Genes associated with “epileptic encephalopathy

246 genes foundHPO: Epileptic encephalopathyOpen Targets: Epileptic encephalopathy14838 ClinVar P/LP variants1 PanelApp panel
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

73 genes
1
SCN2A

sodium voltage-gated channel alpha subunit 2

61
score
ClinGen: DefinitiveP2G #25GTR ↑

developmental and epileptic encephalopathy, 11

Frequency
100%
n=1
P/LP Variants
22
OT Score
0.50
2
KCNQ2

potassium voltage-gated channel subfamily Q member 2

61
score
ClinGen: DefinitiveP2G #8GTR ↑

developmental and epileptic encephalopathy, 7

Frequency
100%
n=1
P/LP Variants
22
OT Score
0.62
3
CHD2

chromodomain helicase DNA binding protein 2

61
score
ClinGen: DefinitiveP2G #27GTR ↑

developmental and epileptic encephalopathy 94

Frequency
-
P/LP Variants
18
OT Score
0.56
4
SCN1A

sodium voltage-gated channel alpha subunit 1

60
score
ClinGen: DefinitiveP2G #20GTR ↑

developmental and epileptic encephalopathy, 6A

Frequency
-
P/LP Variants
46
OT Score
0.51
5
SYNGAP1

synaptic Ras GTPase activating protein 1

59
score
ClinGen: DefinitiveP2G #41GTR ↑

intellectual disability, autosomal dominant 5

Frequency
-
P/LP Variants
22
OT Score
0.45
6
STXBP1

syntaxin binding protein 1

57
score
ClinGen: DefinitiveP2G #40GTR ↑

developmental and epileptic encephalopathy, 4

Frequency
-
P/LP Variants
16
OT Score
0.53
7
SCN8A

sodium voltage-gated channel alpha subunit 8

56
score
ClinGen: DefinitiveP2G #29GTR ↑

developmental and epileptic encephalopathy, 13

Frequency
-
P/LP Variants
15
OT Score
0.53
8
DNM1

dynamin 1

56
score
ClinGen: DefinitiveP2G #36GTR ↑

developmental and epileptic encephalopathy, 31A

Frequency
100%
n=5
P/LP Variants
3
OT Score
0.49
9
GRIN2B

glutamate ionotropic receptor NMDA type subunit 2B

53
score
ClinGen: DefinitiveP2G #4GTR ↑

developmental and epileptic encephalopathy, 27

Frequency
-
P/LP Variants
7
OT Score
0.40
49HNRNPU
Def

developmental and epileptic encephalopathy, 54

49SPTAN1
Def

developmental and epileptic encephalopathy, 5

49GABRB3
Def#16

developmental and epileptic encephalopathy, 43

48KCNA2
Def

developmental and epileptic encephalopathy, 32

48GRIN1
Def#3

developmental and epileptic encephalopathy 101

47GABRA1
Def#11

developmental and epileptic encephalopathy, 19

46KCNB1
Def#15

developmental and epileptic encephalopathy, 26

45GABBR2
Mod#9

developmental and epileptic encephalopathy, 59

developmental and epileptic encephalopathy, 42

44WWOX
Def

developmental and epileptic encephalopathy, 28

44ARHGEF9
Def

developmental and epileptic encephalopathy, 8

43CDKL5
Def

developmental and epileptic encephalopathy, 2

43SYNJ1
Def

developmental and epileptic encephalopathy, 53

43ARX
Def

developmental and epileptic encephalopathy, 1

43SMC1A
Def

structural maintenance of chromosomes 1A

42SLC1A2
Def#14

developmental and epileptic encephalopathy, 41

41DOCK7
Def

developmental and epileptic encephalopathy, 23

40GNAO1
Def#12

developmental and epileptic encephalopathy, 17

40KCNT1
Def

developmental and epileptic encephalopathy, 14

38FGF12
Def

developmental and epileptic encephalopathy, 47

36NRXN1
Def#1

Pitt-Hopkins-like syndrome 2

36CACNA1E
Def#17

developmental and epileptic encephalopathy, 69

36GRIN2D
Def#5

developmental and epileptic encephalopathy, 46

36PLCB1
Def#6

developmental and epileptic encephalopathy, 12

36GABRB2
Def

developmental and epileptic encephalopathy 92

35HCN1
Def

developmental and epileptic encephalopathy, 24

35PIGA
Def

multiple congenital anomalies-hypotonia-seizures syndrome 2

35NUS1
Def

intellectual disability, autosomal dominant 55, with seizures

35GABRG2
Def

developmental and epileptic encephalopathy, 74

35SLC35A2
Def

SLC35A2-congenital disorder of glycosylation

35SZT2
Def

developmental and epileptic encephalopathy, 18

34FRRS1L
Def

developmental and epileptic encephalopathy, 37

34PNKP
Def
30SCN3A
Def

developmental and epileptic encephalopathy, 62

30PPP3CA
Str

developmental and epileptic encephalopathy 91

developmental and epileptic encephalopathy, 25

28PNPO
Def

developmental and epileptic encephalopathy, 3

28CAD
Def

developmental and epileptic encephalopathy, 50

27UBA5
Def

developmental and epileptic encephalopathy, 44

27PCDH19
Def
27MEF2C
Def

neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language

27CACNA2D2
Mod#10

cerebellar atrophy with seizures and variable developmental delay

26BRAT1
Def
26EEF1A2
Def

developmental and epileptic encephalopathy, 33

26KCNH5
Def

developmental and epileptic encephalopathy 112

26KMT2E
Def

O'Donnell-Luria-Rodan syndrome

25SCN1B
Def

developmental and epileptic encephalopathy, 52

25KCNC1
Def
24LGI1
Def
24CYFIP2
Def

developmental and epileptic encephalopathy, 65

24DNM1L
Def

encephalopathy, lethal, due to defective mitochondrial peroxisomal fission 1

24PACS2
Def

developmental and epileptic encephalopathy, 66

23KCNC2
Def

developmental and epileptic encephalopathy 103

23ALG13
Def

ALG13 UDP-N-acetylglucosaminyltransferase subunit

23GRIA2
Def
22UGDH
Dis

developmental and epileptic encephalopathy, 84

22TBC1D24
Def

developmental and epileptic encephalopathy, 16

21ATP1A2
Def
21GAD1
Def
21ITPA
Def
21CACNA1B
Mod#7

neurodevelopmental disorder with seizures and nonepileptic hyperkinetic movements

20GRIN2A
Def
20LINS1
Def

Consider

68 genes

developmental and epileptic encephalopathy, 49

20CUX2
Mod

developmental and epileptic encephalopathy, 67

developmental and epileptic encephalopathy, 48

19ST3GAL3
Mod

developmental and epileptic encephalopathy, 15

developmental and epileptic encephalopathy, 57

18NECAP1
Mod

developmental and epileptic encephalopathy, 21

18GLUL
Mod

developmental and epileptic encephalopathy 116

18ATP6V1A
Lim

developmental and epileptic encephalopathy 93

developmental and epileptic encephalopathy, 60

17GLS
Def#18

developmental and epileptic encephalopathy, 71

16DHDDS
Def

developmental delay and seizures with or without movement abnormalities

16PARS2
Mod

developmental and epileptic encephalopathy, 75

15PIGP
Mod

developmental and epileptic encephalopathy, 55

15CASK
Def
15BOLA3
Def

multiple mitochondrial dysfunctions syndrome 2

developmental and epileptic encephalopathy 102

14GABRB1
Lim#19

developmental and epileptic encephalopathy, 45

developmental and epileptic encephalopathy, 39

gamma-aminobutyric acid type A receptor subunit alpha2

14CLCN4
Def

intellectual disability, X-linked 49

developmental and epileptic encephalopathy, 72

13FLNA
Def

filamin A

13ROGDI
Def

amelocerebrohypohidrotic syndrome

13UBE3A
Def

ubiquitin protein ligase E3A

13ALG9
Def

ALG9-congenital disorder of glycosylation

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 13; DEE13

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 45; DEE45

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 53; DEE53

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 57; DEE57

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 7; DEE7

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 76; DEE76

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 78; DEE78

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 79; DEE79

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 81; DEE81

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 82; DEE82

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 83; DEE83

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 85 WITH OR WITHOUT MIDLINE BRAIN DEFECTS; DEE85

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 86; DEE86

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 90; DEE90

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 93; DEE93

13RS1
Def
13COQ4
Def

neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome

developmental and epileptic encephalopathy, 63

12CARS2
Mod

combined oxidative phosphorylation defect type 27

12FARS2
Def
12SLC2A1
Def

solute carrier family 2 member 1

developmental and epileptic encephalopathy, 38

12AARS1
Def

developmental and epileptic encephalopathy, 29

12TWNK
Def

mitochondrial DNA depletion syndrome 7 (hepatocerebral type)

intellectual disability, autosomal dominant 46

11FCSK
Lim

congenital disorder of glycosylation with defective fucosylation 2

11SIK1
Lim

developmental and epileptic encephalopathy, 30

multiple mitochondrial dysfunctions syndrome 6

10MECP2
Def

methyl-CpG binding protein 2

10SLC12A5
Lim

peptidyl-tRNA hydrolase 1 homolog

10ADSL
Def

adenylosuccinate lyase

developmental and epileptic encephalopathy, 58

developmental and epileptic encephalopathy, 51

9ATP2B2
Def

ATPase plasma membrane Ca2+ transporting 2

developmental and epileptic encephalopathy, 61

9ENG
Def

developmental and epileptic encephalopathy, 40

developmental and epileptic encephalopathy, 70

developmental and epileptic encephalopathy, 73

9TIMM50
Def

translocase of inner mitochondrial membrane 50

Possible

100 genes — click to expand
8PHGDH
Def

phosphoglycerate dehydrogenase

developmental and epileptic encephalopathy 97

7BLM
Def
7EPG5
Def
7HYDIN
Def
7IDH2
Def
7LRSAM1
Def
7NR2F2
Def
7TERT
Def
7VPS33B
Def

ubiquitin specific peptidase 19

developmental and epileptic encephalopathy 108

KINSSHIP syndrome

UDP-glucose pyrophosphorylase 2

potassium channel tetramerization domain containing 3

nucleoporin 214

La ribonucleoprotein 7, transcriptional regulator

WASP family member 1

5ALG10
Lim

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 14; DEE14

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 15; DEE15

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 16; DEE16

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 17; DEE17

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 18; DEE18

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 19; DEE19

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 71; DEE71

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 9; DEE9

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 94; DEE94

5MAN2A2
Lim

tyrosine kinase non receptor 2

5TRIT1
Def

combined oxidative phosphorylation deficiency 35

4PCSK6
No
4HNRNPR
Def

neurodevelopmental disorder with dysmorphic facies and skeletal and brain abnormalities

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