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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 v3.151 | RRAS | Sarah Leigh edited their review of gene: RRAS: Added comment: RRAS variants have not associated with a phenotype in OMIM or MONDO, but Gen2Phen lists a strong association between RRAS variants and RRAS-related atypical Noonan syndrome. Three germline RRAS variants have been reported (PMID: 24705357; 32815881; 34935735), associated with a RASopathy, which includes myelodysplastic syndrome and contributes to leukaemogenesis.; Changed rating: GREEN; Changed publications to: 24705357, 32815881, 34935735 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v1.945 | MYBPC3 |
Arina Puzriakova Added comment: Comment on list classification: New gene added to this panel by Rhiannon Mellis (GOSH). Rating Amber inline with this review, awaiting further evidence supporting that this gene can cause a fetal phenotype. Note that the two fetal cases reported in literature harboured homozygous variants (PMID:19858127; 28749478) although expert reviewer suggests an MOI of 'both mono- and biallelic' |
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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 v1.864 | 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 v1.717 | GNB1 | Sarah Leigh Added comment: Comment on mode of pathogenicity: Gen2Phen entry for GNB1 (https://www.ebi.ac.uk/gene2phenotype/gfd?dbID=2121) lists the mutation consequence summary as Activating | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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 v1.185 | 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 v1.49 | 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 v1.41 | TUBA8 | Rebecca Foulger Added comment: Comment on list classification: The reanalysis in PMID:28388629 casts doubt that TUBA8 is responsible for the morphological phenotypes initially reported in PMID:19896110. Only 2 families (of possible shared descent) were reported. Therefore insufficient evidence for Green rating. Downgraded from Green to Amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.309 | ALPL | Rebecca Foulger Added comment: Comment on mode of inheritance: Changed MOI from BIALLELIC to 'BOTH monoallelic and biallelic' following advice by Anna de Burca (Genomics England clinical team). AD variant reported in Chandler et al (PMID:29595812) for Hypophosphatasia phenotype. OMIM lists AR inheritance for Hypophosphatasia, infantile/Hypophosphatasia, childhood. And AD/AR for Hypophosphatasia, adult and Odontohypophosphatasia. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.308 | ALPL | Rebecca Foulger Added comment: Comment on mode of inheritance: Changed MOI from BIALLELIC to 'BOTH monoallelic and biallelic' following advice by Anna de Burca (Genomics England clinical team). AD variant reported in Chandler et al (PMID:29595812) for Hypophosphatasia phenotype. OMIM lists AR inheritance for Hypophosphatasia, infantile/Hypophosphatasia, childhood. And AD/AR for Hypophosphatasia, adult and Odontohypophosphatasia. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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 v0.222 | DARS2 | Rebecca Foulger edited their review of gene: DARS2: 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: Slowly progressive and manifests later. Action taken: Demoted DARS2 gene rating from Amber to Red.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.199 | COG4 |
Rebecca Foulger commented on gene: COG4: COG4 is Green on the fetal panel based on 'confirmed' rating for a biallelic glycosylation disorder (COG4-CDG) and expert clinical review. A probable gene:disease disorder also exists in DD-Gene2Phenotype: Saul-Wilson syndrome. DDG2P Disease confidence: probable. DDG2P mode of pathogenicity/mutation consequence: all missense/in frame, gain of function. DDG2P mode of inheritance: monoallelic. Saul-Wilson syndrome is a rare form of primordial dwarfism with severe pre-and postnatal growth retardation, and characteristic facial and radiographic features (PMID:30290151). Fetal relevance was confirmed by Anna de Burca but the evidence requires further investigation before the MOI is expanded to include monoallelic variants. |
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| Fetal anomalies v0.197 | DSTYK | Rebecca Foulger commented on gene: DSTYK: Note that a new gene:disorder association was added to DDG2P in March 2019: Autosomal Recessive Complicated Spastic Paraparesis SPG23. DDG2P Disease confidence: probable. DDG2P mode of pathogenicity/mutation consequence: loss of function. DDG2P mode of inheritance: biallelic. Not yet included the spastic paraplegia phenotype (or biallelic inheritance) on this Fetal anomalies panel for DSTYK because the 3 families identified in PMID:28157540 have the same variant, and haplotype analysis suggests a Founder effect. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.165 | STS |
Rebecca Foulger Source Expert Review Red was added to STS. Rating Changed from Green List (high evidence) to Red List (low evidence) |
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| Fetal anomalies v0.161 | STS | Rebecca Foulger edited their review of gene: STS: 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: Cutaneous patches only. Action taken: Demoted STS gene rating from Green to Red.; Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.110 | SNORD118 | Rebecca Foulger commented on gene: SNORD118: Changed rating to Amber to reflect DDG2P Disease confidence of 'DD and IF' for Leukoencephalopathy with cerebral calcification & cysts. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.62 | CDKN1C | Rebecca Foulger Added comment: Comment on mode of inheritance: Updated MOI from 'Monoallelic, imprinted status unknown' to 'Monoallelic, paternally imprinted (maternal allele expressed). This reflects DDG2P update which now lists 'imprinted' MOI for both BECKWITH-WIEDEMANN SYNDROME and IMAGe Syndrome. This MOI is taken from the PanelApp 'Imprinted Genes' panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.50 | PIEZO1 | Rebecca Foulger Added comment: Comment on mode of inheritance: Anna's suggestion of biallelic MOI is based on Lymphatic malformation 6 phenotype (MIM:616843) which has AR inheritance and fetally-relevant phenotype. After further discussion we agreed to include AD inheritance for PIEZO1 based on reviews on the Fetal hydrops panel: in summary, PMID:26333996 (Fotiou et al., 2015) reports that NIHF variably occurs in DHS (with AD inheritance), and a review by Tessa Homfray lists both AD and AR inheritance. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.28 | RBPJ | Rebecca Foulger Added comment: Comment on list classification: Updated rating from Amber to Green: Rated Green on relevant V1 panel(s) PLUS phenotype (ADAMS OLIVER SYNDROME) appropriate for fetal panel, as noted by Helen Brittain and Anna de Burca (Genomics England Clinical team). Although OMIM lists 2 unrelated cases, further cases supporting causation are provided in PMID:28160419, as detailed on the 'Limb disorders' panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.9 | STS | Rebecca Foulger reviewed gene: STS: Rating: AMBER; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v0.1 | STS |
Rebecca Foulger gene: STS was added gene: STS was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: STS was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Phenotypes for gene: STS were set to ICHTHYOSIS, X-LINKED |
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| Fetal anomalies v0.1 | SNORD118 |
Rebecca Foulger gene: SNORD118 was added gene: SNORD118 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: SNORD118 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: SNORD118 were set to Leukoencephalopathy with cerebral calcification & cysts |
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| Fetal anomalies v0.1 | MLC1 |
Rebecca Foulger gene: MLC1 was added gene: MLC1 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: MLC1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: MLC1 were set to LEUKOENCEPHALOPATHY MEGALENCEPHALIC WITH SUBCORTICAL CYSTS |
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| Fetal anomalies v0.1 | LAMA1 |
Rebecca Foulger gene: LAMA1 was added gene: LAMA1 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: LAMA1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: LAMA1 were set to CEREBELLAR DYSPLASIA WITH CYSTS WITH OR WITHOUT RETINAL DYSTROPHY |
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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 | CTC1 |
Rebecca Foulger gene: CTC1 was added gene: CTC1 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: CTC1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: CTC1 were set to CEREBRORETINAL MICROANGIOPATHY WITH CALCIFICATIONS AND CYSTS |
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