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Genetic Epilepsy

Gene: CPA6

Red List (low evidence)
CPA6 (carboxypeptidase A6)
EnsemblGeneIds (GRCh38): ENSG00000165078
EnsemblGeneIds (GRCh37): ENSG00000165078
OMIM: 609562, Gene2Phenotype
CPA6 is in 3 panels

3 reviews

Bryony Thompson (Royal Melbourne Hospital)

Comment on list classification: ClinGen Epilepsy GCEP has reviewed both inheritances for gene-disease associations with epilepsy: AR disease is Disputed - There is contradictory case level and experimental data regarding any association between CPA6 and autosomal recessive epilepsy. Classification - 07/29/2021 AD disease is Refuted- There is very limited evidence supporting a gene-disease association. Many of the reported pathogenic variants have been subsequently identified as having a high minor allele frequency in population databases. Classification - 07/29/2021
Created: 11 Nov 2021, 4:49 a.m. | Last Modified: 11 Nov 2021, 4:49 a.m.
Panel Version: 0.1379
Created: 11 Nov 2021, 4:49 a.m.
Last Modified: 11 Nov 2021, 4:49 a.m.
Panel version: 0.1379

Elena Savva (Victorian Clinical Genetics Services)

Red List (low evidence)

Almost all variants reported in these papers are highly prevalent in gnomAD, especially african american cohorts (>250 hets, 0.3-0.9% MAF in this subpopulation)

Sapio (2012), Salazza (2012), Sapio (2015): co-authors on each other's papers, use functional studies to prove LOF (DN excluded) but there are many PTCs in gnomAD and VUS PTCs in ClinVar. Authors acknowledge variants are found in control cohorts but disregard.
Only p.R36H and p.N271S are rare (2015 paper).

PMID: 32207733 paper describes an additional case but paper inaccessible (Russian)

No additional papers in panelapp or pubmed to established gene-disease association
Created: 4 Jan 2021, 12:11 a.m. | Last Modified: 4 Jan 2021, 12:11 a.m.
Panel Version: 0.990

Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal

Phenotypes
Epilepsy, familial temporal lobe, 5 MIM#614417; Febrile seizures, familial, 11 MIM#614418

Publications

Created: 4 Jan 2021, 12:11 a.m.
Last Modified: 4 Jan 2021, 12:11 a.m.
Panel version: 0.990

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

I don't know

Homozygous p.A270V variant reported in four siblings with Febrile seizures, familial, 11 (MIM 614418)(PMID:21922598), some functional data. Present in gnomad as hets but no homs. Also note one of the heterozygous individuals initially reported was subsequently found to have a second missense variant, PMID 23105115.

Disputed association between mono allelic variants and disease.
Created: 4 Jan 2021, 1:09 a.m. | Last Modified: 4 Jan 2021, 1:11 a.m.
Panel Version: 0.990

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Epilepsy, familial temporal lobe, 5, MIM#614417; Febrile seizures, familial, 11, MIM#614418

Publications

Created: 29 Nov 2019, 10:20 p.m.
Last Modified: 4 Jan 2021, 1:11 a.m.
Panel version: 0.990

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Red
  • Victorian Clinical Genetics Services
  • Australian Genomics Health Alliance Epilepsy Flagship
Phenotypes
  • Epilepsy, familial temporal lobe, 5, MIM#614417
  • Febrile seizures, familial, 11, MIM#614418
Tags
refuted disputed
OMIM
609562
Clinvar variants
Variants in CPA6
Penetrance
None
Publications
Panels with this gene

History Filter Activity

11 Nov 2021, Gel status: 1

Added Tag, Added Tag

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Tag refuted tag was added to gene: CPA6. Tag disputed tag was added to gene: CPA6.

11 Nov 2021, Gel status: 1

Entity classified by Genomics England curator

Bryony Thompson (Royal Melbourne Hospital)

Gene: cpa6 has been classified as Red List (Low Evidence).

4 Jan 2021, Gel status: 2

Set mode of inheritance

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Mode of inheritance for gene: CPA6 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal

4 Jan 2021, Gel status: 2

Entity classified by Genomics England curator

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Gene: cpa6 has been classified as Amber List (Moderate Evidence).

29 Nov 2019, Gel status: 3

Entity classified by Genomics England curator

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Gene: cpa6 has been classified as Green List (High Evidence).

29 Nov 2019, Gel status: 3

Set Phenotypes

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Phenotypes for gene: CPA6 were changed from to Epilepsy, familial temporal lobe, 5, MIM#614417; Febrile seizures, familial, 11, MIM#614418

29 Nov 2019, Gel status: 3

Set publications

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Publications for gene: CPA6 were set to

29 Nov 2019, Gel status: 3

Set mode of inheritance

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Mode of inheritance for gene: CPA6 was changed from Unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal

17 Nov 2019, Gel status: 3

Created, Added New Source, Set mode of inheritance

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

gene: CPA6 was added gene: CPA6 was added to Genetic Epilepsy_AustralianGenomics_VCGS. Sources: Australian Genomics Health Alliance Epilepsy Flagship,Expert Review Green,Victorian Clinical Genetics Services Mode of inheritance for gene: CPA6 was set to Unknown