Genes associated with “epileptic encephalopathy”

297 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

81 genes
1
SCN2A →

sodium voltage-gated channel alpha subunit 2

61
score
ClinGen: DefinitiveP2G #25GTR ↑

Epileptic encephalopathy

Frequency
100%
n=1
P/LP Variants
20
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
26
OT Score
0.62
3
CHD2 →

chromodomain helicase DNA binding protein 2

61
score
ClinGen: DefinitiveP2G #27GTR ↑

Epileptic encephalopathy

Frequency
-
P/LP Variants
12
OT Score
0.56
4
SCN1A →

sodium voltage-gated channel alpha subunit 1

60
score
ClinGen: DefinitiveP2G #20GTR ↑

Epileptic encephalopathy

Frequency
-
P/LP Variants
60
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
11
OT Score
0.53
7
SCN8A →

sodium voltage-gated channel alpha subunit 8

56
score
ClinGen: DefinitiveP2G #29GTR ↑

Epileptic encephalopathy

Frequency
-
P/LP Variants
17
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
7
OT Score
0.40
50KCNB1
Def#15

Epileptic encephalopathy

49HNRNPU
Def

Epileptic encephalopathy

49SPTAN1
Def

Epileptic encephalopathy

48GRIN1
Def#3

Epileptic encephalopathy

47GABRA1
Def#11

Epileptic encephalopathy

46KCNA2
Def

Epileptic encephalopathy

46GABRB3
Def#16

Epileptic encephalopathy

46GNAO1
Def#12

Epileptic encephalopathy

44CACNA1A
#2

Epileptic encephalopathy

44WWOX
Def

Epileptic encephalopathy

44ARHGEF9
Def

Epileptic encephalopathy

43CDKL5
Def

Epileptic encephalopathy

43SYNJ1
Def

Epileptic encephalopathy

43PPP3CA
Def

Epileptic encephalopathy

42SLC1A2
Def#14

Epileptic encephalopathy

41DOCK7
Def

Epileptic encephalopathy

40KCNT1
Def

Epileptic encephalopathy

39SMC1A
Def

structural maintenance of chromosomes 1A

38ARX
Def

Epileptic encephalopathy

38FGF12
Def

Epileptic encephalopathy

38GABRB2
Def

Epileptic encephalopathy

37PIGA
Def

Epileptic encephalopathy

36NRXN1
Def#1

Epileptic encephalopathy

36PLCB1
Def#6

Epileptic encephalopathy

35HCN1
Def

Epileptic encephalopathy

35NUS1
Def

Epileptic encephalopathy

35AP3B2
Def

Epileptic encephalopathy

35SLC35A2
Def

Epileptic encephalopathy

34CACNA1E
Def#17

Epileptic encephalopathy

34FRRS1L
Def

Epileptic encephalopathy

34SZT2
Def

Epileptic encephalopathy

34PNKP
Def
33GRIN2D
Def#5

Epileptic encephalopathy

33CAD
Def

Epileptic encephalopathy

33SCN3A
Def

Epileptic encephalopathy

32MEF2C
Def

Epileptic encephalopathy

31EEF1A2
Def

Epileptic encephalopathy

30GABBR2
Mod#9

Epileptic encephalopathy

30GABRG2
Def

Epileptic encephalopathy

28SLC13A5

Epileptic encephalopathy

28PNPO
Def
28SLC25A22
Def

Epileptic encephalopathy

28UGDH
Dis

Epileptic encephalopathy

27UBA5
Def

Epileptic encephalopathy

27BRAT1
Def
27PCDH19
Def
27CACNA2D2
Mod#10

Epileptic encephalopathy

26KCNH5
Def

Epileptic encephalopathy

26KMT2E
Def

Epileptic encephalopathy

25TBC1D24
Def

Epileptic encephalopathy

25SCN1B
Def

Epileptic encephalopathy

25KCNC1
Def
25DENND5A

Epileptic encephalopathy

24LGI1
Def
24CYFIP2
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

21GAD1
Def
21GRIA2
Def
21ITPA
Def
21AP1S2
Def
21CACNA1B
Mod#7

Epileptic encephalopathy

20ATP1A2
Def
20DEPDC5
Def
20FRMPD4
Def
20GRIN2A
Def
20LINS1
Def
20RNU2-2
Str
20TRA2B
Def

Epileptic encephalopathy

Consider

70 genes
20CUX2
Mod

Epileptic encephalopathy

19ST3GAL3
Mod

Epileptic encephalopathy

19CLCN4
Def

Epileptic encephalopathy

18KCNT2

Epileptic encephalopathy

18NECAP1
Mod

Epileptic encephalopathy

18ATP6V1A
Lim

Epileptic encephalopathy

17GLS
Def#18

Epileptic encephalopathy

16DHDDS
Def

Epileptic encephalopathy

16NEUROD2

Epileptic encephalopathy

15PIGP
Mod

Epileptic encephalopathy

15CASK
Def
15BOLA3
Def

Epileptic encephalopathy

14GABRB1
Lim#19

Epileptic encephalopathy

14SLC25A12
Mod

Epileptic encephalopathy

13FLNA
Def

filamin A

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

13DEE67

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 67; DEE67

13DEE69

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 69; DEE69

13DEE7

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 7; DEE7

13DEE70

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 70; DEE70

13DEE71

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 71; DEE71

13DEE72

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 72; DEE72

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
13CNPY3
13COQ4
Def

Epileptic encephalopathy

13CPLX1

Epileptic encephalopathy

12CARS2
Mod

Epileptic encephalopathy

12FARS2
Def
12SLC2A1
Def

solute carrier family 2 member 1

12ARV1

Epileptic encephalopathy

12AARS1
Def

Epileptic encephalopathy

12TWNK
Def

Epileptic encephalopathy

11KCNQ5

Epileptic encephalopathy

11ASPM
Def
11FCSK
Lim

Epileptic encephalopathy

11GLUL
Mod

Epileptic encephalopathy

11SIK1
Lim

Epileptic encephalopathy

11PARS2
Mod

Epileptic encephalopathy

10PMPCB

Epileptic encephalopathy

10MECP2
Def

methyl-CpG binding protein 2

10BAIAP2
10SLC12A5
Lim
10PTRH1

peptidyl-tRNA hydrolase 1 homolog

10ADSL
Def

adenylosuccinate lyase

10NTRK2

Epileptic encephalopathy

9SLC38A3

Epileptic encephalopathy

9MDH2

Epileptic encephalopathy

9ATP2B2
Def

ATPase plasma membrane Ca2+ transporting 2

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

gamma-aminobutyric acid type A receptor subunit alpha2

9GUF1

Epileptic encephalopathy

9PHACTR1

Epileptic encephalopathy

9RNF13

Epileptic encephalopathy

9TIMM50
Def

translocase of inner mitochondrial membrane 50

8UBE3A
Def

ubiquitin protein ligase E3A

Possible

139 genes — click to expand
8PHGDH
Def

phosphoglycerate dehydrogenase

7SLC32A1
7ACTL6B
7ANGPTL3
Def
7BLM
Def
7EPG5
Def
7GPR143
Def
7HYDIN
Def
7IDH2
Def
7LRSAM1
Def
7NR2F2
Def
7RTEL1
Def
7SET
Def
7VPS33B
Def
6CIZ1
6LRRC37A2
6SV2A
6USP19

ubiquitin specific peptidase 19

6IGF1R
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

5DEE1

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 1; DEE1

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

5DMXL2
Lim
5MAN2A2
Lim
5TNK2

tyrosine kinase non receptor 2

5TRIT1
Def

Epileptic encephalopathy

4ACE2
4ACE2-DT
4ADAMTS17
4ALDH1A3
4AMELX
4ARHGAP6
4ARRDC4
4ASB11
4ASB7
4ASB9
4ATP6V0A1
4ATXN3L
4C15ORF32
4CA5B
4CA5BP1-CA5B
4CDK19
4CDK9
4CERS3
4CFAP157
4CHSY1
4CIB1
4CLDN34
4CLTRN
4CNPY3-GNMT
4CRTC3
4CTPS2
4EGFL6
4FAM174B
4FAM9C
4FNDC11
4FURIN
4FZR1
4GARNL3
4GDPGP1
4GEMIN8
4GLRA2
4GMEB2
4GPM6B
4GS1-600G8.3
4HCCS-DT
4HDDC3
4HELZ2
4INE2
4IQGAP1
4LRRC28
4LRRK1
4LYSMD4
4MAGEB17
4MCTP2
4MEF2A
4MOSPD2
4MSL3-DT
4NIBAN2
4NPHP3-ACAD11
4OR4F15
4OR4F6
4PCSK6
No
4PGPEP1L
4PIR-FIGF
4PPDPF
4PRC1
4PRPS2
4PTK6
4RAB9A
4RBBP7
4RCCD1
4REPS2
4RPL12
4S100G
4SELENOS
4SEMA4B
4SH2D3C
4SHROOM2
4SLC2A8
4SLCO3A1
4SNRPA1
4SPATA8
4ST8SIA2
4STMN3
4SV2B
4SYAP1
4TARS3
4TBL1X
4TCEANC
4TLR8
4TM2D3
4TMSB4X
4TOR2A
4TTC16
4TTC23
4TXLNG
4UNC45A
4VEGFD
4WDR74
4WWC3
4ZFHX3
4ZNF710
4ZNF774
4ZNF79
4ZRSR2
4HNRNPR
Def

Epileptic encephalopathy

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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.