Mendeliome
Gene: CCDC88C Green List (high evidence)I don't know
PMID: 38173219 – Cohort of individuals with epilepsy. Identified novel CCDC88C variants, including two de novo missense and two biallelic variants, in four unrelated individuals with focal (partial) epilepsy. The two heterozygous variants were of de novo origin. The two pairs of compound heterozygous mutations were inherited from their asymptomatic parents. Patients with de novo variants presented with adult-onset epilepsy, whereas patients with biallelic variants displayed infant-onset epilepsy.Created: 1 Feb 2024, 12:44 a.m. | Last Modified: 1 Feb 2024, 12:44 a.m.
Panel Version: 1.1511
Mode of inheritance
BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Phenotypes
monogenic epilepsy MONDO:0015653, CCDC88C-related
Publications
I don't know
Heterozygous missense variant (gnomad: 1 het) reported in a 48-year-old Sudanese female presented with pure early onset hereditary spastic paraplegia. In contrast to previous reports, she developed neurological symptoms in early childhood and showed neither features of cerebellar ataxia, extrapyramidal signs, nor evidence of intellectual involvement. Functional studies showed the varaint induced JNK hyper-phosphorylation and enhanced apoptosis. 4 unaffected family members did not have the variant.
NB: Rated Amber as this phenotype appears to be sufficiently dissimilar to the 2 previously reported SCA families to not constitute a 3rd supporting report in that context. Gene remains Green for the AR ID phenotype.Created: 8 Apr 2021, 2:46 a.m. | Last Modified: 8 Apr 2021, 2:51 a.m.
Panel Version: 0.7056
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes
Eearly-onset pure hereditary spastic paraplegia
Publications
Variants in this GENE are reported as part of current diagnostic practice
Green List (high evidence)
Three families for AR ID (green), amber for AD SCA (2 families only).Created: 27 Jan 2020, 5:27 a.m. | Last Modified: 27 Jan 2020, 5:27 a.m.
Panel Version: 0.982
Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Phenotypes
Spinocerebellar ataxia 40, MIM#616053; Hydrocephalus, nonsyndromic, autosomal recessive 236600 AR
Publications
Variants in this GENE are reported as part of current diagnostic practice
I don't know
Two families, no functional data.Created: 28 Dec 2019, 12:17 a.m. | Last Modified: 28 Dec 2019, 12:17 a.m.
Panel Version: 0.434
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Phenotypes
Spinocerebellar ataxia 40, MIM#616053
Publications
Phenotypes for gene: CCDC88C were changed from Spinocerebellar ataxia 40, MIM#616053; Hydrocephalus, nonsyndromic, autosomal recessive 236600; Eearly-onset pure hereditary spastic paraplegia to Spinocerebellar ataxia 40, MIM#616053; Hydrocephalus, nonsyndromic, autosomal recessive 236600; Early-onset pure hereditary spastic paraplegia
Phenotypes for gene: CCDC88C were changed from Spinocerebellar ataxia 40, MIM#616053; Hydrocephalus, nonsyndromic, autosomal recessive 236600 AR to Spinocerebellar ataxia 40, MIM#616053; Hydrocephalus, nonsyndromic, autosomal recessive 236600; Eearly-onset pure hereditary spastic paraplegia
Publications for gene: CCDC88C were set to 23042809; 21031079; 25062847; 30398676
Phenotypes for gene: CCDC88C were changed from Spinocerebellar ataxia 40, MIM#616053 to Spinocerebellar ataxia 40, MIM#616053; Hydrocephalus, nonsyndromic, autosomal recessive 236600 AR
Publications for gene: CCDC88C were set to 25062847; 30398676
Mode of inheritance for gene: CCDC88C was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Gene: ccdc88c has been classified as Green List (High Evidence).
Mode of inheritance for gene: CCDC88C was changed from BIALLELIC, autosomal or pseudoautosomal to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Gene: ccdc88c has been classified as Amber List (Moderate Evidence).
Phenotypes for gene: CCDC88C were changed from to Spinocerebellar ataxia 40, MIM#616053
Publications for gene: CCDC88C were set to
Mode of inheritance for gene: CCDC88C was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal
Gene: ccdc88c has been classified as Amber List (Moderate Evidence).
gene: CCDC88C was added gene: CCDC88C was added to Mendeliome_VCGS. Sources: Expert Review Green,Victorian Clinical Genetics Services Mode of inheritance for gene: CCDC88C was set to Unknown
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 panelapp@genomicsengland.co.uk
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.