Fetal anomalies
Gene: SLC25A46 Green List (high evidence)Green List (high evidence)
The rating of this gene has been updated to Green and the mode of inheritance set to BIALLELIC, autosomal or pseudoautosomal following NHS Genomic Medicine Service approval.Created: 10 Oct 2023, 3:39 p.m. | Last Modified: 10 Oct 2023, 3:39 p.m.
Panel Version: 3.111
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Green List (high evidence)
This gene and phenotype were reviewed during a meeting on 23rd Feb 2023 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Natalie Chandler (North Thames GLH), and Stephanie Allen, Esther Kinning and Megan Horton-Bell (Central & South GLH). Outcome of review: Confirmed that the phenotype is fetally relevant, support adding to the Fetal anomalies panel as a Green gene.Created: 5 May 2023, 3 p.m. | Last Modified: 5 May 2023, 3 p.m.
Panel Version: 3.8
On 16 panels, inc. IEM, severe paediatric disorders. Associated with Neuropathy, hereditary motor and sensory, type VIB (AR), Pontocerebellar hypoplasia, type 1E (AR). Wan et al., 2016 PMID 27543974: Index px of family 1: born at 38wks gestation, polyhydramnios. Affected sister born at 37.5wks, polyhydramnios, Similar postnatal clinical features: hypotonia, severe DD, small cerebellum and brainstem. Died at 4 / 2 weeks respectively. Index px of family 2: polyhydramnios, preterm labour, placental haemorrhage - delivery at 36wks. Weight and head circumference <5th centile. Brain MRI anomalies. Affected sister with same phenotype. Died 6 / 3 weeks respectively. Nguyen et al., 2016 PMID 26951855: Index px: polyhydramnios. Postnatal: respiratory insufficiency, clubfoot, hypotonia, double-sided optic atrophy. Myoclonic. Died of respiratory deficiency at 7do. Braunisch et al., 2017 PMID 28653766: German family 1: index px born at 40+3wks; pregnancy complicated by polyhydramnios and congenital talipes equinovarus. Died at 23do. Brother born at 39+0wks; pregnancy complicated by polyhydramnios. Died 1do. Yamada et al., 2022 PMID 35012485: Proband: 36wks gestation = polyhydramnios, fetal effusion and fetal ascites. Died 19do. Cerebellar hypoplasia. Elder brother - polyhydramnios, born at 36+6wks; died at 12ho due to severe neonatal asphyxia and cardiopulmonary failure with hypoplastic lungs. Conclusion: link to prenatal phenotypes (polyhydramnios, talipes, foetal effusion and ascites. RelevantCreated: 5 May 2023, 3 p.m. | Last Modified: 5 May 2023, 3 p.m.
Panel Version: 3.8
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Phenotypes
Pontocerebellar hypoplasia, type 1E, OMIM:619303
Publications
Tag Q2_23_promote_green was removed from gene: SLC25A46. Tag Q2_23_NHS_review was removed from gene: SLC25A46.
Source Expert Review Green was added to SLC25A46. Source NHS GMS was added to SLC25A46. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
Publications for gene: SLC25A46 were set to
Tag Q2_23_promote_green tag was added to gene: SLC25A46. Tag Q2_23_NHS_review tag was added to gene: SLC25A46.
gene: SLC25A46 was added gene: SLC25A46 was added to Fetal anomalies. Sources: Expert Review Amber Mode of inheritance for gene: SLC25A46 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: SLC25A46 were set to Pontocerebellar hypoplasia, type 1E, OMIM:619303
If promoting or demoting a gene, please provide comments to justify a decision to move it.
Genes included in a Genomics England gene panel for a rare disease category (green list) should fit the criteria A-E outlined below.
These guidelines were developed as a combination of the ClinGen DEFINITIVE evidence for a causal role of the gene in the disease(a), and the Developmental Disorder Genotype-Phenotype (DDG2P) CONFIRMED DD Gene evidence level(b) (please see the original references provided below for full details). These help provide a guideline for expert reviewers when assessing whether a gene should be on the green or the red list of a panel.
A. There are plausible disease-causing mutations(i) within, affecting or encompassing an interpretable functional region(ii) of this gene identified in multiple (>3) unrelated cases/families with the phenotype(iii).
OR
B. There are plausible disease-causing mutations(i) within, affecting or encompassing cis-regulatory elements convincingly affecting the expression of a single gene identified in multiple (>3) unrelated cases/families with the phenotype(iii).
OR
C. As definitions A or B but in 2 or 3 unrelated cases/families with the phenotype, with the addition of convincing bioinformatic or functional evidence of causation e.g. known inborn error of metabolism with mutation in orthologous gene which is known to have the relevant deficient enzymatic activity in other species; existence of an animal model which recapitulates the human phenotype.
AND
D. Evidence indicates that disease-causing mutations follow a Mendelian pattern of causation appropriate for reporting in a diagnostic setting(iv).
AND
E. No convincing evidence exists or has emerged that contradicts the role of the gene in the specified phenotype.
(i)Plausible disease-causing mutations: Recurrent de novo mutations convincingly affecting gene function. Rare, fully-penetrant mutations - relevant genotype never, or very rarely, seen in controls. (ii) Interpretable functional region: ORF in protein coding genes miRNA stem or loop. (iii) Phenotype: the rare disease category, as described in the eligibility statement. (iv) Intermediate penetrance genes should not be included.
It’s assumed that loss-of-function variants in this gene can cause the disease/phenotype unless an exception to this rule is known. We would like to collect information regarding exceptions. An example exception is the PCSK9 gene, where loss-of-function variants are not relevant for a hypercholesterolemia phenotype as they are associated with increased LDL-cholesterol uptake via LDLR (PMID: 25911073).
If a curated set of known-pathogenic variants is available for this gene-phenotype, please contact us at [email protected]
We classify loss-of-function variants as those with the following Sequence Ontology (SO) terms:
Term descriptions can be found on the PanelApp homepage and Ensembl.
If you are submitting this evaluation on behalf of a clinical laboratory please indicate whether you report variants in this gene as part of your current diagnostic practice by checking the box
Standardised terms were used to represent the gene-disease mode of inheritance, and were mapped to commonly used terms from the different sources. Below each of the terms is described, along with the equivalent commonly-used terms.
A variant on one allele of this gene can cause the disease, and imprinting has not been implicated.
A variant on the paternally-inherited allele of this gene can cause the disease, if the alternate allele is imprinted (function muted).
A variant on the maternally-inherited allele of this gene can cause the disease, if the alternate allele is imprinted (function muted).
A variant on one allele of this gene can cause the disease. This is the default used for autosomal dominant mode of inheritance where no knowledge of the imprinting status of the gene required to cause the disease is known. Mapped to the following commonly used terms from different sources: autosomal dominant, dominant, AD, DOMINANT.
A variant on both alleles of this gene is required to cause the disease. Mapped to the following commonly used terms from different sources: autosomal recessive, recessive, AR, RECESSIVE.
The disease can be caused by a variant on one or both alleles of this gene. Mapped to the following commonly used terms from different sources: autosomal recessive or autosomal dominant, recessive or dominant, AR/AD, AD/AR, DOMINANT/RECESSIVE, RECESSIVE/DOMINANT.
A variant on one allele of this gene can cause the disease, however a variant on both alleles of this gene can result in a more severe form of the disease/phenotype.
A variant in this gene can cause the disease in males as they have one X-chromosome allele, whereas a variant on both X-chromosome alleles is required to cause the disease in females. Mapped to the following commonly used term from different sources: X-linked recessive.
A variant in this gene can cause the disease in males as they have one X-chromosome allele. A variant on one allele of this gene may also cause the disease in females, though the disease/phenotype may be less severe and may have a later-onset than is seen in males. X-linked inactivation and mosaicism in different tissues complicate whether a female presents with the disease, and can change over their lifetime. This term is the default setting used for X-linked genes, where it is not known definitately whether females require a variant on each allele of this gene in order to be affected. Mapped to the following commonly used terms from different sources: X-linked dominant, x-linked, X-LINKED, X-linked.
The gene is in the mitochondrial genome and variants within this can cause this disease, maternally inherited. Mapped to the following commonly used term from different sources: Mitochondrial.
Mapped to the following commonly used terms from different sources: Unknown, NA, information not provided.
For example, if the mode of inheritance is digenic, please indicate this in the comments and which other gene is involved.