Genes associated with “seizures”

Diagnostic yield calculator →
438 genes foundHPO: Hypocalcemic seizuresOpen Targets: Seizure
How are genes scored? (0–100 composite)
-5–15
ClinGen
0–15
HPO Freq
0–15
Open Targets
0–12
Phen2Gene
0–10
ClinVar
0–8
Constraint
0–8
Dosage
0–8
OMIM CS
0–8
PanelApp
0–5
OMIM
0–5
G2P
0–4
Breadth
Tiers:Strong Candidates (≥20)Consider (≥8)Possible (≥3)
Evidence dots:
HPOClinVarPhen2GeneOpen TargetsPanelApp
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Strong Candidates

28 genes
1
SCN1A →

sodium voltage-gated channel alpha subunit 1

53
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
9
OT Score
0.79
2
KCNQ2 →

potassium voltage-gated channel subfamily Q member 2

47
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
4
OT Score
0.67
3
GABRG2 →

gamma-aminobutyric acid type A receptor subunit gamma2

37
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
185
OT Score
0.75
4
SCN2A →

sodium voltage-gated channel alpha subunit 2

35
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
709
OT Score
0.79
5
SCN8A →

sodium voltage-gated channel alpha subunit 8

33
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
6
OT Score
0.74
6
CACNA1E →

calcium voltage-gated channel subunit alpha1 E

33
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
-
OT Score
0.72
7
CACNA1C →

calcium voltage-gated channel subunit alpha1 C

31
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
7
OT Score
0.67
8
SCN3A →

sodium voltage-gated channel alpha subunit 3

30
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
-
OT Score
0.72
9
29
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
2
OT Score
-
29STXBP1
Def
27NPRL3
Def
26NUS1
Def
26SLC2A1
Def

solute carrier family 2 member 1

25CUL3
Def
25GABRB3
Def

gamma-aminobutyric acid type A receptor subunit beta3

24GABRA1
Def

gamma-aminobutyric acid type A receptor subunit alpha1

24DEPDC5
Def
24SCN4A
Def

sodium voltage-gated channel alpha subunit 4

23PRRT2
Def
23TANC2
Def
22CACNA1B
Mod

calcium voltage-gated channel subunit alpha1 B

21AP3B2
Def
20ALDH7A1
Def
20CNNM2
Def
20KCNT1
Def
20LGI1
Def
20QARS1
Def
20STX1B
Def

Consider

178 genes
20CACNA1A

calcium voltage-gated channel subunit alpha1 A

19CASK
Def
19CHD7
Def
18ADGRV1
Def

adhesion G protein-coupled receptor V1

17CHD2
Def
17GRIA3
Def

glutamate ionotropic receptor AMPA type subunit 3

16TBCE
Mod#2

Hypocalcemic seizures

15ASXL3
Def
15CHD8
Def
15KDM6A
Def
15KMT2D
Def
15MECP2
Def
15MED13L
Def
15NSD1
Def
15POGZ
Def
15SLC6A8
Def
14CACNA2D1
Dis

calcium voltage-gated channel auxiliary subunit alpha2delta 1

14CTCF
Def
14DYRK1A
Def
14NARS1
Mod
14TSC2
SF
13GABRB2
Def

gamma-aminobutyric acid type A receptor subunit beta2

13ALPL
Def
13ARSA
Def
13ASXL1
Def
13ATP7B
DefSF
13BFIS1

Seizures, benign familial infantile, 1

13BFNS1

SEIZURES, BENIGN FAMILIAL NEONATAL, 1; BFNS1

13BFNS2

SEIZURES, BENIGN FAMILIAL NEONATAL, 2; BFNS2

13DOORS

DEAFNESS, ONYCHODYSTROPHY, OSTEODYSTROPHY, IMPAIRED INTELLECTUAL DEVELOPMENT, AND SEIZURES SYNDROME; DOORS

13FEB1

Febrile seizures, familial, 1

13FEB4

FEBRILE SEIZURES, FAMILIAL, 4; FEB4

13FOXG1
Def
13GEFSP1

GENERALIZED EPILEPSY WITH FEBRILE SEIZURES PLUS, TYPE 1; GEFSP1

13GRIN2B
Def
13IKBKG
Def
13PASNA

PRIMARY ALDOSTERONISM, SEIZURES, AND NEUROLOGIC ABNORMALITIES; PASNA

13PIGN
Def
13RPS6KA3
Def
13RTTN
Def
13SLC9A6
Def
13SON
Def
13TCF4
Def
13GRIK2
Def

glutamate ionotropic receptor kainate type subunit 2

12GRIN2A
Def

glutamate ionotropic receptor NMDA type subunit 2A

12AGA
Def
12GFAP
Def
12GRIN1
Def
12MBD5
Def
12TRIO
Def
12UBE3A
Def
12KCNQ3
Def

potassium voltage-gated channel subfamily Q member 3

12CYP27A1
Def
12ALDH5A1
Def

aldehyde dehydrogenase 5 family member A1

12SCN5A
DefSF

sodium voltage-gated channel alpha subunit 5

12CACNA1D
Def

calcium voltage-gated channel subunit alpha1 D

12CACNA1G
Def

calcium voltage-gated channel subunit alpha1 G

12SCN11A
Def

sodium voltage-gated channel alpha subunit 11

12CACNA1F
Def

calcium voltage-gated channel subunit alpha1 F

12CACNA2D4
Def

calcium voltage-gated channel auxiliary subunit alpha2delta 4

12CYP27B1
Def#3

Hypocalcemic seizures

11ADNP
Def
11AHDC1
Def
11BCL11A
Def
11DCX
Def
11DDX3X
Def
11GLI3
Def
11KMT2E
Def
11MEF2C
Def
11NFIX
Def
11SATB2
Def
11CACNA2D2
Mod

calcium voltage-gated channel auxiliary subunit alpha2delta 2

11CACNA1S
ModSF

calcium voltage-gated channel subunit alpha1 S

11COL4A1
Def
11HNRNPU
Def
11IRF2BPL
Def
11MMACHC
Def
11NGLY1
Def
11PAH
Def
11CSNK2A1
Def
10CACNG2
Lim

calcium voltage-gated channel auxiliary subunit gamma 2

10KCND2
Mod
10SNX27
10VPS13A
10GABRA2

gamma-aminobutyric acid type A receptor subunit alpha2

9GABRA5

gamma-aminobutyric acid type A receptor subunit alpha5

9ACAN
Def
9ALPK3
Def
9AP4M1
Def
9ASPM
Def
9ATP1A3
Def
9BLM
Def
9CLCN7
Def
9CORO1A
Def
9EFL1
Def
9EHMT1
Def
9EPM2A
Def
9FA2H
Def
9FANCI
Def
9FUCA1
Def
9GM2A
Def
9HEXB
Def
9IDH2
Def
9IVD
Def
9KCNJ10
Def
9KIF1A
Def
9MMAA
Def
9MMUT
Def
9MTHFR
Def
9MTOR
Def
9MTRR
Def
9PCCA
Def
9PCCB
Def
9PLIN1
Def
9RLBP1
Def
9SETD1B
Def
9SPTBN4
Def
9ST3GAL5
Def
9TBCK
Def
9UBE3B
Def
9VPS33B
Def
9ADPRS
9MDGA2
9PI4KA
9MAPK3
9SCN7A

sodium voltage-gated channel alpha subunit 7

9ARF3

ARF GTPase 3

9SV2A

synaptic vesicle glycoprotein 2A

9CACNA1H

calcium voltage-gated channel subunit alpha1 H

9SCN10A
Dis

sodium voltage-gated channel alpha subunit 10

9CACNA1I

calcium voltage-gated channel subunit alpha1 I

9CACNB3

calcium voltage-gated channel auxiliary subunit beta 3

9CACNG4

calcium voltage-gated channel auxiliary subunit gamma 4

9CACNA2D3

calcium voltage-gated channel auxiliary subunit alpha2delta 3

9CACNB2
Dis

calcium voltage-gated channel auxiliary subunit beta 2

9CACNG1

calcium voltage-gated channel auxiliary subunit gamma 1

9CACNG3

calcium voltage-gated channel auxiliary subunit gamma 3

9CACNG5

calcium voltage-gated channel auxiliary subunit gamma 5

9CACNG6

calcium voltage-gated channel auxiliary subunit gamma 6

9CACNG7

calcium voltage-gated channel auxiliary subunit gamma 7

9DLG4
Def
9ELN
Def
9KANSL1
Def
9NFIA
Def
9SYNGAP1
Def
9WDR26
Def
8HOMER2
Mod
8MESP1
Mod
8PPOX
Str
8RPS17
8SLC6A1
8ATP6V0A2
Def
8CSNK2B
Def
8TCIRG1
Def
8ALDOA
8ASPHD1
8C16ORF54
8CDIPT
8CDIPTOSP
8DOC2A
8FIMP1
8GDPD3
8HIRIP3
8INO80E
8KCTD13
8KCTD13-DT
8KIF22
8MVP-DT
8PAGR1
8PPP4C
8SEZ6L2
8TAOK2
8TBX6
8TLCD3B
8TMEM219
8YPEL3
8YPEL3-DT
8ZG16

Possible

232 genes — click to expand
7MAN2A2
Lim
7POLG
Lim
7ACADM
Def
7ACTB
Def
7AMACR
Def
7AP4B1
Def
7ASL
Def
7BRAF
Def
7CBS
Def
7CPT2
Def
7DHTKD1
Def
7DIAPH1
Def
7DNAJC30
Def
7DNMT3A
Def
7FARS2
Def
7FASTKD2
Def
7FBP1
Def
7FGFR3
Def
7FKTN
Def
7FOLR1
Def
7GAN
Def
7GLB1
Def
7HECW2
Def
7ISCA2
Def
7LMBRD1
Def
7MAGEL2
Def
7MBTPS1
Def
7MN1
Def
7MYRF
Def
7NHLRC1
Def
7NPC1
Def
7NPC2
Def
7PEX26
Def
7PEX3
Def
7PEX6
Def
7PIGT
Def
7PMM2
Def
7PPP2R1A
Def
7PURA
Def
7RNU4ATAC
Def
7SCO2
Def
7SLC19A3
Def
7TRPM3
Def
7TUBGCP6
Def
7TYMP
Def
7UNC80
Def
7VLDLR
Def
7ZMYM2
Def
6ABHD2
6ADAMTSL3
6AGBL1
6AKAP13
6ANPEP
6AP3S2
6ARPIN
6ARPIN-AP3S2
6BNC1
6BTBD1
6C15ORF32
6C15ORF40
6CARMAL
6CEMIP
Dis
6CFAP161
6CIB1
6CPEB1
6CRAT37
6CRTC3
6DET1
6FAM174B
6FSD2
6FURIN
6GDPGP1
6GOLGA6L10
6GOLGA6L4
6GOLGA6L9
6HACE1
6HAPLN3
6HDDC3
6HDGFL3
6IDH2-DT
6IL16
6IQGAP1
6ISG20
6KIF7
6KLHL25
6KRIT1
6MESP2
6MEX3B
6MFGE8
6MRPL46
6MRPS11
6NTRK3
Dis
6PDE8A
6PEX11A
No
6PIRC76
6POLG-DT
6POLGARF
6PPFIBP1
6PRC1
6PRMT7
6RAMAC
6RCCD1
6SAXO2
6SCARNA15
6SEC11A
6SEMA4B
6SH3GL3
6SLC28A1
6SLCO3A1
6SNHG21
6ST8SIA2
6STARD5
6SV2B
6TICRR
6TLNRD1
6TM6SF1
6TMC3
6TRR-TCG1-1
6TTLL13
6UNC45A
6VPS33B-DT
6VPS50
6WDR73
6WDR93
6WHAMM
6ZNF592
6ZNF710
6ZNF774
6ZSCAN2
6GCM2
#9

Hypocalcemic seizures

6PPP1R12A
Str
6PRICKLE1
Lim
6SBF1
Mod
5CLDN16
Def

Hypocalcemic seizures

5MAPK11
5MAPK12
5BCL9
Lim
5CHD1
Lim
5CHD1L
Lim
5GEFSP2

GENERALIZED EPILEPSY WITH FEBRILE SEIZURES PLUS, TYPE 2; GEFSP2

5HOMGSMR1

HYPOMAGNESEMIA, SEIZURES, AND IMPAIRED INTELLECTUAL DEVELOPMENT 1; HOMGSMR1

5MCAHS2

MULTIPLE CONGENITAL ANOMALIES-HYPOTONIA-SEIZURES SYNDROME 2; MCAHS2

5MCAHS3

MULTIPLE CONGENITAL ANOMALIES-HYPOTONIA-SEIZURES SYNDROME 3; MCAHS3

5MRD55

INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 55, WITH SEIZURES; MRD55

5MRD60

INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 60, WITH SEIZURES; MRD60

5NEDHELS

NEURODEVELOPMENTAL DISORDER WITH HYPOTONIA AND IMPAIRED EXPRESSIVE LANGUAGE AND WITH OR WITHOUT SEIZURES; NEDHELS

5OPA10

OPTIC ATROPHY 10 WITH OR WITHOUT ATAXIA, IMPAIRED INTELLECTUAL DEVELOPMENT, AND SEIZURES; OPA10

5ROBO1
Lim
5TNFRSF11A
#7

Hypocalcemic seizures

5SCN9A
Ref

sodium voltage-gated channel alpha subunit 9

4CACNB4
Ref

calcium voltage-gated channel auxiliary subunit beta 4

4ABHD11
4ACP6
4ADM2
4BAZ1B
4BCL7B
4BOLA2B
4BUD23
4C1QTNF3-AMACR
4CHKB-CPT1B
4CHKB-DT
4CIMAP1B
4CLASP1
4CLDN3
4CLDN4
4CLIP2
4CPT1B
No
4DENND6B
4EIF4H
4EMC10
4EPM2A-DT
4FKBP6
4FMO5
Dis
4FZD9
4GJA5
Dis
4GJA8
4GPHRB
4GRM7
4GTF2I
4GTF2IRD1
4HBA-LCR
4HDAC10
4KLHDC7B
4KLHDC7B-DT
4LAT2
4LIMK1
4LMF2
4MAPK8IP2
4MED11
4METTL27
4MLXIPL
4NBPF11
4NCAPH2
4NSUN5
4ODC1
4PI4K2A
4PIEZO2
4PLXNB2
4PPIAL4G
4PPP6R2
4PRKAB2
Dis
4RECQL
Dis
4RFC2
4RNVU1-1
4RNVU1-3
4RNVU1-7
4RNVU1-8
4SELENOO
4SEMA3E
4SLC46A1
4SLX1A
4SLX1A-SULT1A3
4SNHG14
4STX1A
4SULT1A3
4SYCE3
4TANGO2
4TBL2
4TCP1
4TMEM270
4TRH-GTG1-2
4TRH-GTG1-3
4TRH-GTG1-4
4TRIM50
4TRN-GTT9-2
4TRQ-CTG3-2
4TRQ-CTG4-1
4TRQ-CTG7-1
4TSEN2
4TSEN54
4VPS37D
4WASF1

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Data aggregated from HPO/Monarch, ClinVar, OMIM (phenotypes + clinical synopsis), Open Targets, PanelApp, Phen2Gene, and Gene2Phenotype. Click a gene to view full details.