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Relevance to Autism

6 missense variants in the HCN1 gene, 5 of which were de novo in origin and were experimentally shown to alter channel properties, were identified in patients with epileptic encephalopathy; individuals with these variants had clinical features resembling those of Dravet syndrome with progression towards atypical absences, intellectual disability, and autistic features (Nava et al., 2014).

Molecular Function

The membrane protein encoded by this gene is a hyperpolarization-activated cation channel that contributes to the native pacemaker currents in heart and neurons. The encoded protein can homodimerize or heterodimerize with other pore-forming subunits to form a potassium channel. Detected in brain, in particular in amygdala and hippocampus.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
De novo mutations in HCN1 cause early infantile epileptic encephalopathy.
Epilepsy/seizures, ID
Autistic features, ADHD
Positive Association
Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection.
SCZ
Support
Large-scale discovery of novel genetic causes of developmental disorders.
Unknown diagnosis
Support
Impaired Color Recognition in HCN1 Epilepsy: A Single Case Report
ADHD, DD, epilepsy/seizures
Support
Mutational Landscape of Autism Spectrum Disorder Brain Tissue
ASD
Support
Genome sequencing of 320 Chinese children with epilepsy: a clinical and molecular study
DD, epilepsy/seizures
Support
Genomic insights from a deeply phenotyped highly consanguineous neurodevelopmental disorders cohort
DD, epilepsy/seizures
Support
A novel de novo HCN1 loss-of-function mutation in genetic generalized epilepsy causing increased neuronal excitability.
Epilepsy/seizures
Support
ASD
DD, ID, epilepsy/seizures
Support
Diagnostic Targeted Resequencing in 349 Patients with Drug-Resistant Pediatric Epilepsies Identifies Causative Mutations in 30 Different Genes.
Epilepsy/seizures
Support
Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability
ID
Support
Integrating de novo and inherited variants in 42
ASD
Recent Recommendation
HCN1 mutation spectrum: from neonatal epileptic encephalopathy to benign generalized epilepsy and beyond.
Early infantile epileptic encephalopathy-24 (EIEE2
Recent Recommendation
Autism-associated SHANK3 haploinsufficiency causes Ih channelopathy in human neurons.

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN611R001 
 missense_variant 
 c.1201G>C 
 p.Asp401His 
 De novo 
  
 Simplex 
 GEN611R002 
 missense_variant 
 c.299C>T 
 p.Ser100Phe 
 De novo 
  
 Simplex 
 GEN611R003 
 missense_variant 
 c.814T>C 
 p.Ser272Pro 
 De novo 
  
 Simplex 
 GEN611R004 
 missense_variant 
 c.890G>C 
 p.Arg297Thr 
 De novo 
  
 Simplex 
 GEN611R005 
 missense_variant 
 c.835C>T 
 p.His279Tyr 
 De novo 
  
 Simplex 
 GEN611R006 
 missense_variant 
 c.140G>T 
 p.Gly47Val 
 Unknown 
  
 Simplex 
 GEN611R007 
 copy_number_loss 
  
 p.Asn338_Lys410del 
 Familial 
 Paternal 
 Simplex 
 GEN611R008 
 missense_variant 
 c.913A>C 
 p.Met305Leu 
 De novo 
  
 Unknown 
 GEN611R009 
 missense_variant 
 c.1145G>C 
 p.Gly382Ala 
 De novo 
  
  
 GEN611R010 
 missense_variant 
 c.1172G>A 
 p.Gly391Asp 
 De novo 
  
  
 GEN611R011 
 missense_variant 
 c.459G>C 
 p.Met153Ile 
 De novo 
  
  
 GEN611R012 
 missense_variant 
 c.469C>G 
 p.Leu157Val 
 De novo 
  
 Multiplex 
 GEN611R013 
 missense_variant 
 c.428T>A 
 p.Phe143Tyr 
 De novo 
  
  
 GEN611R014 
 missense_variant 
 c.459G>C 
 p.Met153Ile 
 De novo 
  
  
 GEN611R015 
 missense_variant 
 c.459G>T 
 p.Met153Ile 
 De novo 
  
  
 GEN611R016 
 missense_variant 
 c.514A>C 
 p.Thr172Pro 
 De novo 
  
  
 GEN611R017 
 missense_variant 
 c.728T>G 
 p.Met243Arg 
 De novo 
  
  
 GEN611R018 
 missense_variant 
 c.728T>G 
 p.Met243Arg 
 De novo 
  
  
 GEN611R019 
 missense_variant 
 c.779C>T 
 p.Thr260Ile 
 De novo 
  
  
 GEN611R020 
 missense_variant 
 c.790A>T 
 p.Ser264Cys 
 De novo 
  
  
 GEN611R021 
 missense_variant 
 c.824T>C 
 p.Ile275Thr 
 De novo 
  
  
 GEN611R022 
 missense_variant 
 c.913A>T 
 p.Met305Leu 
 De novo 
  
  
 GEN611R023 
 missense_variant 
 c.913A>C 
 p.Met305Leu 
 De novo 
  
  
 GEN611R024 
 missense_variant 
 c.1172G>A 
 p.Gly391Asp 
 De novo 
  
  
 GEN611R025 
 missense_variant 
 c.1172G>A 
 p.Gly391Asp 
 De novo 
  
  
 GEN611R026 
 missense_variant 
 c.1171G>A 
 p.Gly391Ser 
 De novo 
  
  
 GEN611R027 
 missense_variant 
 c.1171G>A 
 p.Gly391Ser 
 De novo 
  
  
 GEN611R028 
 missense_variant 
 c.1171G>T 
 p.Gly391Cys 
 De novo 
  
  
 GEN611R029 
 missense_variant 
 c.1189A>C 
 p.Ile397Leu 
 De novo 
  
  
 GEN611R030 
 missense_variant 
 c.1195T>C 
 p.Ser399Pro 
 De novo 
  
  
 GEN611R031 
 missense_variant 
 c.1769G>A 
 p.Arg590Gln 
 De novo 
  
  
 GEN611R032 
 missense_variant 
 c.512C>G 
 p.Thr171Arg 
 Familial 
 Paternal 
 Multi-generational 
 GEN611R033 
 missense_variant 
 c.986G>C 
 p.Cys329Ser 
 Familial 
  
 Multi-generational 
 GEN611R034 
 missense_variant 
 c.1240G>A 
 p.Val414Met 
 Familial 
  
 Multi-generational 
 GEN611R035 
 missense_variant 
 c.2039C>A 
 p.Ser680Tyr 
 Familial 
  
 Multi-generational 
 GEN611R036a 
 missense_variant 
 c.781A>G 
 p.Lys261Glu 
 Unknown 
  
  
 GEN611R036b 
 splice_site_variant 
 c.1377+1G>A 
  
 Unknown 
  
  
 GEN611R037 
 frameshift_variant 
 c.414del 
 p.Tyr138Ter 
 De novo 
  
  
 GEN611R038 
 missense_variant 
 c.1136T>G 
 p.Met379Arg 
 De novo 
  
  
 GEN611R039 
 copy_number_loss 
  
  
 Familial 
 Paternal 
  
 GEN611R040 
 missense_variant 
 c.254A>C 
 p.Glu85Ala 
 Familial 
 Maternal 
  
 GEN611R041 
 missense_variant 
 c.1232A>G 
 p.Tyr411Cys 
 Familial 
 Paternal 
  
 GEN611R042 
 missense_variant 
 c.2143C>G 
 p.Arg715Gly 
 Familial 
 Paternal 
  
 GEN611R043 
 missense_variant 
 c.2507C>G 
 p.Pro836Arg 
 Unknown 
  
  
 GEN611R044 
 missense_variant 
 c.905T>C 
 p.Ile302Thr 
 Unknown 
  
  
 GEN611R045 
 missense_variant 
 c.737A>C 
 p.Glu246Ala 
 De novo 
  
  
 GEN611R046a 
 synonymous_variant 
 c.2238T>A 
 p.Thr746= 
 De novo 
  
 Simplex 
 GEN611R046b 
 missense_variant 
 c.2236A>C 
 p.Thr746Pro 
 De novo 
  
 Simplex 
 GEN611R047 
 missense_variant 
 c.457A>G 
 p.Met153Val 
 De novo 
  
 Simplex 
 GEN611R048 
 missense_variant 
 c.862A>C 
 p.Thr288Pro 
 De novo 
  
  
 GEN611R049 
 missense_variant 
 c.1691T>C 
 p.Leu564Pro 
 De novo 
  
  
 GEN611R050 
 missense_variant 
 c.1460T>C 
 p.Met487Thr 
 Familial 
 Maternal 
 Simplex 
 GEN611R051 
 missense_variant 
 c.2068C>A 
 p.Pro690Thr 
 Unknown 
  
  

Common

Variant ID
Polymorphism
SNP ID
Allele Change
Residue Change
Population Origin
Population Stage
Author, Year
 GEN611C001 
 intron_variant 
 rs16902086 
 c.1618+17949T>C 
  
 40,675 SCZ cases and 64,643 controls (CLOZUK and independent PGC datasets) 
 Discovery 
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
5
Deletion-Duplication
 10
 
5
Deletion-Duplication
 6
 
5
Duplication
 1
 
5
Duplication
 1
 
5
Duplication
 1
 
5
Duplication
 1
 
5
Duplication
 1
 
5
Duplication
 1
 
5
Duplication
 1
 

Model Summary

HCN1 loss of function is associated with ataxia and ASD. A homozygous knockout mouse model of HCN1 shows impairments in motor coordination and balance. The severity of the motor phenotype is dependent on the genetic background strain. The knockout also shows a decrease in GABA tone in the cerebellum. Chronic treatment with gabapentin, a voltage-gated calcium channel modulator, ameliorates the motor coordination phenotype.

References

Type
Title
Author, Year
Primary
Gabapentin treatment improves motor coordination in a mice model of progressive ataxia

M_HCN1_1_KO_HM

Model Type: Genetic
Model Genotype: Homozygous
Mutation: Two loxP sites were inserted flanking the pore-S6 domain containing exon. Excision of the targeted exon was done through Cre recombinase expression in targeted ES cells. Hcn1 mRNA and protein expression is absent in mice homozygous for this allele (MGI:2686951). This model has a mixed genetic background after one generation of inbreeding (F1).
Allele Type: Knockout
Strain of Origin: 129S/SvEv
Genetic Background: 129S/SvEv*C57BL6/J
ES Cell Line: MM13
Mutant ES Cell Line:
Model Source: Jackson

M_HCN1_2_KO_HM

Model Type: Genetic
Model Genotype: Homozygous
Mutation: Two loxP sites were inserted flanking the pore-S6 domain containing exon. Excision of the targeted exon was done through Cre recombinase expression in targeted ES cells. Hcn1 mRNA and protein expression is absent in mice homozygous for this allele (MGI:2686951). This model has more uniform genetic background after three to six generations of inbreeding.
Allele Type: Knockout
Strain of Origin: 129S/SvEv
Genetic Background: B6129S
ES Cell Line: MM13
Mutant ES Cell Line:
Model Source: Jackson

M_HCN1_1_KO_HM

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Motor coordination and balance1
Decreased
Description: 6-month-old knockout mice completely fail to balance on the Rotarod cylinder, while wildtype mice progressively improve motor performance during the 3 days of training. These mice are in the first generation of inbreeding.
 Accelerating rotarod test
 6 months
Size/growth1
 No change
 General observations
 Not reported
Motor coordination and balance1
 No change
 Accelerating rotarod test
 2 months
 Not Reported:

M_HCN1_2_KO_HM

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Motor coordination and balance1
Decreased
Description: 2-month-old knockout mice completely fail to balance on the Rotarod cylinder, while wildtype mice progressively improve motor performance during the 3 days of training. These mice are in the sixth generation of inbreeding. The phenotype is also evident at 4 months of age. Inbred crossing caused a worsening of motor coordination impairment.
 Accelerating rotarod test
 2, 4 months
Neurotransmitter release: GABA1
Decreased
Description: GABA content was lower in the cerebellum of knockout mice compared to wildtype mice.
Exp Paradigm: Cerebellum
 High-performance liquid chromatography (HPLC)
 6 months
Neurotransmitter release: GABA1
Decreased
Description: The expression level of the mRNA for the GABA synthesis enzyme GAD67 is reduced in knockout mice compared to wildtype mice.
Exp Paradigm: GAD67 (GABA synthesis enzyme)
 Quantitative PCR (qRT-PCR)
 8 months
Cerebellar morphology: granule cell layer thickness1
 No change
 Histology
 1, 12.5 months
Cerebellar morphology: molecular layer thickness1
 No change
 Histology
 1, 12.5 months
Neuronal number1
 No change
 Cell counting
 1.5, 6, 8.5 months
Neuronal number: Purkinje cells1
 No change
 Histology
 1, 12.5 months
 Not Reported:


Interactor Symbol Interactor Name Interactor Organism Entrez ID Uniprot ID Interaction Type Evidence Reference
NEDD4L neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase 23327 Q96PU5 IP/WB
Wilkars W , et al. 2014
SHANK3 SH3 and multiple ankyrin repeat domains 3 85358 Q9BYB0 IP/WB
Yi F , et al. 2016
UBC ubiquitin C 7316 P63279 LC-MS/MS
Vanderwerf SM , et al. 2009
HCN1 hyperpolarization-activated, cyclic nucleotide-gated K+ 1 15165 O88704 Y2H
Proenza C , et al. 2002
HCN2 hyperpolarization-activated, cyclic nucleotide-gated K+ 2 15166 O88703 IP/WB; Electrophysiology
Much B , et al. 2003
Hcn2 hyperpolarization-activated, cyclic nucleotide-gated K+ 2 15166 O88703 IP/WB
Omrani A , et al. 2015
HCN3 hyperpolarization-activated, cyclic nucleotide-gated K+ 3 15168 O88705 IP/WB; Electrophysiology
Much B , et al. 2003
HCN4 hyperpolarization activated cyclic nucleotide-gated potassium channel 4 10021 Q9Y3Q4 IP/WB; Electrophysiology
Much B , et al. 2003
HCN4 Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 O70507 IP/WB; Electrophysiology
Much B , et al. 2003
NF1 neurofibromatosis 1 18015 Q04690 IP; LC-MS/MS; IP/WB
Omrani A , et al. 2015
Pex5l peroxisomal biogenesis factor 5-like 58869 Q8C437 IP/WB
Omrani A , et al. 2015

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