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Genetic epilepsy syndromes

Gene: HCN2

Green List (high evidence)

HCN2 (hyperpolarization activated cyclic nucleotide gated potassium and sodium channel 2)
EnsemblGeneIds (GRCh38): ENSG00000099822
EnsemblGeneIds (GRCh37): ENSG00000099822
OMIM: 602781, Gene2Phenotype
HCN2 is in 1 panel

6 reviews

Helen Lord (Oxford Medical Genetics Laboratories)

I don't know

No phenotype association on OMIM. HGMD Pro: no of reported variants associated with epilepsy phenotypes: Li et al 2018 (29064616): 4 different variants identified in HCN2 (3 missense 1 fs - all AD inheritance)- all affecteds had a seizure phenotype: 2 unrelated individuals with seizures had the same missense variant. In one family it was shown to segregate with disease in aff brother and mother. The fs variant did not appear to segregate with disease. Functional studies on two of the missense variants (Ser632Trp & Val246Met) suggest GOF. Dibbens et al, 2010 (20437590): in frame deletion of 3 AA in HCN2 which was found to be het in 3/65 GEFS+ unrelated patients, 3/61 FS unrelated patients, and 3/772 blood bank controls.Dewar et al, 2017 (28807990) - reclassified this variant as benign. DiFrancesco, 2019 & 2011 (30986657 & 221311395) 2011 paper identified first recessive missense variant - causing a nearly complete LOF of the channel, het carriers didn't appear to have any features. In the 2019 paper, identify 6 het missense variants - however they only think that the Glu515Lys variant (that they prev reported in a hom case) as being of interest. Nakamura et al, 2013 (24324597) - 2 unrelated children with FS where carriers of a het missense HCN2 variant. In one family the mother also had the variant and suffered from FS. I think class as amber.
Created: 5 Sep 2019, 2:22 p.m. | Last Modified: 5 Sep 2019, 2:22 p.m.
Panel Version: 1.261

Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal

Alison Callaway (Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust)

Green List (high evidence)

No phenotype association link in OMIM; 5 DM variants in HGMDPro with an association with an epilepsy phenotype. PMID 29064616 details several individuals with mainly missense variants in this gene and epilepsy/seizures (pedigrees suggest a dominant MOI). Functional studies in this paper also showed a depolarising shift in activation fot the p.(Ser632Trp) and p.(Val246Met) variants consistent with a gain-of-function. Additionally, PMID 22131395 identified the p.(Glu515Lys) variant in a large family and suggested that homozygosity is associated with epilepsy in this instance as this variant exhibits LOF.
Created: 23 Aug 2019, 9:54 a.m. | Last Modified: 23 Aug 2019, 9:54 a.m.
Panel Version: 1.256

Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal

Publications

Tracy Lester (Genetics laboratory, Oxford UK)

I don't know

more information required
Created: 6 Aug 2019, 8:31 p.m. | Last Modified: 6 Aug 2019, 8:31 p.m.
Panel Version: 1.188

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Publications

Rebecca Foulger (Genomics England curator)

I don't know

As discussed with members of the GMS Neurology Specialist Test Group on the Webex call 22nd November 2019 for Clinical Indication R59 Early onset or syndromic epilepsy: Agreed that there is enough evidence to rate this gene Green. Although this is a borderline case with questions over phenotype segregation, there are sufficient cases to support inclusion. Although seizures aren’t one of the cardinal phenotypes, most cases will be trios and therefore there will be less issues in being inclusive. Kept rating of HCN2 as Green with the option of review on subsequent panel versions.
Created: 25 Nov 2019, 8:17 p.m. | Last Modified: 25 Nov 2019, 8:17 p.m.
Panel Version: 1.426
Comment on mode of inheritance: Kept MOI as 'BOTH monoallelic and biallelic' as supported by reviews from Helen Lord and Alison Callaway, and literature (PMID:22131395).
Created: 19 Nov 2019, 10:37 p.m. | Last Modified: 19 Nov 2019, 10:37 p.m.
Panel Version: 1.408
Review and rating collated by Helen Lord (Oxford University Hospitals NHS Foundation Trust, 2019_08_30) on behalf of West Midlands, Oxford and Wessex GLH for GMS Neurology specialist test group. This gene is part of a subset that were re-reviewed following the group Webex call on 2019_08_08 for Clinical Indication R59 Early onset or syndromic epilepsy.
Created: 5 Sep 2019, 2:26 p.m. | Last Modified: 5 Sep 2019, 2:26 p.m.
Panel Version: 1.262
Review and rating collated by Tracy Lester (Oxford Medical Genetics Laboratories Oxford University Hospitals NHS Foundation Trust, 2019_02_06) on behalf of Wessex and West Midlands GLH for GMS Neurology specialist test group, for Clinical Indication R59 'Early onset or syndromic epilepsy'. Review contributors: John Taylor. Suggested gene rating: Amber.
Created: 6 Aug 2019, 8:38 p.m. | Last Modified: 6 Aug 2019, 8:38 p.m.
Panel Version: 1.189
Comment on mode of inheritance: PMID:22131395: DiFrancesco et al. 2011 report a homozygous HCN2 variant (p.E515K) in a patient with idiopathic generalized epilepsy. Of 17 screened members of the same family, the proband was the only one affected and homozygous for the variant. This is the first evidence in humans for a single-point, homozygous loss-of-function mutation in HCN2 potentially associated with generalized epilepsy with recessive inheritance. Hence MOI listed as BOTH monoallelic and biallelic.
Created: 11 Jul 2019, 4:27 p.m. | Last Modified: 13 Aug 2019, 10:49 a.m.
Panel Version: 1.198

Ivone Leong (Genomics England Curator)

Comment on list classification: Promoted from amber to green. No phenotypes have been associated with HCN2 in OMIM or Gene2Phenotype. There are 2 papers (PMID: 29064616, 17931874) reporting misssense, frameshift and small deletion variants in HCN2 associated with Genetic epilepsy with febrile seizures plus disorders and other epilepsy/seizure disorders (e.g. Idiopathic generalized epilepsy). There is also evidence that these variants cause gain-of-function effects (PMID: 29064616). Another study reported on a patient with sporadic idiopathic generalised seizures who had a recessive loss-of-function missense variant. An HCN2 knockout mouse model (PMID: 12514127) had absence seizures.
Created: 23 Nov 2018, 4:35 p.m.

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Multiple patients reported with different seizure disorders and variants in this gene. There is evidence that the variants are gain-of-function.
Created: 15 Aug 2018, 12:56 a.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
GEFS+ and other seizure disorders

Publications

Mode of pathogenicity
Other

Variants in this GENE are reported as part of current diagnostic practice

Details

Mode of Inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Wessex and West Midlands GLH
  • NHS GMS
  • Victorian Clinical Genetics Services
Phenotypes
  • Genetic epilepsy with febrile seizures plus
  • Other seizure disorders
OMIM
602781
Clinvar variants
Variants in HCN2
Penetrance
None
Publications
Panels with this gene

History Filter Activity

25 Nov 2019, Gel status: 3

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: hcn2 has been classified as Green List (High Evidence).

19 Nov 2019, Gel status: 3

Set mode of inheritance

Rebecca Foulger (Genomics England curator)

Mode of inheritance for gene: HCN2 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal

6 Aug 2019, Gel status: 3

Added New Source

Rebecca Foulger (Genomics England curator)

Source Wessex and West Midlands GLH was added to HCN2.

6 Aug 2019, Gel status: 3

Added New Source

Rebecca Foulger (Genomics England curator)

Source NHS GMS was added to HCN2.

11 Jul 2019, Gel status: 3

Set mode of inheritance

Rebecca Foulger (Genomics England curator)

Mode of inheritance for gene: HCN2 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal

11 Dec 2018, Gel status: 3

Panel promoted to version 1.0

Sarah Leigh (Genomics England Curator)

Zornitza Stark: Multiple patients reported wit

26 Nov 2018, Gel status: 3

Entity classified by Genomics England curator

Ivone Leong (Genomics England Curator)

Gene: hcn2 has been classified as Green List (High Evidence).

23 Nov 2018, Gel status: 3

Entity classified by Genomics England curator

Ivone Leong (Genomics England Curator)

Gene: hcn2 has been classified as Green List (High Evidence).

23 Nov 2018, Gel status: 2

Set Phenotypes

Ivone Leong (Genomics England Curator)

Phenotypes for gene: HCN2 were changed from Genetic epilepsy with efbrile seizures plus; Other seizure disorders to Genetic epilepsy with febrile seizures plus; Other seizure disorders

23 Nov 2018, Gel status: 2

Set Phenotypes

Ivone Leong (Genomics England Curator)

Phenotypes for gene: HCN2 were changed from to Genetic epilepsy with efbrile seizures plus; Other seizure disorders

23 Nov 2018, Gel status: 2

Set mode of inheritance

Ivone Leong (Genomics England Curator)

Mode of inheritance for gene: HCN2 was changed from to BOTH monoallelic and biallelic, autosomal or pseudoautosomal

23 Nov 2018, Gel status: 2

Set publications

Ivone Leong (Genomics England Curator)

Publications for gene: HCN2 were set to 29064616; 20437590; 12514127; 17931874

23 Nov 2018, Gel status: 2

Set publications

Ivone Leong (Genomics England Curator)

Publications for gene: HCN2 were set to

25 Jun 2018, Gel status: 2

Added New Source

Sarah Leigh (Genomics England Curator)

Expert Review Amber was added to HCN2. Panel: Genetic Epilepsy Syndromes

25 Jun 2018, Gel status: 1

Added New Source

Sarah Leigh (Genomics England Curator)

HCN2 was added to Genetic Epilepsy Syndromes panel. Sources: Victorian Clinical Genetics Services

25 Jun 2018, Gel status: 1

Created

Sarah Leigh (Genomics England Curator)

HCN2 was created by Sarah Leigh