Genes associated with “infantile spasms

262 genes foundHPO: Infantile spasmsOpen Targets: infantile spasms2663 ClinVar P/LP variants3 PanelApp panels
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:
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Strong Candidates

18 genes
1
CDKL5

cyclin dependent kinase like 5

40
score
ClinGen: DefinitiveP2G #37GTR ↑

developmental and epileptic encephalopathy, 2

Frequency
60%
n=5
P/LP Variants
17
OT Score
0.86
2
ARX

aristaless related homeobox

38
score
ClinGen: DefinitiveP2G #43GTR ↑

developmental and epileptic encephalopathy, 1

Frequency
100%
n=1
P/LP Variants
21
OT Score
0.81
3
GRIN2B

glutamate ionotropic receptor NMDA type subunit 2B

38
score
ClinGen: DefinitiveP2G #7GTR ↑

developmental and epileptic encephalopathy, 27

Frequency
100%
n=2
P/LP Variants
2
OT Score
0.77
4
SPTAN1

spectrin alpha, non-erythrocytic 1

35
score
ClinGen: DefinitiveP2G #6GTR ↑

developmental delay with or without epilepsy

Frequency
5%
n=21
P/LP Variants
2
OT Score
0.79
5
SCN2A

sodium voltage-gated channel alpha subunit 2

33
score
ClinGen: DefinitiveP2G #39GTR ↑
Frequency
-
P/LP Variants
2
OT Score
0.64
6
SCN1A

sodium voltage-gated channel alpha subunit 1

31
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
127
OT Score
0.51
7
STXBP1

syntaxin binding protein 1

31
score
ClinGen: DefinitiveP2G #19GTR ↑
Frequency
-
P/LP Variants
50
OT Score
0.46
8
GABRB3

gamma-aminobutyric acid type A receptor subunit beta3

28
score
ClinGen: DefinitiveGTR ↑

developmental and epileptic encephalopathy, 43

Frequency
75%
n=4
P/LP Variants
7
OT Score
0.43
9
SCN8A

sodium voltage-gated channel alpha subunit 8

28
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
5
OT Score
0.38
24TSC2
DefSF#1

tuberous sclerosis 2

24KCNQ2
Def

potassium voltage-gated channel subfamily Q member 2

23PLCB1
Def#5

phospholipase C beta 1

23DNM1
Def

developmental and epileptic encephalopathy, 31B

23TBC1D24
Def

TBC1 domain family member 24

22WWOX
Def

WW domain containing oxidoreductase

gamma-aminobutyric acid type A receptor subunit alpha5

20PRRT2
Def

infantile convulsions and choreoathetosis

Consider

78 genes
19OCA2
DefP:G
19SLC9A6
Def
19DEPDC5
Def

developmental and epileptic encephalopathy 111

17TSC1
DefSF#2

tuberous sclerosis 1

gamma-aminobutyric acid type A receptor subunit gamma3

17ST3GAL3
Mod#15

ST3 beta-galactoside alpha-2,3-sialyltransferase 3

15PIGA
Def#20

multiple congenital anomalies-hypotonia-seizures syndrome 2

15PNKP
Def

polynucleotide kinase 3'-phosphatase

14NPRL3
Def

phosphatase and actin regulator 1

14TRPM3
Def

neurodevelopmental disorder with hypotonia, dysmorphic facies, and skeletal anomalies, with or without seizures

microcephaly-capillary malformation syndrome

13SLC2A1
Def

solute carrier family 2 member 1

13ALDH7A1
Def
13IRF2BPL
Def
13MAGEL2
Def
13UBE3A
Def

canopy FGF signaling regulator 3

12KCNH5
Def

developmental and epileptic encephalopathy 112

12RS1
Def

retinoschisin 1

GTP binding elongation factor GUF1

11NR4A2
Def
11GABRG2
Def

developmental and epileptic encephalopathy, 74

11WDR45
Def

WD repeat domain 45

10GCSH
Def

multiple mitochondrial dysfunctions syndrome 7

10SIK1
Lim

salt inducible kinase 1

10UBA5
Def

developmental and epileptic encephalopathy, 44

developmental and epileptic encephalopathy 106

10ABAT
Mod

4-aminobutyrate aminotransferase

10PACS2
Def

phosphofurin acidic cluster sorting protein 2

10ALG13
Def

developmental and epileptic encephalopathy, 36

9PLCG2
P:A
9NTRK2
#18

neurotrophic receptor tyrosine kinase 2

9GABRA1
Def

gamma-aminobutyric acid type A receptor subunit alpha1

9CHD2
Def
9KMT2E
Def
9NSMCE3
Lim
9POGZ
Def
9TCF20
Def
9TJP1
Lim
9GABRB2
Def

gamma-aminobutyric acid type A receptor subunit beta2

9KCNC2
Def

potassium voltage-gated channel subfamily C member 2

9KCNA2
Def

potassium voltage-gated channel subfamily A member 2

9SYNJ1
Def

synaptojanin 1

8NARS1
Mod

Possible

129 genes — click to expand

epilepsy, early-onset, 3, with or without developmental delay

8GABRD
Mod

gamma-aminobutyric acid type A receptor subunit delta

8GNAO1
Def#14

neurodevelopmental disorder with involuntary movements

7TRIM8
Def

focal segmental glomerulosclerosis and neurodevelopmental syndrome

7OTUD7A
Lim

neurodevelopmental disorder with hypotonia and seizures

7ACVRL1
Def
7ASNS
Def
7GAN
Def
7MOGS
Def
7RFX5
Def
7THOC6
Def
7TRPM1
Def
7TRRAP
Def
7CUL3
Def

neurodevelopmental disorder with or without autism or seizures

7GABRB1
Lim

gamma-aminobutyric acid type A receptor subunit beta1

7SMC1A
Def

developmental and epileptic encephalopathy, 85, with or without midline brain defects

glucosamine-6-phosphate deaminase 2

casein kinase 1 epsilon

6CDK5
Mod
6KLF13
Mod

developmental and epileptic encephalopathy, 72

gamma-aminobutyric acid type A receptor subunit epsilon

gamma-aminobutyric acid type A receptor subunit alpha2

gamma-aminobutyric acid type A receptor subunit alpha3

gamma-aminobutyric acid type A receptor subunit alpha4

gamma-aminobutyric acid type A receptor subunit alpha6

gamma-aminobutyric acid type A receptor subunit gamma1

gamma-aminobutyric acid type A receptor subunit pi

gamma-aminobutyric acid type A receptor subunit theta

melanocortin 2 receptor

6NACC1
Def

neurodevelopmental disorder with epilepsy, cataracts, feeding difficulties, and delayed brain myelination

5GNB1
Def

intellectual disability, autosomal dominant 42

5FAN1
Lim
5KCNB1
Def

developmental and epileptic encephalopathy, 26

5DPAGT1
Def

DPAGT1-congenital disorder of glycosylation

5ERCC5
Def

xeroderma pigmentosum group G

4DMXL2
Lim

developmental and epileptic encephalopathy, 81

4GABBR2
Mod

developmental and epileptic encephalopathy, 59

4HCFC1
Def

methylmalonic acidemia with homocystinuria, type cblX

4D2HGDH
Def

D-2-hydroxyglutaric aciduria 1

4EEF1A2
Def

intellectual disability, autosomal dominant 38

4TUBB2A
Def

complex cortical dysplasia with other brain malformations 5

intellectual developmental disorder with severe speech and ambulation defects

developmental and epileptic encephalopathy 93

4CHRNA7
Ref
4SCN9A
Ref
4DOCK7
Def

developmental and epileptic encephalopathy, 23

4TUBG1
Def

complex cortical dysplasia with other brain malformations 4

4RUSC2
Mod

intellectual disability, autosomal recessive 61

4FDXR
Def

multiple mitochondrial dysfunctions syndrome 9b

4TUBB2B
Def

complex cortical dysplasia with other brain malformations 7

4ALG2
Str

ALG2-congenital disorder of glycosylation

4NAXD
Def

NAD(P)HX dehydratase deficiency

4NEDD4L
Def

periventricular nodular heterotopia 7

4NEXMIF
Def

X-linked intellectual disability, Cantagrel type

cortical dysplasia-focal epilepsy syndrome

3SUCLA2
Def

mitochondrial DNA depletion syndrome, encephalomyopathic form with methylmalonic aciduria

3ALG14
Lim

intellectual developmental disorder with epilepsy, behavioral abnormalities, and coarse facies

3CHD3
Def

Snijders Blok-Campeau syndrome

3FBXL4
Def

mitochondrial DNA depletion syndrome 13

3MACF1
Mod

lissencephaly 9 with complex brainstem malformation

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