We collected the data of 33 affected individuals carrying 18 different novel HCN1 missense variants classified as pathogenic or likely pathogenic using the ACMG criteria, all absent from the GnomAD database (Fig. 1 and Supplementary Table 1). Overall, 14 different variants occurred de novo in 19 sporadic patients (Table 1). Four variants segregated with epilepsy in at least two affected family members of four families (Table 2). All 18 variants led to missense substitutions altering amino acids highly conserved in orthologues and/or paralogues (Supplementary Fig. 1). Five amino acid substitutions (Met153Ile, Met243Arg, Met305Leu, Gly391Ser and Gly391Asp) were each observed twice, Met305Leu and Met153Ile resulting from different nucleotides substitutions. Three different base changes altering glycine 391 (Gly391Ser, Gly391Cys and Gly391Asp) were observed in five patients.

Table 1

Clinical and genetic summary of the 19 sporadic patients with de novo HCN1 variants

Patient numberGenderAge at the studySeizure onsetSeizure type at onsetSeizure type at follow-upSensitivity to feverSeizure frequencyResistance to AEDsDevelopmentEpilepsy type/ syndromesMutation
1F12 y 6 m12 mTCSTCS, AtNoDailyYesSevere IDEIEEp.Phe143Tyr
2F7 y 3 m5 mFSFc, TCSYesWeekly to dailyYesMild IDEIEEp.Met153Ile
3M2 y 8 m9 mTCSTCS, FcNoWeeklyYesMild language delayUncl epilepsy infantile onsetp.Met153Ile
4F42 y7 mFSFS, afebrile TC, Tn and absenceYesLast seizure at 20 yNoMild ID + autistic traitsGGE-TCSp.Thr172Pro
5F17 y13 mFSFS, afebrile TCS, absenceYesRNoModerate IDFS+p.Met243Arg
6F2 y 6 m10 mFS (Tn)FSYesWith feverNoNormalFSp.Met243Arg
7F2 y8 mFS (Cl)Cl GenYesMonthlyNoNormalFS+p.Thr260Ile
8M5 y 10 m9 mFc (Cl)TCSNoRNoNormal, mild language delayUncl epilepsy infantile onsetp. Ser264Cys
9F9 y42 mFcFc > TCS; MyNoDailyYesModerate IDChildhood focal epilepsyp.Ile275Thr
10F12 m3 mTCSTCSYes4 m seizure-freeYesMild DDUncl epilepsy infantile onsetp.Met305Leu
11F14 y2 mTCSTCS, Tn, Fc, ClYesMonthlyYesSevere ID, microcephalyEIEEp.Met305Leu
12MDied at 14 m30 hTn asymmetric, prolongedTn asymmetric ± Cl, prolonged apnoea and cyanosisNoDailyYesSevere ID, microcephalyNOEE (MMPSI)p.Gly391Asp
13MDied at 15 m48 hTn asymmetric, prolongedSimilar but with cyanosisNoDailyYesSevere IDNOEEp.Gly391Asp
14F6 y 3 m5 mProlonged FS (20 min)FS; afebrile TCS: Fc (LOC, hypotonia, cyanosis, vomit)YesYearlyNoNormalFS+p.Gly391Ser
15M2 y 5 m7 mHemiClFc, TCSYesYearlyNoMild IDGEFS+p.Gly391Ser
16F29 yInfancyEyelid MyTCS, Fc, absence, MyNAMonthly to weeklyYesModerate ID, autistic traitsGen epilepsy with eyelid Myp.Gly391Cys
17M15 y5 mHypotonia and cyanosis few h after vaccinationMA; Fc (hypomotor with psychomotor arrest) TCSYesDailyYesSevere ID, autistic traitsEIEEp.Ile397Leu
18M7 y4 mProlonged FSTCS, with apnoeaYesDailyYesSevere IDEIEEp.Ser399Pro
19M15 y72 mAbsenceabsence + single TCSNoDailyYesNormalCAEp.Arg590Gln
Patient numberGenderAge at the studySeizure onsetSeizure type at onsetSeizure type at follow-upSensitivity to feverSeizure frequencyResistance to AEDsDevelopmentEpilepsy type/ syndromesMutation
1F12 y 6 m12 mTCSTCS, AtNoDailyYesSevere IDEIEEp.Phe143Tyr
2F7 y 3 m5 mFSFc, TCSYesWeekly to dailyYesMild IDEIEEp.Met153Ile
3M2 y 8 m9 mTCSTCS, FcNoWeeklyYesMild language delayUncl epilepsy infantile onsetp.Met153Ile
4F42 y7 mFSFS, afebrile TC, Tn and absenceYesLast seizure at 20 yNoMild ID + autistic traitsGGE-TCSp.Thr172Pro
5F17 y13 mFSFS, afebrile TCS, absenceYesRNoModerate IDFS+p.Met243Arg
6F2 y 6 m10 mFS (Tn)FSYesWith feverNoNormalFSp.Met243Arg
7F2 y8 mFS (Cl)Cl GenYesMonthlyNoNormalFS+p.Thr260Ile
8M5 y 10 m9 mFc (Cl)TCSNoRNoNormal, mild language delayUncl epilepsy infantile onsetp. Ser264Cys
9F9 y42 mFcFc > TCS; MyNoDailyYesModerate IDChildhood focal epilepsyp.Ile275Thr
10F12 m3 mTCSTCSYes4 m seizure-freeYesMild DDUncl epilepsy infantile onsetp.Met305Leu
11F14 y2 mTCSTCS, Tn, Fc, ClYesMonthlyYesSevere ID, microcephalyEIEEp.Met305Leu
12MDied at 14 m30 hTn asymmetric, prolongedTn asymmetric ± Cl, prolonged apnoea and cyanosisNoDailyYesSevere ID, microcephalyNOEE (MMPSI)p.Gly391Asp
13MDied at 15 m48 hTn asymmetric, prolongedSimilar but with cyanosisNoDailyYesSevere IDNOEEp.Gly391Asp
14F6 y 3 m5 mProlonged FS (20 min)FS; afebrile TCS: Fc (LOC, hypotonia, cyanosis, vomit)YesYearlyNoNormalFS+p.Gly391Ser
15M2 y 5 m7 mHemiClFc, TCSYesYearlyNoMild IDGEFS+p.Gly391Ser
16F29 yInfancyEyelid MyTCS, Fc, absence, MyNAMonthly to weeklyYesModerate ID, autistic traitsGen epilepsy with eyelid Myp.Gly391Cys
17M15 y5 mHypotonia and cyanosis few h after vaccinationMA; Fc (hypomotor with psychomotor arrest) TCSYesDailyYesSevere ID, autistic traitsEIEEp.Ile397Leu
18M7 y4 mProlonged FSTCS, with apnoeaYesDailyYesSevere IDEIEEp.Ser399Pro
19M15 y72 mAbsenceabsence + single TCSNoDailyYesNormalCAEp.Arg590Gln

At = atonic; CAE = childhood absence epilepsy; Cl = clonic; DD = developmental delay; F = female; Fc = focal; FS = febrile seizures; FS+ febrile seizure plus; Gen = generalized; ID = intellectual disability; LOC = loss of consciousness; M = male; MA = myoclonic-atonic; My = myoclonic; NA = unavailable; NOEE = neonatal-onset epileptic encephalopathy; Tn = tonic; TCS = tonic-clonic seizure(s); Uncl = unclassified. Detailed clinical information, including Brain MRI, EEG findings and antiepileptic treatment is provided for Patients 1–19 in Supplementary Table 2.

Table 1

Clinical and genetic summary of the 19 sporadic patients with de novo HCN1 variants

Patient numberGenderAge at the studySeizure onsetSeizure type at onsetSeizure type at follow-upSensitivity to feverSeizure frequencyResistance to AEDsDevelopmentEpilepsy type/ syndromesMutation
1F12 y 6 m12 mTCSTCS, AtNoDailyYesSevere IDEIEEp.Phe143Tyr
2F7 y 3 m5 mFSFc, TCSYesWeekly to dailyYesMild IDEIEEp.Met153Ile
3M2 y 8 m9 mTCSTCS, FcNoWeeklyYesMild language delayUncl epilepsy infantile onsetp.Met153Ile
4F42 y7 mFSFS, afebrile TC, Tn and absenceYesLast seizure at 20 yNoMild ID + autistic traitsGGE-TCSp.Thr172Pro
5F17 y13 mFSFS, afebrile TCS, absenceYesRNoModerate IDFS+p.Met243Arg
6F2 y 6 m10 mFS (Tn)FSYesWith feverNoNormalFSp.Met243Arg
7F2 y8 mFS (Cl)Cl GenYesMonthlyNoNormalFS+p.Thr260Ile
8M5 y 10 m9 mFc (Cl)TCSNoRNoNormal, mild language delayUncl epilepsy infantile onsetp. Ser264Cys
9F9 y42 mFcFc > TCS; MyNoDailyYesModerate IDChildhood focal epilepsyp.Ile275Thr
10F12 m3 mTCSTCSYes4 m seizure-freeYesMild DDUncl epilepsy infantile onsetp.Met305Leu
11F14 y2 mTCSTCS, Tn, Fc, ClYesMonthlyYesSevere ID, microcephalyEIEEp.Met305Leu
12MDied at 14 m30 hTn asymmetric, prolongedTn asymmetric ± Cl, prolonged apnoea and cyanosisNoDailyYesSevere ID, microcephalyNOEE (MMPSI)p.Gly391Asp
13MDied at 15 m48 hTn asymmetric, prolongedSimilar but with cyanosisNoDailyYesSevere IDNOEEp.Gly391Asp
14F6 y 3 m5 mProlonged FS (20 min)FS; afebrile TCS: Fc (LOC, hypotonia, cyanosis, vomit)YesYearlyNoNormalFS+p.Gly391Ser
15M2 y 5 m7 mHemiClFc, TCSYesYearlyNoMild IDGEFS+p.Gly391Ser
16F29 yInfancyEyelid MyTCS, Fc, absence, MyNAMonthly to weeklyYesModerate ID, autistic traitsGen epilepsy with eyelid Myp.Gly391Cys
17M15 y5 mHypotonia and cyanosis few h after vaccinationMA; Fc (hypomotor with psychomotor arrest) TCSYesDailyYesSevere ID, autistic traitsEIEEp.Ile397Leu
18M7 y4 mProlonged FSTCS, with apnoeaYesDailyYesSevere IDEIEEp.Ser399Pro
19M15 y72 mAbsenceabsence + single TCSNoDailyYesNormalCAEp.Arg590Gln
Patient numberGenderAge at the studySeizure onsetSeizure type at onsetSeizure type at follow-upSensitivity to feverSeizure frequencyResistance to AEDsDevelopmentEpilepsy type/ syndromesMutation
1F12 y 6 m12 mTCSTCS, AtNoDailyYesSevere IDEIEEp.Phe143Tyr
2F7 y 3 m5 mFSFc, TCSYesWeekly to dailyYesMild IDEIEEp.Met153Ile
3M2 y 8 m9 mTCSTCS, FcNoWeeklyYesMild language delayUncl epilepsy infantile onsetp.Met153Ile
4F42 y7 mFSFS, afebrile TC, Tn and absenceYesLast seizure at 20 yNoMild ID + autistic traitsGGE-TCSp.Thr172Pro
5F17 y13 mFSFS, afebrile TCS, absenceYesRNoModerate IDFS+p.Met243Arg
6F2 y 6 m10 mFS (Tn)FSYesWith feverNoNormalFSp.Met243Arg
7F2 y8 mFS (Cl)Cl GenYesMonthlyNoNormalFS+p.Thr260Ile
8M5 y 10 m9 mFc (Cl)TCSNoRNoNormal, mild language delayUncl epilepsy infantile onsetp. Ser264Cys
9F9 y42 mFcFc > TCS; MyNoDailyYesModerate IDChildhood focal epilepsyp.Ile275Thr
10F12 m3 mTCSTCSYes4 m seizure-freeYesMild DDUncl epilepsy infantile onsetp.Met305Leu
11F14 y2 mTCSTCS, Tn, Fc, ClYesMonthlyYesSevere ID, microcephalyEIEEp.Met305Leu
12MDied at 14 m30 hTn asymmetric, prolongedTn asymmetric ± Cl, prolonged apnoea and cyanosisNoDailyYesSevere ID, microcephalyNOEE (MMPSI)p.Gly391Asp
13MDied at 15 m48 hTn asymmetric, prolongedSimilar but with cyanosisNoDailyYesSevere IDNOEEp.Gly391Asp
14F6 y 3 m5 mProlonged FS (20 min)FS; afebrile TCS: Fc (LOC, hypotonia, cyanosis, vomit)YesYearlyNoNormalFS+p.Gly391Ser
15M2 y 5 m7 mHemiClFc, TCSYesYearlyNoMild IDGEFS+p.Gly391Ser
16F29 yInfancyEyelid MyTCS, Fc, absence, MyNAMonthly to weeklyYesModerate ID, autistic traitsGen epilepsy with eyelid Myp.Gly391Cys
17M15 y5 mHypotonia and cyanosis few h after vaccinationMA; Fc (hypomotor with psychomotor arrest) TCSYesDailyYesSevere ID, autistic traitsEIEEp.Ile397Leu
18M7 y4 mProlonged FSTCS, with apnoeaYesDailyYesSevere IDEIEEp.Ser399Pro
19M15 y72 mAbsenceabsence + single TCSNoDailyYesNormalCAEp.Arg590Gln

At = atonic; CAE = childhood absence epilepsy; Cl = clonic; DD = developmental delay; F = female; Fc = focal; FS = febrile seizures; FS+ febrile seizure plus; Gen = generalized; ID = intellectual disability; LOC = loss of consciousness; M = male; MA = myoclonic-atonic; My = myoclonic; NA = unavailable; NOEE = neonatal-onset epileptic encephalopathy; Tn = tonic; TCS = tonic-clonic seizure(s); Uncl = unclassified. Detailed clinical information, including Brain MRI, EEG findings and antiepileptic treatment is provided for Patients 1–19 in Supplementary Table 2.

Table 2

Clinical and genetic summary of affected members of families with HCN1 variants

Family/ patient numberGenderAge at studySeizure onssetSeizure typeSeizure at follow-upAEDsEEGBrain MRIDevelopmentEpilepsy type/ syndromesMutation
Family T
20M66 y8 mFS and afebrile TCSSeizure until age 6 y then single TCS in adult agePB, currently no AEDsNormalNANAGEFS+p.Thr171Arg
21M32 y8 mFS; TCS, possible focal onset >TCSSeizure-free from age 12 yPB + GVG + VPA currently no AEDsNormalNormalBorderlineGEFS+
22F21 y10 mFSFS and afebrile TCS, seizure-free for >3 yVPA, ESM, currently no AEDsGSWNormalMild ID (TIQ = 50)GEFS+
23F21 y11 mFSFS and afebrile TCS, seizure-free for from 10 to 18 yVPANormalNormalMild ID (TIQ = 66)GEFS+
Family M1
24F49 y3 mFS, febrile, afebrile TCSSeizure-free from age 12 y after CBZCBZNANANormalGEFS+p.Cys329Ser
25F29 y1 yFSSeizure-free after VPAVPANANANormalFS
26F6 y18 mTCS without feverStatus epilepticus episode treated by PHT then seizure-free on VPAVPANormalNormalNormalGGE
27M23 y8 mFebrile TCSFS and afebrile seizure and absence from age 4 y; non-progressive action myoclonus from age 8 y; seizure-free after VPAVPANormalNormalMild ID (TIQ = 52; VIQ = 46; PIQ = 70)GGE
28F20 y13 mFSSeizure-free with CBZ until 13 y; CBZ was suspended: seizure recurrence. Seizure-free after CBZ reintroductionCBZNormalNormal CT scanNormalGEFS+
Family M2
29F8 y18 mFS, febrile and afebrile TCSSeizure-free after VPAVPAFast activityNormalBorderline (WIPPSI: IQ = 77)GEFS+p.Val414Met
30F5 y18 mFSSeizure-freeNo AEDsRare focal PA, fast activityNormalBorderline (DQ Griffith scale = 70)GEFS+
31M59 y12 mFSSeizure-freeNo AEDsNANANormalFS
Family O
32F7 y7 yTCSSeizure-freeVPAGSW during IPSNormalNormalGGEp.Ser680Tyr
33FUnknownChildhoodAbsenceAbsence and single TCS in childhood, then seizure-freeNo AEDsGSWNormalNormalCAE
Family/ patient numberGenderAge at studySeizure onssetSeizure typeSeizure at follow-upAEDsEEGBrain MRIDevelopmentEpilepsy type/ syndromesMutation
Family T
20M66 y8 mFS and afebrile TCSSeizure until age 6 y then single TCS in adult agePB, currently no AEDsNormalNANAGEFS+p.Thr171Arg
21M32 y8 mFS; TCS, possible focal onset >TCSSeizure-free from age 12 yPB + GVG + VPA currently no AEDsNormalNormalBorderlineGEFS+
22F21 y10 mFSFS and afebrile TCS, seizure-free for >3 yVPA, ESM, currently no AEDsGSWNormalMild ID (TIQ = 50)GEFS+
23F21 y11 mFSFS and afebrile TCS, seizure-free for from 10 to 18 yVPANormalNormalMild ID (TIQ = 66)GEFS+
Family M1
24F49 y3 mFS, febrile, afebrile TCSSeizure-free from age 12 y after CBZCBZNANANormalGEFS+p.Cys329Ser
25F29 y1 yFSSeizure-free after VPAVPANANANormalFS
26F6 y18 mTCS without feverStatus epilepticus episode treated by PHT then seizure-free on VPAVPANormalNormalNormalGGE
27M23 y8 mFebrile TCSFS and afebrile seizure and absence from age 4 y; non-progressive action myoclonus from age 8 y; seizure-free after VPAVPANormalNormalMild ID (TIQ = 52; VIQ = 46; PIQ = 70)GGE
28F20 y13 mFSSeizure-free with CBZ until 13 y; CBZ was suspended: seizure recurrence. Seizure-free after CBZ reintroductionCBZNormalNormal CT scanNormalGEFS+
Family M2
29F8 y18 mFS, febrile and afebrile TCSSeizure-free after VPAVPAFast activityNormalBorderline (WIPPSI: IQ = 77)GEFS+p.Val414Met
30F5 y18 mFSSeizure-freeNo AEDsRare focal PA, fast activityNormalBorderline (DQ Griffith scale = 70)GEFS+
31M59 y12 mFSSeizure-freeNo AEDsNANANormalFS
Family O
32F7 y7 yTCSSeizure-freeVPAGSW during IPSNormalNormalGGEp.Ser680Tyr
33FUnknownChildhoodAbsenceAbsence and single TCS in childhood, then seizure-freeNo AEDsGSWNormalNormalCAE

AED = anti-epileptic drug; CBZ = carbamazepine; DQ = developmental quotient; ESM = ethosuximide; F = female; FS = febrile seizure; FS+ = febrile seizure plus; GSW = generalized spike and wave; GVG = vigabatrin; ID = intellectual disability; IPS = intermittent photic stimulation; IQ = intellectual quotient; M = male; NA = unavailable; PA = paroxysmal activity; PB = phenobarbital; PHT = phenytoin; PIQ = performance intellectual quotient; TCS = tonic-clonic seizure(s); TIQ = full-scale intellectual quotient; WIPPSI = Wechsler preschool and primary scale of intelligence; VIQ = verbal intellectual quotient; VPA = sodium valproate.

Table 2

Clinical and genetic summary of affected members of families with HCN1 variants

Family/ patient numberGenderAge at studySeizure onssetSeizure typeSeizure at follow-upAEDsEEGBrain MRIDevelopmentEpilepsy type/ syndromesMutation
Family T
20M66 y8 mFS and afebrile TCSSeizure until age 6 y then single TCS in adult agePB, currently no AEDsNormalNANAGEFS+p.Thr171Arg
21M32 y8 mFS; TCS, possible focal onset >TCSSeizure-free from age 12 yPB + GVG + VPA currently no AEDsNormalNormalBorderlineGEFS+
22F21 y10 mFSFS and afebrile TCS, seizure-free for >3 yVPA, ESM, currently no AEDsGSWNormalMild ID (TIQ = 50)GEFS+
23F21 y11 mFSFS and afebrile TCS, seizure-free for from 10 to 18 yVPANormalNormalMild ID (TIQ = 66)GEFS+
Family M1
24F49 y3 mFS, febrile, afebrile TCSSeizure-free from age 12 y after CBZCBZNANANormalGEFS+p.Cys329Ser
25F29 y1 yFSSeizure-free after VPAVPANANANormalFS
26F6 y18 mTCS without feverStatus epilepticus episode treated by PHT then seizure-free on VPAVPANormalNormalNormalGGE
27M23 y8 mFebrile TCSFS and afebrile seizure and absence from age 4 y; non-progressive action myoclonus from age 8 y; seizure-free after VPAVPANormalNormalMild ID (TIQ = 52; VIQ = 46; PIQ = 70)GGE
28F20 y13 mFSSeizure-free with CBZ until 13 y; CBZ was suspended: seizure recurrence. Seizure-free after CBZ reintroductionCBZNormalNormal CT scanNormalGEFS+
Family M2
29F8 y18 mFS, febrile and afebrile TCSSeizure-free after VPAVPAFast activityNormalBorderline (WIPPSI: IQ = 77)GEFS+p.Val414Met
30F5 y18 mFSSeizure-freeNo AEDsRare focal PA, fast activityNormalBorderline (DQ Griffith scale = 70)GEFS+
31M59 y12 mFSSeizure-freeNo AEDsNANANormalFS
Family O
32F7 y7 yTCSSeizure-freeVPAGSW during IPSNormalNormalGGEp.Ser680Tyr
33FUnknownChildhoodAbsenceAbsence and single TCS in childhood, then seizure-freeNo AEDsGSWNormalNormalCAE
Family/ patient numberGenderAge at studySeizure onssetSeizure typeSeizure at follow-upAEDsEEGBrain MRIDevelopmentEpilepsy type/ syndromesMutation
Family T
20M66 y8 mFS and afebrile TCSSeizure until age 6 y then single TCS in adult agePB, currently no AEDsNormalNANAGEFS+p.Thr171Arg
21M32 y8 mFS; TCS, possible focal onset >TCSSeizure-free from age 12 yPB + GVG + VPA currently no AEDsNormalNormalBorderlineGEFS+
22F21 y10 mFSFS and afebrile TCS, seizure-free for >3 yVPA, ESM, currently no AEDsGSWNormalMild ID (TIQ = 50)GEFS+
23F21 y11 mFSFS and afebrile TCS, seizure-free for from 10 to 18 yVPANormalNormalMild ID (TIQ = 66)GEFS+
Family M1
24F49 y3 mFS, febrile, afebrile TCSSeizure-free from age 12 y after CBZCBZNANANormalGEFS+p.Cys329Ser
25F29 y1 yFSSeizure-free after VPAVPANANANormalFS
26F6 y18 mTCS without feverStatus epilepticus episode treated by PHT then seizure-free on VPAVPANormalNormalNormalGGE
27M23 y8 mFebrile TCSFS and afebrile seizure and absence from age 4 y; non-progressive action myoclonus from age 8 y; seizure-free after VPAVPANormalNormalMild ID (TIQ = 52; VIQ = 46; PIQ = 70)GGE
28F20 y13 mFSSeizure-free with CBZ until 13 y; CBZ was suspended: seizure recurrence. Seizure-free after CBZ reintroductionCBZNormalNormal CT scanNormalGEFS+
Family M2
29F8 y18 mFS, febrile and afebrile TCSSeizure-free after VPAVPAFast activityNormalBorderline (WIPPSI: IQ = 77)GEFS+p.Val414Met
30F5 y18 mFSSeizure-freeNo AEDsRare focal PA, fast activityNormalBorderline (DQ Griffith scale = 70)GEFS+
31M59 y12 mFSSeizure-freeNo AEDsNANANormalFS
Family O
32F7 y7 yTCSSeizure-freeVPAGSW during IPSNormalNormalGGEp.Ser680Tyr
33FUnknownChildhoodAbsenceAbsence and single TCS in childhood, then seizure-freeNo AEDsGSWNormalNormalCAE

AED = anti-epileptic drug; CBZ = carbamazepine; DQ = developmental quotient; ESM = ethosuximide; F = female; FS = febrile seizure; FS+ = febrile seizure plus; GSW = generalized spike and wave; GVG = vigabatrin; ID = intellectual disability; IPS = intermittent photic stimulation; IQ = intellectual quotient; M = male; NA = unavailable; PA = paroxysmal activity; PB = phenobarbital; PHT = phenytoin; PIQ = performance intellectual quotient; TCS = tonic-clonic seizure(s); TIQ = full-scale intellectual quotient; WIPPSI = Wechsler preschool and primary scale of intelligence; VIQ = verbal intellectual quotient; VPA = sodium valproate.

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