Genes associated with “epilepsy

290 genes foundHPO: Sudden unexpected death in epilepsyOpen Targets: epilepsy21835 ClinVar P/LP variants1 PanelApp panel
Some sources returned errors (2)

omim: Error: OMIM search: 429

omimClinSyn: Error: OMIM CS: 429

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
hover for details

Strong Candidates

82 genes
1
SCN1A

sodium voltage-gated channel alpha subunit 1

62
score
ClinGen: DefinitivePanel: GreenGTR ↑

developmental and epileptic encephalopathy 6B

Frequency
11%
n=9
P/LP Variants
11
OT Score
0.93
2
SCN2A

sodium voltage-gated channel alpha subunit 2

61
score
ClinGen: DefinitivePanel: GreenGTR ↑
Frequency
-
P/LP Variants
149
OT Score
0.90
3
SYNGAP1

synaptic Ras GTPase activating protein 1

59
score
ClinGen: DefinitivePanel: GreenGTR ↑
Frequency
-
P/LP Variants
19
OT Score
0.82
4
SCN8A

sodium voltage-gated channel alpha subunit 8

58
score
ClinGen: DefinitivePanel: GreenGTR ↑

developmental and epileptic encephalopathy, 13

Frequency
0%
n=7
P/LP Variants
7
OT Score
0.90
5
KCNQ2

potassium voltage-gated channel subfamily Q member 2

56
score
ClinGen: DefinitivePanel: GreenGTR ↑
Frequency
-
P/LP Variants
4
OT Score
0.84
6
STXBP1

syntaxin binding protein 1

55
score
ClinGen: DefinitivePanel: GreenGTR ↑
Frequency
-
P/LP Variants
3
OT Score
0.87
7
GRIN2B

glutamate ionotropic receptor NMDA type subunit 2B

53
score
ClinGen: DefinitivePanel: GreenGTR ↑
Frequency
-
P/LP Variants
6
OT Score
0.80
8
GABRA1

gamma-aminobutyric acid type A receptor subunit alpha1

52
score
ClinGen: DefinitivePanel: GreenGTR ↑
Frequency
-
P/LP Variants
4
OT Score
0.89
9
PCDH19

protocadherin 19

51
score
ClinGen: DefinitivePanel: GreenGTR ↑
Frequency
-
P/LP Variants
14
OT Score
0.87
49SCN3A
DefP:G

sodium voltage-gated channel alpha subunit 3

49GRIN2A
DefP:G

glutamate ionotropic receptor NMDA type subunit 2A

49DEPDC5
DefP:G

DEP domain containing 5, GATOR1 subcomplex subunit

49GABRB3
DefP:G

gamma-aminobutyric acid type A receptor subunit beta3

48LGI1
DefP:G

leucine rich glioma inactivated 1

46WWOX
DefP:G

developmental and epileptic encephalopathy, 28

45GABRG2
DefP:G

gamma-aminobutyric acid type A receptor subunit gamma2

45CDKL5
DefP:G

cyclin dependent kinase like 5

45PRRT2
DefP:G

proline rich transmembrane protein 2

45ALDH7A1
DefP:G

aldehyde dehydrogenase 7 family member A1

44KCNT1
DefP:G

potassium sodium-activated channel subfamily T member 1

42GRIN2D
DefP:G

glutamate ionotropic receptor NMDA type subunit 2D

41KCTD7
DefP:G

potassium channel tetramerization domain containing 7

41CHD2
DefP:G

chromodomain helicase DNA binding protein 2

39NBEA
DefP:G
39NPRL3
DefP:G
37SYN1
DefP:G
37ZEB2
DefP:G

zinc finger E-box binding homeobox 2

36DNM1
DefP:G

dynamin 1

36PLCB1
DefP:G

phospholipase C beta 1

36KCNMA1
DefP:G

potassium calcium-activated channel subfamily M alpha 1

35ARX
DefP:G

aristaless related homeobox

35ARHGEF9
DefP:G
35TBC1D24
DefP:G

developmental and epileptic encephalopathy, 16

34SLC12A5
LimP:G

solute carrier family 12 member 5

34GLDC
DefP:G
34GABRB2
DefP:G

gamma-aminobutyric acid type A receptor subunit beta2

33PIGA
DefP:G

phosphatidylinositol glycan anchor biosynthesis class A

33PNKP
DefP:G

polynucleotide kinase 3'-phosphatase

33SPTAN1
DefP:G

spectrin alpha, non-erythrocytic 1

33CNTN2
DefP:G
33SCN1B
DefP:G

sodium voltage-gated channel beta subunit 1

33UBA5
DefP:G

ubiquitin like modifier activating enzyme 5

33SZT2
DefP:G

SZT2 subunit of KICSTOR complex

33PNPO
DefP:G

pyridoxamine 5'-phosphate oxidase

33SCARB2
DefP:G

scavenger receptor class B member 2

33EEF1A2
DefP:G

eukaryotic translation elongation factor 1 alpha 2

33DYRK1A
DefP:G
33NUS1
DefP:G
32CACNA1A
P:G

calcium voltage-gated channel subunit alpha1 A

31CNTNAP2
DefP:G
31GRIN1
DefP:G
31KCNC1
DefP:G
31KCNQ3
DefP:G
30PIGQ
DefP:G
29HNRNPK
Def
29PPP3CA
StrP:G

protein phosphatase 3 catalytic subunit alpha

29EPM2A
DefP:G

EPM2A glucan phosphatase, laforin

29NPRL2
DefP:G
29STX1B
DefP:G
27CSNK2B
DefP:G
27GOSR2
DefP:G
27RORB
DefP:G
27DLG4
Def
27KMT2E
DefP:G
27SLC35A2
DefP:G
27CSTB
DefP:G

cystatin B

27NHLRC1
DefP:G

NHL repeat containing E3 ubiquitin protein ligase 1

25ANK2
DefP:G
25ANKRD17
Def
25CHRNA4
DefP:G
25CHRNB2
DefP:G
25GRIA2
DefP:G
25HNRNPH2
DefP:G
25NEXMIF
DefP:G
25GNAO1
DefP:G

G protein subunit alpha o1

24SLC2A1
DefP:G

solute carrier family 2 member 1

23AFG2A
Def
22RELN
DefP:G
22SLC6A1
P:G
21ARID1B
DefP:G
21SLC6A8
DefP:G
20GABRB1
LimP:G

gamma-aminobutyric acid type A receptor subunit beta1

Consider

59 genes
19DYNC1H1
DefP:G
19GAMT
DefP:G
18CACNA1C
DefP:G
18GABRA2
P:G

gamma-aminobutyric acid type A receptor subunit alpha2

18GABRA5
P:G

gamma-aminobutyric acid type A receptor subunit alpha5

17CLCN4
DefP:G
17EHMT1
DefP:G
16PRICKLE1
LimP:A
16SETD1A
P:G
15MLC1
DefP:G
15ROGDI
DefP:G
15EFTUD2
DefP:G
15FOXG1
DefP:G
15KMT2A
Def
15SETBP1
DefP:G
15SHANK3
Def
15SLC9A6
DefP:G
15TET3
DefP:A
14UNC13A
LimP:A
14HACE1
P:G
14NARS1
Mod
14SUCLG1
ModP:A
13CLPB
LimP:G
13MTR
DefP:A
13RAB3GAP2
DefP:A
13ASAH1
DefP:G
13CEP85L
DefP:G
13GNB1
DefP:G
13HEPACAM
DefP:G
13KCNA1
DefP:G
13NR2F1
Def
13RS1
Def
13SMARCA2
DefP:G
13SMARCC2
DefP:G
12P4HTM
P:G
12PLPBP
P:G
12BICRA
Def
12CHRNA2
LimP:G
11KANSL1
Def
11WDR26
Def
11SLC32A1
P:G

generalized epilepsy with febrile seizures plus, type 12

11SCO2
DefP:A
11USP7
DefP:A
11WDR62
DefP:A
10COL4A2
P:G
10KCNT2
P:G
10STAMBP
P:G
10STRADA
P:G
10TRPM6
P:G
9ADGRV1
DefP:R
9FOXP1
Def
9GATM
DefP:R
9PHF6
Def

Possible

149 genes — click to expand
7SHQ1
P:G

neurodevelopmental disorder with dystonia and seizures

7ACTB
Def
7ARSA
Def
7CSF1R
Def
7DSE
Def
7IVD
Def
7KCNH2
DefSF
7KYNU
Def
7MT-CO3
Def
7MT-ND3
Def
7MT-ND4
Def
7MT-ND5
Def
7MT-TH
Def
7MT-TL2
Def
7MT-TS2
Def
7PLN
DefSF
7RFX6
Def
7RSPH4A
Def
7SCN9A
RefP:R
7SKIC3
Def
7TRDN
DefSF
7TYMP
Def
7CPLX1
P:G

developmental and epileptic encephalopathy, 63

7UBR7
P:G

Li-Campeau syndrome

6FIG4
DefP:R

bilateral parasagittal parieto-occipital polymicrogyria

6CHD1
Lim
6MT-TG
Mod
6MT-TR
Mod
6SBF1
Mod
5GJA1
Lim
5HEY2
Lim
5GUF1
P:A

developmental and epileptic encephalopathy, 40

4CPT1B
No
4PCSK5
Dis
4USP25
Dis

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