Genes associated with “infantile spasms”

Diagnostic yield calculator →
275 genes foundHPO: Infantile spasmsOpen Targets: infantile spasms3 PanelApp panels
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

18 genes
1
CDKL5 →

cyclin dependent kinase like 5

43
score
ClinGen: DefinitiveP2G #37GTR ↑

Infantile spasms

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

aristaless related homeobox

41
score
ClinGen: DefinitiveP2G #43GTR ↑

Infantile spasms

Frequency
100%
n=1
P/LP Variants
20
OT Score
0.81
3
39
score
ACMG SFP2G #1GTR ↑

Infantile spasms

Frequency
57%
n=76
P/LP Variants
8
OT Score
-
4
GRIN2B →

glutamate ionotropic receptor NMDA type subunit 2B

38
score
ClinGen: DefinitiveP2G #7GTR ↑

Infantile spasms

Frequency
100%
n=2
P/LP Variants
2
OT Score
0.78
5
SPTAN1 →

spectrin alpha, non-erythrocytic 1

34
score
ClinGen: DefinitiveP2G #6GTR ↑

Infantile spasms

Frequency
5%
n=21
P/LP Variants
2
OT Score
0.79
6
STXBP1 →

syntaxin binding protein 1

31
score
ClinGen: DefinitiveP2G #19GTR ↑
Frequency
-
P/LP Variants
48
OT Score
0.46
7
SCN1A →

sodium voltage-gated channel alpha subunit 1

30
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
133
OT Score
0.48
8
GABRB3 →

gamma-aminobutyric acid type A receptor subunit beta3

29
score
ClinGen: DefinitiveGTR ↑

Infantile spasms

Frequency
75%
n=4
P/LP Variants
6
OT Score
0.52
9
SCN8A →

sodium voltage-gated channel alpha subunit 8

24
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
2
OT Score
0.39
24KCNQ2
Def

potassium voltage-gated channel subfamily Q member 2

23PLCB1
Def#5

phospholipase C beta 1

23WWOX
Def

WW domain containing oxidoreductase

22DNM1
Def

Infantile spasms

22TBC1D24
Def

TBC1 domain family member 24

22GABRA5

gamma-aminobutyric acid type A receptor subunit alpha5

22PAFAH1B1
#3
21TRA2B
Def

Infantile spasms

20PRRT2
Def

Infantile spasms

Consider

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

Infantile spasms

18SCN2A
Def

sodium voltage-gated channel alpha subunit 2

18GABRG3

gamma-aminobutyric acid type A receptor subunit gamma3

17ST3GAL3
Mod#15

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

15PIGA
Def#20

Infantile spasms

15PNKP
Def

polynucleotide kinase 3'-phosphatase

15NPRL3
Def
15TRPM3
Def

Infantile spasms

14PHACTR1

phosphatase and actin regulator 1

14TSC1
SF#2

Infantile spasms

13STAMBP

Infantile spasms

13ALDH7A1
Def
13IRF2BPL
Def
13MAGEL2
Def
13NEDIES

NEURODEVELOPMENTAL DISORDER WITH INFANTILE EPILEPTIC SPASMS; NEDIES

13UBE3A
Def
13ALG13
Def

Infantile spasms

12GUF1
Lim

GTP binding elongation factor GUF1

12KCNH5
Def

Infantile spasms

12RS1
Def

retinoschisin 1

12GABRG2
Def

Infantile spasms

11NR4A2
Def
11WDR45
Def

WD repeat domain 45

11ABAT
Mod

4-aminobutyrate aminotransferase

10GABRA1
Def

gamma-aminobutyric acid type A receptor subunit alpha1

10GCSH
Def

Infantile spasms

10SIK1
Lim

salt inducible kinase 1

10UBA5
Def

Infantile spasms

10GABRB2
Def

gamma-aminobutyric acid type A receptor subunit beta2

10ATP10A
10ATP10A-DT
10HERC2
10MKRN3
10NPAP1
10PWAR1
10PWAR4
10PWAR5
10PWAR6
10PWARSN
10PWRN1
10PWRN2
10PWRN3
10PWRN4
10SNRPN
10SNURF
10SNX27
10TRE-TTC2-2
10NTRK2
#18

neurotrophic receptor tyrosine kinase 2

9PLCG2
P:A
9CYFIP1
9GOLGA6L1
9GOLGA6L2
9GOLGA6L26
9GOLGA8S
9NIPA1
9NIPA2
9TUBGCP5
9CNPY3

canopy FGF signaling regulator 3

9GABRD
Mod

gamma-aminobutyric acid type A receptor subunit delta

9CHD2
Def
9KMT2E
Def
9POGZ
Def
9TCF20
Def
9KCNC2
Def

potassium voltage-gated channel subfamily C member 2

9PACS2
Def

phosphofurin acidic cluster sorting protein 2

8KCNT1
Def

potassium sodium-activated channel subfamily T member 1

8SNAP25
Def

synaptosome associated protein 25

8NARS1
Mod
8TUBA1A
Def

tubulin alpha 1a

8GABRB1
Lim

gamma-aminobutyric acid type A receptor subunit beta1

8GOLGA6L24
8GOLGA8F

Possible

141 genes — click to expand
8ATP6V0C

Infantile spasms

8GNAO1
Def#14

Infantile spasms

7TRIM8
Def

Infantile spasms

7NSMCE3
Lim
7TJP1
Lim
7GABRP

gamma-aminobutyric acid type A receptor subunit pi

7OTUD7A
Lim

Infantile spasms

7GABRE

gamma-aminobutyric acid type A receptor subunit epsilon

7MC2R

melanocortin 2 receptor

7GABRA2

gamma-aminobutyric acid type A receptor subunit alpha2

7GABRA3

gamma-aminobutyric acid type A receptor subunit alpha3

7GABRA4

gamma-aminobutyric acid type A receptor subunit alpha4

7GABRA6

gamma-aminobutyric acid type A receptor subunit alpha6

7GABRG1

gamma-aminobutyric acid type A receptor subunit gamma1

7GABRQ

gamma-aminobutyric acid type A receptor subunit theta

7FAN1
Def
7GAN
Def
7RFX5
Def
7THOC6
Def
7TRPM1
Def
7TRRAP
Def
7CUL3
Def

Infantile spasms

7SMC1A
Def

Infantile spasms

6GNPDA2

glucosamine-6-phosphate deaminase 2

6APBA2
6CUX1
6ENTREP2
6GOLGA6L25
6GOLGA6L7
6GOLGA8G
6GOLGA8M
6HBA-LCR
6KLF9-DT
6LCIIAR
6CDK5
Mod
6CLDN9
Mod
6KLF13
Mod
6SELENBP1
Mod
6SRRM2
6NEUROD2

Infantile spasms

6NR3C1

nuclear receptor subfamily 3 group C member 1

6CNR1

cannabinoid receptor 1

6NACC1
Def

Infantile spasms

5GNB1
Def

Infantile spasms

5ACOGS

AGENESIS OF CORPUS CALLOSUM, CARDIAC, OCULAR, AND GENITAL SYNDROME; ACOGS

5COQ10D8

COENZYME Q10 DEFICIENCY, PRIMARY, 8; COQ10D8

5DEE2

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 2; DEE2

5DEE89

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 89; DEE89

5DEE93

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 93; DEE93

5DEE96

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 96; DEE96

5IDDEBF

INTELLECTUAL DEVELOPMENTAL DISORDER WITH EPILEPSY, BEHAVIORAL ABNORMALITIES, AND COARSE FACIES; IDDEBF

5IDDSSAD

INTELLECTUAL DEVELOPMENTAL DISORDER WITH SEVERE SPEECH AND AMBULATION DEFECTS; IDDSSAD

5NEDBAVC

NEURODEVELOPMENTAL DISORDER WITH BRAIN ANOMALIES AND WITH OR WITHOUT VERTEBRAL OR CARDIAC ANOMALIES; NEDBAVC

5NEDMSC

NEURODEVELOPMENTAL DISORDER WITH MICROCEPHALY, SEIZURES, AND NEONATAL CHOLESTASIS; NEDMSC

5NMOAS

NEUROMUSCULAR OCULOAUDITORY SYNDROME; NMOAS

5YOBELN

YOON-BELLEN NEURODEVELOPMENTAL SYNDROME; YOBELN

5KCNB1
Def

Infantile spasms

5SPOUT1

Infantile spasms

5ARFGEF1
Def

Infantile spasms

5DPAGT1
Def

Infantile spasms

5ERCC5
Def

Infantile spasms

4DMXL2
Lim

Infantile spasms

4GABBR2
Mod

Infantile spasms

4HCFC1
Def

Infantile spasms

4D2HGDH
Def

Infantile spasms

4EEF1A2
Def

Infantile spasms

4TUBB2A
Def

Infantile spasms

4ACTL6B

Infantile spasms

4ATP6V1A
Lim

Infantile spasms

4AMDHD2
4ANO4
4ARHGAP11B
4ARHGAP11B-DT
4ATMIN
4BCO1
4BICDL2
4C16ORF46
4CCDC82
4CDYL2
4CEMP1
4CENPN
4CHRFAM7A
4CHRNA7
Ref
4CLDN6
4CMC2
4DEAF1
4DYNLRB2
4FLYWCH1
4FLYWCH2
4GOLGA8H
4GOLGA8J
4GOLGA8Q
4GOLGA8R
4GOLGA8T
4HCFC1R1
4IL32
4KCTD5
4KREMEN2
4MMP25
4MTMR10
4NOA3
4NPHP3-ACAD11
4PAQR4
4PDPK1
4PKD1L2
4PKMYT1
4PRR14L
4PRSS21
4PRSS22
4PRSS27
4PRSS33
4PRSS41
4PSMB4
4REPS2
4TBC1D7-LOC100130357
4TNFRSF12A
4TUFT1
4UGP2
4YWHAE
4YWHAH
4ZG16B
4ZP2
4ZSCAN10
4DOCK7
Def

Infantile spasms

4TUBG1
Def

Infantile spasms

4RUSC2
Mod

Infantile spasms

4FDXR
Def

Infantile spasms

4TUBB2B
Def

Infantile spasms

4ALG2
Str

Infantile spasms

4KLHL20
Mod

Infantile spasms

4NAXD
Def

Infantile spasms

4NEDD4L
Def

Infantile spasms

4NEXMIF
Def

Infantile spasms

4CDH2
Def

Infantile spasms

4CNTNAP2
Def

Infantile spasms

3SUCLA2
Def

Infantile spasms

3ALG14
Lim

Infantile spasms

3SPTBN1
Def

Infantile spasms

3CHD3
Def

Infantile spasms

3FBXL4
Def

Infantile spasms

3MACF1
Mod

Infantile spasms

Related phenotype searches

Intellectual disabilityGlobal developmental delaySpeech/language delayNeurodegenerationDevelopmental regressionSeizuresEpileptic encephalopathyStatus epilepticus

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