Severe Paediatric Disorders
Gene: CPA6 Red List (low evidence)Red List (low evidence)
ClinGen has refuted the association between biallelic CPA6 variants and epilepsy and had disputed the association between monoallelic CPA6 variants and epilepsy (https://search.clinicalgenome.org/kb/gene-validity?page=1&size=25&search=CPA6)Created: 28 Nov 2023, 1:53 p.m. | Last Modified: 28 Nov 2023, 1:53 p.m.
Panel Version: 1.176
Red List (low evidence)
This gene should be retracted from the green list for all panels.
It is regarded as "disputed" and "refuted" evidence respectively by ClinGen curation.
The evidence supporting the association is largely based on observation of three variants which are common in the general population in studies by Salzmann et al 2012 & Sapio et al 2012.
https://www.deciphergenomics.org/sequence-variant/8-67483797-G-A/annotation/maf/both - this variant p.Ala270Val was seen in homozygosity in a small family but is also common in gnomAD with 2x homozygotes. It has not been replicated and is now considered benign/LB.
p.Gly267Arg and p.Gln207Glu were both observed in a single case by Sapio et al 2012, but these co-segregate extensively in gnomAD (approx. 1 in 160 European individuals has these variants, likely on the same haplotype) and no parental testing was done to determine phase. Both variants are likely to be benign.
There are no large cohort studies, functional evidence or other collaborating studies other than single observations since these two papers. The gene is not a particularly compelling candidate for epilepsy mechanistically and the animal model isn't convincing. This should not be green in my opinion and should be removed from this panel.Created: 16 May 2023, 2:53 p.m. | Last Modified: 16 May 2023, 2:53 p.m.
Panel Version: 1.153
Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
I don't know
Initial gene list (NGC_genelist-20190823_GREEN_dis_moi_forCuration_20200211.xlsx) collated by Dr Courtney French (University of Cambridge University Hospital NHS Foundation), Dr Karyn Megy (Clinical Feedback Lead, NIHR BioResource - Rare Diseases Study, University of Cambridge University Hospital NHS Foundation), Dr Alba Sanchis-Juan (NIHR BioResource - Rare Diseases Study, University of Cambridge University Hospital NHS Foundation) and Lucy Raymond (Professor of Medical Genetics and Neurodevelopment, University of Cambridge University Hospital NHS Foundation). Submitted to the PanelApp resource January 2020 on behalf of the Next Generation Children Project, Addenbrookes' Hospital, Cambridge. Gene Symbol submitted: CPA6; Recommended initial gene rating: Green List (high evidence); Phenotypes: Epilepsy, familial temporal lobe, 5, 614417 (3) | Febrile seizures, familial, 11, 614418 (3); Mode of inheritance: Autosomal recessive, Autosomal dominant | Autosomal recessiveCreated: 20 Feb 2020, 5:17 p.m. | Last Modified: 20 Feb 2020, 5:17 p.m.
Panel Version: 0.12
Gene: cpa6 has been classified as Red List (Low Evidence).
Mode of inheritance for gene CPA6 was changed from to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene CPA6 were updated from to 30847515
Added phenotypes Epilepsy, familial temporal lobe, 5, 614417; Febrile seizures, familial, 11, 614418 for gene: CPA6
Added phenotypes Epilepsy, familial temporal lobe, 5, 614417; Febrile seizures, familial, 11, 614418 for gene: CPA6
Added phenotypes Epilepsy, familial temporal lobe, 5, 614417; Febrile seizures, familial, 11, 614418 for gene: CPA6
Added phenotypes Febrile seizures, familial, 11, 614418; Epilepsy, familial temporal lobe, 5, 614417 for gene: CPA6
Source Next Generation Children Project was added to CPA6.
Source Expert Review Green was added to CPA6. Rating Changed from Red List (low evidence) to Green List (high evidence)
gene: CPA6 was added gene: CPA6 was added to Severe Paediatric Disorders. Sources: Expert list Mode of inheritance for gene: CPA6 was set to
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.