'CAKUT' panels states "Confirmed with the clinical team that this gene has enough evidence to be green". | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.22 | HAAO | Rebecca Foulger Added comment: Comment on list classification: Updated rating from Amber to Green: Rated Green on relevant V1 panel(s) PLUS phenotype (MIM:617660) appropriate for fetal panel, as noted by Helen Brittain and Anna de Burca (Genomics England Clinical team). The literature evidence amounts to 2 unrelated patients, each born of consanguineous parents, with vertebral, cardiac, renal, and limb defects syndrome-1 (MIM:617660) and homozygous truncating variants in HAAO (Shi et al. 2017, PMID:28792876). However, the comment on the 'VACTERL-like phenotypes', 'Undiagnosed metabolic disorders' and 'CAKUT' panels states "Confirmed with the clinical team that this gene has enough evidence to be green". | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.9 | TUBB | Rebecca Foulger commented on gene: TUBB: DDG2P rating in original PAGE list: Confirmed for CORTICAL DYSPLASIA, COMPLEX, WITH OTHER BRAIN MALFORMATIONS 6 and Confirmed for Circumferential Skin Creases Kunze Type. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.9 | SIX5 | Rebecca Foulger commented on gene: SIX5: DDG2P rating in original PAGE list: Confirmed for BRANCHIOOTORENAL SYNDROME TYPE 2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.9 | REN | Rebecca Foulger reviewed gene: REN: Rating: AMBER; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.9 | OCRL | Rebecca Foulger commented on gene: OCRL: DDG2P rating in original PAGE list: Confirmed for LOWE OCULOCEREBRORENAL SYNDROME and Confirmed for DENT DISEASE TYPE 2. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.9 | NEK8 | Rebecca Foulger commented on gene: NEK8: DDG2P rating in original PAGE list: Probable for NEPHRONOPHTHISIS 9 and Probable for RENAL-HEPATIC-PANCREATIC DYSPLASIA 2. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.9 | MAPRE2 | Rebecca Foulger commented on gene: MAPRE2: DDG2P rating in original PAGE list: Confirmed for Circumferential Skin Creases Kunze Type | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.9 | GNAS | Rebecca Foulger commented on gene: GNAS: DDG2P rating in original PAGE list: Confirmed for PSEUDOHYPOPARATHYROIDISM TYPE 1B, Confirmed for ACTH-INDEPENDENT MACRONODULAR ADRENAL HYPERPLASIA, Confirmed for ALBRIGHT HEREDITARY OSTEODYSTROPHY and Confirmed for GNAS HYPERFUNCTION. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.9 | CLDN19 | Rebecca Foulger commented on gene: CLDN19: DDG2P rating in original PAGE list: Confirmed for HYPOMAGNESEMIA 5, RENAL, WITH OCULAR INVOLVEMENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.7 | SLC4A1 | Rebecca Foulger commented on gene: SLC4A1: Rating in original PAGE file: 'both DD and IF' for RENAL TUBULAR ACIDOSIS, DISTAL, AD and RENAL TUBULAR ACIDOSIS, DISTAL, AR. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.7 | RET | Rebecca Foulger commented on gene: RET: Rating in original PAGE file: 'both DD and IF' for RENAL AGENESIS and MULTIPLE ENDOCRINE NEOPLASIA IIB. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.7 | COL4A2 | Rebecca Foulger commented on gene: COL4A2: Rating in original PAGE file: 'both DD and IF' for PORENCEPHALY 2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.7 | COL4A1 | Rebecca Foulger commented on gene: COL4A1: Rating in original PAGE file: 'both DD and IF' for PORENCEPHALY 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.6 | RET | Rebecca Foulger commented on gene: RET: Rating in original PAGE file: 'Both DD and IF' for RENAL AGENESIS and MULTIPLE ENDOCRINE NEOPLASIA IIB. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | TCTN1 | Rebecca Foulger commented on gene: TCTN1: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | BGN | Rebecca Foulger commented on gene: BGN: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | TBC1D20 | Rebecca Foulger commented on gene: TBC1D20: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | ITPR1 | Rebecca Foulger commented on gene: ITPR1: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | BMP2 | Rebecca Foulger commented on gene: BMP2: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | SUFU | Rebecca Foulger commented on gene: SUFU: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | KMT2C | Rebecca Foulger commented on gene: KMT2C: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | ERCC4 | Rebecca Foulger commented on gene: ERCC4: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | IL11RA | Rebecca Foulger commented on gene: IL11RA: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | PIEZO1 | Rebecca Foulger commented on gene: PIEZO1: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | DNAH5 | Rebecca Foulger commented on gene: DNAH5: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | EMG1 | Rebecca Foulger commented on gene: EMG1: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | MITF | Rebecca Foulger commented on gene: MITF: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | MAFB | Rebecca Foulger commented on gene: MAFB: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | ATAD3A | Rebecca Foulger commented on gene: ATAD3A: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | DEAF1 | Rebecca Foulger commented on gene: DEAF1: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | TBCE | Rebecca Foulger commented on gene: TBCE: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | ACTB | Rebecca Foulger commented on gene: ACTB: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | IFIH1 | Rebecca Foulger commented on gene: IFIH1: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | TWIST2 | Rebecca Foulger commented on gene: TWIST2: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | MAGEL2 | Rebecca Foulger commented on gene: MAGEL2: 'watchlist' tag added to highlight different DD-G2P ratings for this gene. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.3 | GNAS | Rebecca Foulger commented on gene: GNAS: Mosaicism tag added based on original PAGE file which records Mosaic MOI for ACTH-INDEPENDENT MACRONODULAR ADRENAL HYPERPLASIA. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.1 | VPS33B |
Rebecca Foulger gene: VPS33B was added gene: VPS33B was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype 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 |
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| Fetal anomalies v0.1 | VIPAS39 |
Rebecca Foulger gene: VIPAS39 was added gene: VIPAS39 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype 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 |
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| Fetal anomalies v0.1 | TUBB | Rebecca Foulger Added phenotypes Circumferential Skin Creases Kunze Type for gene: TUBB | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.1 | TRIP4 |
Rebecca Foulger gene: TRIP4 was added gene: TRIP4 was added to Fetal anomalies. Sources: PAGE DD-Gene2Phenotype,Expert Review Amber Mode of inheritance for gene: TRIP4 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: TRIP4 were set to Prenatal Spinal Muscular Atrophy and Congenital Bone Fractures |
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| Fetal anomalies v0.1 | TMEM260 |
Rebecca Foulger gene: TMEM260 was added gene: TMEM260 was added to Fetal anomalies. Sources: PAGE DD-Gene2Phenotype,Expert Review Amber Mode of inheritance for gene: TMEM260 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: TMEM260 were set to Neurodevelopmental, Cardiac, and Renal Syndrome |
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| Fetal anomalies v0.1 | TANGO2 |
Rebecca Foulger gene: TANGO2 was added gene: TANGO2 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: TANGO2 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: TANGO2 were set to Infancy-Onset Recurrent Metabolic Crises with Encephalocardiomyopathy |
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| Fetal anomalies v0.1 | STAR |
Rebecca Foulger gene: STAR was added gene: STAR was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: STAR was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: STAR were set to CHOLESTEROL DESMOLASE-DEFICIENT CONGENITAL ADRENAL HYPERPLASIA |
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| Fetal anomalies v0.1 | SLC4A4 |
Rebecca Foulger gene: SLC4A4 was added gene: SLC4A4 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: SLC4A4 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: SLC4A4 were set to PROXIMAL RENAL TUBULAR ACIDOSIS WITH OCULAR ABNORMALITIES |
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| Fetal anomalies v0.1 | SLC4A1 | Rebecca Foulger Added phenotypes RENAL TUBULAR ACIDOSIS, DISTAL, AR for gene: SLC4A1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.1 | SLC4A1 |
Rebecca Foulger gene: SLC4A1 was added gene: SLC4A1 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: SLC4A1 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal Phenotypes for gene: SLC4A1 were set to RENAL TUBULAR ACIDOSIS, DISTAL, AD |
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| Fetal anomalies v0.1 | SIX5 |
Rebecca Foulger gene: SIX5 was added gene: SIX5 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: SIX5 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene: SIX5 were set to BRANCHIOOTORENAL SYNDROME TYPE 2 |
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| Fetal anomalies v0.1 | SIL1 |
Rebecca Foulger gene: SIL1 was added gene: SIL1 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: SIL1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: SIL1 were set to MARINESCO-SJOEGREN SYNDROME |
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| Fetal anomalies v0.1 | SALL4 |
Rebecca Foulger gene: SALL4 was added gene: SALL4 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: SALL4 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene: SALL4 were set to ACRO-RENAL-OCULAR SYNDROME |
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| Fetal anomalies v0.1 | RET |
Rebecca Foulger gene: RET was added gene: RET was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: RET was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal Phenotypes for gene: RET were set to RENAL AGENESIS |
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| Fetal anomalies v0.1 | REN |
Rebecca Foulger gene: REN was added gene: REN was added to Fetal anomalies. Sources: Expert Review Green,PAGE Additional Gene List Mode of inheritance for gene: REN was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: REN were set to Renal tubular dysgenesis 267430 |
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| Fetal anomalies v0.1 | PQBP1 |
Rebecca Foulger gene: PQBP1 was added gene: PQBP1 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: PQBP1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Phenotypes for gene: PQBP1 were set to RENPENNING S(YNDROME 1 |
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| Fetal anomalies v0.1 | PMP22 | Rebecca Foulger Added phenotypes Neuropathy, recurrent, with pressure palsies 162500 for gene: PMP22 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.1 | PEX5 |
Rebecca Foulger gene: PEX5 was added gene: PEX5 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: PEX5 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: PEX5 were set to ADRENOLEUKODYSTROPHY NEONATAL |
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| Fetal anomalies v0.1 | PEX26 | Rebecca Foulger Added phenotypes ADRENOLEUKODYSTROPHY NEONATAL for gene: PEX26 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.1 | PEX13 |
Rebecca Foulger gene: PEX13 was added gene: PEX13 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: PEX13 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: PEX13 were set to ADRENOLEUKODYSTROPHY NEONATAL |
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| Fetal anomalies v0.1 | PEX10 |
Rebecca Foulger gene: PEX10 was added gene: PEX10 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: PEX10 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: PEX10 were set to ADRENOLEUKODYSTROPHY NEONATAL |
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| Fetal anomalies v0.1 | PEX1 | Rebecca Foulger Added phenotypes ADRENOLEUKODYSTROPHY NEONATAL for gene: PEX1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.1 | PAX2 |
Rebecca Foulger gene: PAX2 was added gene: PAX2 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: PAX2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene: PAX2 were set to RENAL-COLOBOMA SYNDROME |
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| Fetal anomalies v0.1 | OCRL |
Rebecca Foulger gene: OCRL was added gene: OCRL was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: OCRL was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Phenotypes for gene: OCRL were set to LOWE OCULOCEREBRORENAL SYNDROME |
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| Fetal anomalies v0.1 | NR0B1 | Rebecca Foulger Added phenotypes Adrenal hypoplasia, congenital 300200 for gene: NR0B1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.1 | NPHP3 | Rebecca Foulger Added phenotypes RENAL-HEPATIC-PANCREATIC DYSPLASIA for gene: NPHP3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.1 | NEK8 | Rebecca Foulger Added phenotypes RENAL-HEPATIC-PANCREATIC DYSPLASIA 2 for gene: NEK8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.1 | MAPRE2 |
Rebecca Foulger gene: MAPRE2 was added gene: MAPRE2 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: MAPRE2 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: MAPRE2 were set to Circumferential Skin Creases Kunze Type |
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| Fetal anomalies v0.1 | LRPPRC |
Rebecca Foulger gene: LRPPRC was added gene: LRPPRC was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: LRPPRC was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: LRPPRC were set to LEIGH SYNDROME, FRENCH-CANADIAN TYPE |
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| Fetal anomalies v0.1 | KYNU |
Rebecca Foulger gene: KYNU was added gene: KYNU was added to Fetal anomalies. Sources: PAGE Additional Gene List,Expert Review Amber Mode of inheritance for gene: KYNU was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: KYNU were set to 28792876 Phenotypes for gene: KYNU were set to Vertebral, cardiac, renal, and limb defects syndrome 2 617661 |
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| Fetal anomalies v0.1 | ITGA8 |
Rebecca Foulger gene: ITGA8 was added gene: ITGA8 was added to Fetal anomalies. Sources: PAGE DD-Gene2Phenotype,Expert Review Amber Mode of inheritance for gene: ITGA8 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: ITGA8 were set to RENAL HYPODYSPLASIA/APLASIA 1 |
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| Fetal anomalies v0.1 | IARS |
Rebecca Foulger gene: IARS was added gene: IARS was added to Fetal anomalies. Sources: PAGE DD-Gene2Phenotype,Expert Review Amber Mode of inheritance for gene: IARS was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: IARS were set to Growth Retardation with Prenatal Onset, Intellectual Disability, Muscular Hypotonia, and Infantile Hepatopathy |
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| Fetal anomalies v0.1 | HNF1B |
Rebecca Foulger gene: HNF1B was added gene: HNF1B was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: HNF1B was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene: HNF1B were set to RENAL CYSTS AND DIABETES SYNDROME |
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| Fetal anomalies v0.1 | HAAO |
Rebecca Foulger gene: HAAO was added gene: HAAO was added to Fetal anomalies. Sources: PAGE Additional Gene List,Expert Review Amber Mode of inheritance for gene: HAAO was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: HAAO were set to 28792876 Phenotypes for gene: HAAO were set to Vertebral, cardiac, renal, and limb defects syndrome 1 617660 |
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| Fetal anomalies v0.1 | GNAS | Rebecca Foulger Added phenotypes ACTH-INDEPENDENT MACRONODULAR ADRENAL HYPERPLASIA for gene: GNAS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.1 | EYA1 |
Rebecca Foulger gene: EYA1 was added gene: EYA1 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: EYA1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene: EYA1 were set to BRANCHIOOTORENAL SYNDROME TYPE 1 |
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| Fetal anomalies v0.1 | DOCK8 |
Rebecca Foulger gene: DOCK8 was added gene: DOCK8 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: DOCK8 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: DOCK8 were set to HYPERIMMUNOGLOBULIN E RECURRENT INFECTION SYNDROME AUTOSOMAL RECESSIVE |
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| Fetal anomalies v0.1 | DCDC2 |
Rebecca Foulger gene: DCDC2 was added gene: DCDC2 was added to Fetal anomalies. Sources: PAGE DD-Gene2Phenotype,Expert Review Amber Mode of inheritance for gene: DCDC2 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: DCDC2 were set to RENAL-HEPATIC CILIOPATHY |
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| Fetal anomalies v0.1 | CYP21A2 |
Rebecca Foulger gene: CYP21A2 was added gene: CYP21A2 was added to Fetal anomalies. Sources: Expert Review Green,PAGE Additional Gene List Mode of inheritance for gene: CYP21A2 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: CYP21A2 were set to Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency |
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| Fetal anomalies v0.1 | CYP11B1 |
Rebecca Foulger gene: CYP11B1 was added gene: CYP11B1 was added to Fetal anomalies. Sources: Expert Review Green,PAGE Additional Gene List Mode of inheritance for gene: CYP11B1 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal Phenotypes for gene: CYP11B1 were set to Adrenal hyperplasia, congenital, due to 11-beta-hydroxylase deficiency 202010 |
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| Fetal anomalies v0.1 | CYP11A1 |
Rebecca Foulger gene: CYP11A1 was added gene: CYP11A1 was added to Fetal anomalies. Sources: Expert Review Green,PAGE Additional Gene List Mode of inheritance for gene: CYP11A1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: CYP11A1 were set to Adrenal insufficiency, congenital, with 46XY sex reversal, partial or complete 613743 |
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| Fetal anomalies v0.1 | COL4A2 |
Rebecca Foulger gene: COL4A2 was added gene: COL4A2 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: COL4A2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene: COL4A2 were set to PORENCEPHALY 2 |
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| Fetal anomalies v0.1 | COL4A1 |
Rebecca Foulger gene: COL4A1 was added gene: COL4A1 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: COL4A1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene: COL4A1 were set to PORENCEPHALY 1 |
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| Fetal anomalies v0.1 | CLDN19 |
Rebecca Foulger gene: CLDN19 was added gene: CLDN19 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: CLDN19 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: CLDN19 were set to HYPOMAGNESEMIA 5, RENAL, WITH OCULAR INVOLVEMENT |
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| Fetal anomalies v0.1 | ATP6V1B1 |
Rebecca Foulger gene: ATP6V1B1 was added gene: ATP6V1B1 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: ATP6V1B1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: ATP6V1B1 were set to DISTAL RENAL TUBULAR ACIDOSIS WITH DEAFNESS |
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| Fetal anomalies v0.1 | ALDH3A2 |
Rebecca Foulger gene: ALDH3A2 was added gene: ALDH3A2 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: ALDH3A2 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: ALDH3A2 were set to SJOEGREN-LARSSON SYNDROME |
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| Fetal anomalies v0.1 | ACOX1 |
Rebecca Foulger gene: ACOX1 was added gene: ACOX1 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: ACOX1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: ACOX1 were set to ADRENOLEUKODYSTROPHY PSEUDONEONATAL |
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| Fetal anomalies v0.1 | ACE |
Rebecca Foulger gene: ACE was added gene: ACE was added to Fetal anomalies. Sources: Expert Review Green,PAGE Additional Gene List Mode of inheritance for gene: ACE was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: ACE were set to Renal tubular dysgenesis 267430 |
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| Fetal anomalies v0.1 | ABCD1 |
Rebecca Foulger gene: ABCD1 was added gene: ABCD1 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: ABCD1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Phenotypes for gene: ABCD1 were set to ADRENOLEUKODYSTROPHY, X-LINKED |
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