Genes associated with “epileptic encephalopathy”

Diagnostic yield calculator →
347 genes foundHPO: Epileptic encephalopathyOpen Targets: Epileptic encephalopathy1 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:
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Strong Candidates

90 genes
1
SCN2A →

sodium voltage-gated channel alpha subunit 2

62
score
ClinGen: DefinitiveP2G #25GTR ↑

Epileptic encephalopathy

Frequency
100%
n=1
P/LP Variants
31
OT Score
0.50
2
KCNQ2 →

potassium voltage-gated channel subfamily Q member 2

61
score
ClinGen: DefinitiveP2G #8GTR ↑

Epileptic encephalopathy

Frequency
100%
n=1
P/LP Variants
41
OT Score
0.61
3
CHD2 →

chromodomain helicase DNA binding protein 2

61
score
ClinGen: DefinitiveP2G #27GTR ↑

Epileptic encephalopathy

Frequency
-
P/LP Variants
5
OT Score
0.56
4
SCN1A →

sodium voltage-gated channel alpha subunit 1

60
score
ClinGen: DefinitiveP2G #20GTR ↑

Epileptic encephalopathy

Frequency
-
P/LP Variants
43
OT Score
0.51
5
SYNGAP1 →

synaptic Ras GTPase activating protein 1

59
score
ClinGen: DefinitiveP2G #41GTR ↑

Epileptic encephalopathy

Frequency
-
P/LP Variants
16
OT Score
0.45
6
STXBP1 →

syntaxin binding protein 1

57
score
ClinGen: DefinitiveP2G #40GTR ↑

Epileptic encephalopathy

Frequency
-
P/LP Variants
10
OT Score
0.53
7
SCN8A →

sodium voltage-gated channel alpha subunit 8

56
score
ClinGen: DefinitiveP2G #29GTR ↑

Epileptic encephalopathy

Frequency
-
P/LP Variants
13
OT Score
0.53
8
DNM1 →

dynamin 1

54
score
ClinGen: DefinitiveP2G #36GTR ↑

Epileptic encephalopathy

Frequency
100%
n=5
P/LP Variants
2
OT Score
0.49
9
GRIN2B →

glutamate ionotropic receptor NMDA type subunit 2B

53
score
ClinGen: DefinitiveP2G #4GTR ↑

Epileptic encephalopathy

Frequency
-
P/LP Variants
10
OT Score
0.40
50GABRB3
Def#16

Epileptic encephalopathy

50KCNB1
Def#15

Epileptic encephalopathy

49HNRNPU
Def

Epileptic encephalopathy

48GRIN1
Def#3

Epileptic encephalopathy

47GABRA1
Def#11

Epileptic encephalopathy

46KCNA2
Def

Epileptic encephalopathy

46GNAO1
Def#12

Epileptic encephalopathy

45PPP3CA
Def

Epileptic encephalopathy

45CACNA1A
#2

Epileptic encephalopathy

44WWOX
Def

Epileptic encephalopathy

44SYNJ1
Def

Epileptic encephalopathy

44ARHGEF9
Def

Epileptic encephalopathy

43CAD
Def

Epileptic encephalopathy

42SLC1A2
Def#14

Epileptic encephalopathy

42SMC1A
Def

structural maintenance of chromosomes 1A

40DOCK7
Def

Epileptic encephalopathy

40KCNT1
Def

Epileptic encephalopathy

39GABBR2
Mod#9

Epileptic encephalopathy

39SPTAN1
Def

Epileptic encephalopathy

38ARX
Def

Epileptic encephalopathy

38FGF12
Def

Epileptic encephalopathy

38GABRB2
Def

Epileptic encephalopathy

37GABRG2
Def

Epileptic encephalopathy

37AP3B2
Def

Epileptic encephalopathy

36NRXN1
Def#1

Epileptic encephalopathy

36MEF2C
Def

Epileptic encephalopathy

36CACNA1E
Def#17

Epileptic encephalopathy

36PLCB1
Def#6

Epileptic encephalopathy

36SCN3A
Def

Epileptic encephalopathy

35CDKL5
Def

Epileptic encephalopathy

35HCN1
Def

Epileptic encephalopathy

35SLC25A22
Def

Epileptic encephalopathy

35KCNT2
Def

Epileptic encephalopathy

35PIGA
Def

Epileptic encephalopathy

35NUS1
Def

Epileptic encephalopathy

33CYFIP2
Def

Epileptic encephalopathy

33SZT2
Def

Epileptic encephalopathy

31EEF1A2
Def

Epileptic encephalopathy

31CLCN4
Def

Epileptic encephalopathy

30SLC35A2
Def

Epileptic encephalopathy

28KCNC2
Def

Epileptic encephalopathy

28GRIN2D
Def#5

Epileptic encephalopathy

28PNPO
Def
28BRAT1
Def
28UGDH
Dis

Epileptic encephalopathy

28PNKP
Def
27NPRL3
Def
27NR4A2
Def
27PCDH19
Def
27TBR1
Def
26SLC13A5

Epileptic encephalopathy

26KMT2E
Def

Epileptic encephalopathy

25TBC1D24
Def

Epileptic encephalopathy

25SCN1B
Def

Epileptic encephalopathy

25UBA5
Def

Epileptic encephalopathy

25KCNC1
Def
25DENND5A

Epileptic encephalopathy

24DEPDC5
Def
24ITPA
Def
24ADAM22
Def

Epileptic encephalopathy

24FRRS1L
Def

Epileptic encephalopathy

24PACS2
Def

Epileptic encephalopathy

23ALG13
Def

ALG13 UDP-N-acetylglucosaminyltransferase subunit

23ATP1A2
Def
22GLS
Def#18

Epileptic encephalopathy

21GRIA2
Def
21AP1S2
Def
21CNKSR2
Def
21CACNA1B
Mod#7

Epileptic encephalopathy

21KCNH5
Def

Epileptic encephalopathy

20CSNK2B
Def
20FRMPD4
Def
20MBD5
Def
20PIGQ
Def
20PLPBP
Def
20PURA
Def
20RNU2-2
Str
20SLC4A10
Str
20TANC2
Def
20TRA2B
Def

Epileptic encephalopathy

20UNC13A
Def

Epileptic encephalopathy

Consider

74 genes
20CUX2
Mod

Epileptic encephalopathy

19ST3GAL3
Mod

Epileptic encephalopathy

19SLC25A12
Mod

Epileptic encephalopathy

19AARS1
Def

Epileptic encephalopathy

19MECP2
Def

methyl-CpG binding protein 2

18FLNA
Def

filamin A

18NECAP1
Mod

Epileptic encephalopathy

18SLC2A1
Def

solute carrier family 2 member 1

17ARV1

Epileptic encephalopathy

17CACNA2D2
Mod#10

Epileptic encephalopathy

16DHDDS
Def

Epileptic encephalopathy

16KCNQ5

Epileptic encephalopathy

16NEUROD2

Epileptic encephalopathy

15UBE3A
Def

ubiquitin protein ligase E3A

15PIGP
Mod

Epileptic encephalopathy

15CASK
Def
15BOLA3
Def

Epileptic encephalopathy

14MDH2

Epileptic encephalopathy

14GABRB1
Lim#19

Epileptic encephalopathy

14PHACTR1

Epileptic encephalopathy

14RNF13

Epileptic encephalopathy

13ROGDI
Def

Epileptic encephalopathy

13ALG9
Def

Epileptic encephalopathy

13DEE13

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 13; DEE13

13DEE45

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 45; DEE45

13DEE53

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 53; DEE53

13DEE57

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 57; DEE57

13DEE7

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 7; DEE7

13DEE71

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 71; DEE71

13DEE72

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 72; DEE72

13DEE73

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 73; DEE73

13DEE74

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 74; DEE74

13DEE75

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 75; DEE75

13DEE76

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 76; DEE76

13DEE85

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

13DEE86

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 86; DEE86

13DEE90

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 90; DEE90

13DEE93

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 93; DEE93

13RS1
Def
13ATP6V1A
Lim

Epileptic encephalopathy

13COQ4
Def

Epileptic encephalopathy

13CELF2

Epileptic encephalopathy

13CPLX1

Epileptic encephalopathy

12CARS2
Mod

Epileptic encephalopathy

12NSRP1
Mod
12TWNK
Def

Epileptic encephalopathy

11FCSK
Lim

Epileptic encephalopathy

11SIK1
Lim

Epileptic encephalopathy

11PARS2
Mod

Epileptic encephalopathy

11MAST3

Epileptic encephalopathy

11GUF1
Lim

Epileptic encephalopathy

10PMPCB

Epileptic encephalopathy

10MDGA2
10ADSL
Def

adenylosuccinate lyase

10NTRK2

Epileptic encephalopathy

9GABRA5
9ASPM
Def
9ATP1A3
Def
9OCA2
Def
9PIGS
Def
9SLC38A3

Epileptic encephalopathy

9ATP2B2
Def

ATPase plasma membrane Ca2+ transporting 2

9ADNP
Def
9AVPR2
Def
9BCOR
Def
9FANCB
Def
9L1CAM
Def
9MID1
Def
9MSL3
Def
9NHS
Def
9OFD1
Def
9GABRA2

gamma-aminobutyric acid type A receptor subunit alpha2

9KCNMA1
Def

potassium calcium-activated channel subfamily M alpha 1

9TIMM50
Def

translocase of inner mitochondrial membrane 50

Possible

176 genes — click to expand
8PHGDH
Def

phosphoglycerate dehydrogenase

7KCNJ3
7DMXL2
Lim
7ACTC1
DefSF
7ACTL6B
7ACVR1
Def
7ANGPTL3
Def
7EPG5
Def
7FARS2
Def
7GPR143
Def
7HCFC1
Def
7HIBCH
Def
7HYDIN
Def
7IRF2BPL
Def
7KIF1A
Def
7MAGEL2
Def
7NAA10
Def
7OPN1LW
Def
7OPN1MW
Def
7RNASEH2B
Def
7RTEL1
Def
7SET
Def
7TFR2
Def
7WARS2
Def
7GLUL
Mod

Epileptic encephalopathy

6ATP10A
6ATP10A-DT
6FSD1L
6GABRG3
6HERC2
6NPAP1
6PWAR1
6PWAR4
6PWAR5
6PWAR6
6PWARSN
6PWRN1
6PWRN2
6PWRN3
6PWRN4
6SNRPN
6SNURF
6TRE-TTC2-2
6USP19

ubiquitin specific peptidase 19

6BAZ2B
Lim
6CHD1
Lim
6RASA1
Dis
6RYR3
Lim
6TLR7
Mod
6TRAPPC2
6AFF3

Epileptic encephalopathy

6UGP2

UDP-glucose pyrophosphorylase 2

6KCTD3

potassium channel tetramerization domain containing 3

6NUP214

nucleoporin 214

5LARP7

La ribonucleoprotein 7, transcriptional regulator

5WASF1

WASP family member 1

5DEE11

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 11; DEE11

5DEE12

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 12; DEE12

5DEE39

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 39 WITH LEUKODYSTROPHY; DEE39

5DEE4

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 4; DEE4

5DEE5

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 5; DEE5

5TRIT1
Def

Epileptic encephalopathy

4ACE2
4ACE2-DT
4ACVR1C
4AMELX
4ARHGAP4
4ARHGAP6
4ARL6IP6
4ASB11
4ASB9
4ATP6V0A1
4ATXN3L
4CA5B
4CA5BP1-CA5B
4CCDC148
4CD302
4CIZ1
4CLDN34
4CLTRN
4COX7C
4CRE1
4CTPS2
4CYFIP1
4CYTIP
4DALRD3
4DAPL1
4DIAPH2
4DPP4
4EDIL3
4EDIL3-DT
4EGFL6
4FAM133A
4FAM9C
4FNDC11
4GALNT13
4GALNT5
4GEMIN8
4GJD2-DT
4GLRA2
4GMEB2
4GOLGA6L1
4GOLGA6L2
4GOLGA6L24
4GOLGA6L25
4GOLGA6L26
4GOLGA8F
4GOLGA8G
4GOLGA8S
4GPD2
4GPM6B
4GS1-600G8.3
4HAPLN1
4HBA-LCR
4HCCS-DT
4HELZ2
4HID1
4INE2
4IRAK1
4ITGB6
4KCNQ5-DT
4LY75
4LY75-CD302
4MAGEB17
4MARCHF7
4MKRN3
4MOSPD2
4MSL3-DT
4MYRACL
4NAP1L3
4NCAM1
4NIPA1
4NIPA2
4OPN1MW2
4OPN1MW3
4OPSIN-LCR
4PCDH11X
4PIR-FIGF
4PKP4
4PLA2R1
4PPDPF
4PRPS2
4PSMD14
4PTK6
4PTPN23
4RAB9A
4RBBP7
4RBMS1
4RENBP
4REPS2
4RPA4
4S100G
4SEPSECS
4SHROOM2
4STMN3
4SYAP1
4TANC1
4TBC1D7-LOC100130357
4TBL1X
4TCEANC
4TEX28
4TKTL1
4TLR8
4TMEM161B
4TMEM161B-DT
4TMEM187
4TMSB4X
4TRAK1
4TUBGCP5
4TXLNG
4UPP2
4VEGFD
4WDSUB1
4WWC3
4ZRSR2
4HNRNPR
Def

Epileptic encephalopathy

Related phenotype searches

Intellectual disabilityGlobal developmental delaySpeech/language delayNeurodegenerationDevelopmental regressionSeizuresStatus epilepticusInfantile spasms

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