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Intellectual disability

Gene: CACNA1E

Green List (high evidence)
CACNA1E (calcium voltage-gated channel subunit alpha1 E)
EnsemblGeneIds (GRCh38): ENSG00000198216
EnsemblGeneIds (GRCh37): ENSG00000198216
OMIM: 601013, Gene2Phenotype
CACNA1E is in 6 panels

2 reviews

Louise Daugherty (Genomics England Curator)

Comment on list classification: New gene added by external expert and reviewed by curation team, appropriate phenotype, sufficient cases and external expert review all support gene-disease association and relevance to this panel to rate gene to Green.
Created: 21 Feb 2019, 2:31 p.m.
Comment on publications: added Helbig et al. publication that supports the gene-disease association, and upgrading of the gene to Green
Created: 21 Feb 2019, 2:29 p.m.
Comment on phenotypes: added phenotype info from OMIM and MIMid
Created: 21 Feb 2019, 2:25 p.m.
Created: 21 Feb 2019, 2:25 p.m.

Panel version: 2.714

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Helbig et al. (https://doi.org/10.1016/j.ajhg.2018.09.006) report on 30 individuals with pathogenic variants in CACNA1E.

The phenotype was consistent with a developmental and epileptic encephalopathy, with hypotonia, early-onset and refractory seizures, severe to profound developmental delay and intellectual disability. Additional relatively common features included hyperkinetic movement disorder (severe dystonia which was observed in 40%, other dyskinesias in another 20%), congenital joint contractures of variable degree and joint involvement (approx. 40% of individuals) and macrocephaly (approx. 40%). There were no common facial dysmorphic features observed.

Of note, epilepsy was not a feature in 4 cases (age 1 to 4 years) so few of these individuals may be investigated for their developmental delay/intellectual disability or other features.

Missense variants:
All the 30 subjects described harbored a missense variant in CACNA1E which in all cases where parental studies were possible (29/30) occurred as a de novo event. There were 4 recurrent variants, explaining the phenotype in 20 patients in total while the rest of the individuals had private mutations. Functional studies were performed and suggested a gain-of-function effect for these variants (increased calcium inward currents).

Loss-of-function (LoF) variants:
Apart from the main cohort of patients, the authors note the presence of 3 individuals with such variants incl.:
- one individual with a nonsense variant present in the mosaic state (6/22 reads) in peripheral blood.
- one individual with a frameshift variant inherited from his unaffected parent.
- one individual with a nonsense variant for whom parental studies were not possible.

The authors comment that these indivdiduals presented with milder phenotype compared to those with missense variants. More information on these subjects is provided in the supplement as the article focuses on missense SNVs.

As the authors also note, several LoF variants exist in gnomAD, although the gene appears to be LoF intolerant (pLI=1).

Penetrance:
Seems to be complete for missense SNVs and possibly incomplete for LoF ones.

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A previous study by Heyne et al. (PMID: 29942082) implicated de novo variants (DNVs) in CACNA1E with neurodevelopmental disorders for the first time. This study however does not provide clinical details on the phenotype of the affected individuals, while it seems to present overlap as to the individuals reported (eg. includes subjects from the DDD study and others).

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Details as to a few - possibly further - de novo coding variants reported to date can be found at the denovo-db:
http://denovo-db.gs.washington.edu/denovo-db/QueryVariantServlet?searchBy=Gene&target=CACNA1E

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As a result this gene can be considered for inclusion in this panel as green.
Sources: Expert Review, Literature
Created: 19 Oct 2018, 7:58 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Phenotypes
Global developmental delay; Intellectual disability; Seizures; Dystonia; Congenital contracture; Macrocephaly

Publications

Mode of pathogenicity
Other

Created: 19 Oct 2018, 7:58 p.m.

Panel version: 2.510

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Green
Phenotypes
  • Global developmental delay
  • Intellectual disability
  • Seizures
  • Dystonia
  • Congenital contracture
  • Macrocephaly
  • Epileptic encephalopathy, early infantile, 69, 618285
OMIM
601013
Clinvar variants
Variants in CACNA1E
Penetrance
Incomplete
Publications
Mode of Pathogenicity
Other
Panels with this gene

History Filter Activity

21 Feb 2019, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: cacna1e has been classified as Green List (High Evidence).

21 Feb 2019, Gel status: 0

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: CACNA1E were set to 29942082

21 Feb 2019, Gel status: 0

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: CACNA1E were changed from Global developmental delay; Intellectual disability; Seizures; Dystonia; Congenital contracture; Macrocephaly to Global developmental delay; Intellectual disability; Seizures; Dystonia; Congenital contracture; Macrocephaly; Epileptic encephalopathy, early infantile, 69, 618285

19 Oct 2018, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes, Set penetrance, Set mode of pathogenicity

Konstantinos Varvagiannis (Other)

gene: CACNA1E was added gene: CACNA1E was added to Intellectual disability. Sources: Expert Review,Literature Mode of inheritance for gene: CACNA1E was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: CACNA1E were set to 29942082 Phenotypes for gene: CACNA1E were set to Global developmental delay; Intellectual disability; Seizures; Dystonia; Congenital contracture; Macrocephaly Penetrance for gene: CACNA1E were set to Incomplete Mode of pathogenicity for gene: CACNA1E was set to Other Review for gene: CACNA1E was set to GREEN