Genes associated with “epileptic encephalopathy”

Diagnostic yield calculator →
282 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

82 genes
1
SCN2A →

sodium voltage-gated channel alpha subunit 2

62
score
ClinGen: DefinitiveP2G #25GTR ↑

Epileptic encephalopathy

Frequency
100%
n=1
P/LP Variants
26
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
29
OT Score
0.61
3
CHD2 →

chromodomain helicase DNA binding protein 2

61
score
ClinGen: DefinitiveP2G #27GTR ↑

Epileptic encephalopathy

Frequency
-
P/LP Variants
11
OT Score
0.56
4
SCN1A →

sodium voltage-gated channel alpha subunit 1

60
score
ClinGen: DefinitiveP2G #20GTR ↑

Epileptic encephalopathy

Frequency
-
P/LP Variants
55
OT Score
0.51
5
SYNGAP1 →

synaptic Ras GTPase activating protein 1

59
score
ClinGen: DefinitiveP2G #41GTR ↑

Epileptic encephalopathy

Frequency
-
P/LP Variants
17
OT Score
0.45
6
STXBP1 →

syntaxin binding protein 1

57
score
ClinGen: DefinitiveP2G #40GTR ↑

Epileptic encephalopathy

Frequency
-
P/LP Variants
9
OT Score
0.53
7
SCN8A →

sodium voltage-gated channel alpha subunit 8

56
score
ClinGen: DefinitiveP2G #29GTR ↑

Epileptic encephalopathy

Frequency
-
P/LP Variants
16
OT Score
0.53
8
DNM1 →

dynamin 1

56
score
ClinGen: DefinitiveP2G #36GTR ↑

Epileptic encephalopathy

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 ↑

Epileptic encephalopathy

Frequency
-
P/LP Variants
8
OT Score
0.40
50KCNB1
Def#15

Epileptic encephalopathy

49SPTAN1
Def

Epileptic encephalopathy

49HNRNPU
Def

Epileptic encephalopathy

49GABRB3
Def#16

Epileptic encephalopathy

46GNAO1
Def#12

Epileptic encephalopathy

45PPP3CA
Def

Epileptic encephalopathy

44CACNA1A
#2

Epileptic encephalopathy

44WWOX
Def

Epileptic encephalopathy

44KCNA2
Def

Epileptic encephalopathy

44SYNJ1
Def

Epileptic encephalopathy

44ARHGEF9
Def

Epileptic encephalopathy

43CDKL5
Def

Epileptic encephalopathy

43AP3B2
Def

Epileptic encephalopathy

42SLC1A2
Def#14

Epileptic encephalopathy

41DOCK7
Def

Epileptic encephalopathy

41SMC1A
Def

structural maintenance of chromosomes 1A

40KCNT1
Def

Epileptic encephalopathy

39GABBR2
Mod#9

Epileptic encephalopathy

38FGF12
Def

Epileptic encephalopathy

38PLCB1
Def#6

Epileptic encephalopathy

38GABRB2
Def

Epileptic encephalopathy

38GABRA1
Def#11

Epileptic encephalopathy

37ARX
Def

Epileptic encephalopathy

36NRXN1
Def#1

Epileptic encephalopathy

36GRIN1
Def#3

Epileptic encephalopathy

35HCN1
Def

Epileptic encephalopathy

35CAD
Def

Epileptic encephalopathy

35KCNT2
Def

Epileptic encephalopathy

35PIGA
Def

Epileptic encephalopathy

35NUS1
Def

Epileptic encephalopathy

35GABRG2
Def

Epileptic encephalopathy

34PNKP
Def
33SLC25A22
Def

Epileptic encephalopathy

33CACNA1E
Def#17

Epileptic encephalopathy

33FRRS1L
Def

Epileptic encephalopathy

33SCN3A
Def

Epileptic encephalopathy

32MEF2C
Def

Epileptic encephalopathy

31SZT2
Def

Epileptic encephalopathy

31EEF1A2
Def

Epileptic encephalopathy

30SLC35A2
Def

Epileptic encephalopathy

29CYFIP2
Def

Epileptic encephalopathy

28SLC13A5

Epileptic encephalopathy

28GRIN2D
Def#5

Epileptic encephalopathy

28PNPO
Def
28UGDH
Dis

Epileptic encephalopathy

27UBA5
Def

Epileptic encephalopathy

27NPRL3
Def
27PCDH19
Def
27CACNA2D2
Mod#10

Epileptic encephalopathy

26BRAT1
Def
26KMT2E
Def

Epileptic encephalopathy

25SCN1B
Def

Epileptic encephalopathy

25KCNC1
Def
25DENND5A

Epileptic encephalopathy

24TBC1D24
Def

Epileptic encephalopathy

24ADAM22
Def

Epileptic encephalopathy

24DNM1L
Def

Epileptic encephalopathy

24PACS2
Def

Epileptic encephalopathy

23KCNC2
Def

Epileptic encephalopathy

23ALG13
Def

ALG13 UDP-N-acetylglucosaminyltransferase subunit

23ITPA
Def
22FLNA
Def

filamin A

21AP1S2
Def
21CACNA1B
Mod#7

Epileptic encephalopathy

21KCNH5
Def

Epileptic encephalopathy

20ATP1A2
Def
20CSNK2B
Def
20DEPDC5
Def
20FRMPD4
Def
20GRIA2
Def
20GRIN2A
Def
20RNU2-2
Str
20TRA2B
Def

Epileptic encephalopathy

Consider

67 genes
19ST3GAL3
Mod

Epileptic encephalopathy

19CLCN4
Def

Epileptic encephalopathy

18NECAP1
Mod

Epileptic encephalopathy

17ARV1

Epileptic encephalopathy

17GLS
Def#18

Epileptic encephalopathy

17AARS1
Def

Epileptic encephalopathy

16DHDDS
Def

Epileptic encephalopathy

15PIGP
Mod

Epileptic encephalopathy

15MECP2
Def

methyl-CpG binding protein 2

15CASK
Def
15BOLA3
Def

Epileptic encephalopathy

15CUX2
Mod

Epileptic encephalopathy

14GABRB1
Lim#19

Epileptic encephalopathy

14SLC25A12
Mod

Epileptic encephalopathy

14NEUROD2

Epileptic encephalopathy

13ROGDI
Def

Epileptic encephalopathy

13UBE3A
Def

ubiquitin protein ligase E3A

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

13DEE58

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 58; DEE58

13DEE59

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 59; DEE59

13DEE60

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 60; DEE60

13DEE61

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 61; DEE61

13DEE7

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 7; DEE7

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

13DEE92

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 92; DEE92

13DEE93

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 93; DEE93

13RS1
Def
13ATP6V1A
Lim

Epileptic encephalopathy

13COQ4
Def

Epileptic encephalopathy

13CPLX1

Epileptic encephalopathy

12CARS2
Mod

Epileptic encephalopathy

12FARS2
Def
12SLC2A1
Def

solute carrier family 2 member 1

12TWNK
Def

Epileptic encephalopathy

11KCNQ5

Epileptic encephalopathy

11FCSK
Lim

Epileptic encephalopathy

11SIK1
Lim

Epileptic encephalopathy

11PARS2
Mod

Epileptic encephalopathy

11GUF1
Lim

Epileptic encephalopathy

10PMPCB

Epileptic encephalopathy

10MDGA2
10SLC12A5
Lim
10ADSL
Def

adenylosuccinate lyase

10CELF2

Epileptic encephalopathy

10NTRK2

Epileptic encephalopathy

9ASPM
Def
9ATP1A3
Def
9SLC38A3

Epileptic encephalopathy

9MDH2

Epileptic encephalopathy

9ATP2B2
Def

ATPase plasma membrane Ca2+ transporting 2

9FANCB
Def
9L1CAM
Def
9MID1
Def
9MSL3
Def
9NHS
Def
9OFD1
Def
9GABRA2

gamma-aminobutyric acid type A receptor subunit alpha2

9PHACTR1

Epileptic encephalopathy

9RNF13

Epileptic encephalopathy

9TIMM50
Def

translocase of inner mitochondrial membrane 50

Possible

127 genes — click to expand
8PHGDH
Def

phosphoglycerate dehydrogenase

7GABRA5
7ANGPTL3
Def
7EPG5
Def
7GPR143
Def
7HCFC1
Def
7HYDIN
Def
7MAGEL2
Def
7NAA10
Def
7OCA2
Def
7OPN1LW
Def
7OPN1MW
Def
7PIGS
Def
7RTEL1
Def
7SET
Def
7GLUL
Mod

Epileptic encephalopathy

6CIZ1
6USP19

ubiquitin specific peptidase 19

6AVPR2
6CHD1
Lim
6TLR7
Mod
6TRAPPC2
6MAST3

Epileptic encephalopathy

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

5DEE14

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 14; DEE14

5DEE15

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 15; DEE15

5DEE16

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 16; DEE16

5DEE17

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 17; DEE17

5DEE18

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 18; DEE18

5DEE4

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 4; DEE4

5DEE71

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 71; DEE71

5DEE94

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 94; DEE94

5DMXL2
Lim
5PTRH1

peptidyl-tRNA hydrolase 1 homolog

5TNK2

tyrosine kinase non receptor 2

5TRIT1
Def

Epileptic encephalopathy

4ACE2
4ACE2-DT
4AMELX
4ARHGAP4
4ARHGAP6
4ASB11
4ASB9
4ATP10A
4ATP10A-DT
4ATXN3L
4CA5B
4CA5BP1-CA5B
4CLDN34
4CLTRN
4CTPS2
4CYFIP1
4DALRD3
4EGFL6
4FAM9C
4FNDC11
4GABRG3
4GEMIN8
4GLRA2
4GMEB2
4GOLGA6L1
4GOLGA6L2
4GOLGA6L26
4GOLGA8S
4GPM6B
4GS1-600G8.3
4HBA-LCR
4HCCS-DT
4HELZ2
4HERC2
4INE2
4IRAK1
4MAGEB17
4MKRN3
4MOSPD2
4MSL3-DT
4NIPA1
4NIPA2
4NPAP1
4NPHP3-ACAD11
4OPN1MW2
4OPN1MW3
4OPSIN-LCR
4PIR-FIGF
4PPDPF
4PRPS2
4PTK6
4PTPN23
4PWAR1
4PWAR4
4PWAR5
4PWAR6
4PWARSN
4PWRN1
4PWRN2
4PWRN3
4PWRN4
4RAB9A
4RBBP7
4RENBP
4REPS2
4S100G
4SHROOM2
4SNRPN
4SNURF
4STMN3
4SYAP1
4TBL1X
4TCEANC
4TEX28
4TKTL1
4TLR8
4TMEM187
4TMSB4X
4TRAK1
4TRE-TTC2-2
4TUBGCP5
4TXLNG
4VEGFD
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.