Genes associated with “hypotonia”

Diagnostic yield calculator →
756 genes foundHPO: HypotoniaOpen Targets: Hypotonia
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
hover for details

Strong Candidates

19 genes
1
EBF3 →

EBF transcription factor 3

50
score
ClinGen: DefinitiveGTR ↑

Generalized hypotonia

Frequency
100%
n=8
P/LP Variants
4
OT Score
0.49
2
POLR2A →

RNA polymerase II subunit A

44
score
ClinGen: DefinitiveGTR ↑

Frog-leg posture

Frequency
67%
n=15
P/LP Variants
4
OT Score
0.37
3
AHDC1 →

AT-hook DNA binding motif containing 1

28
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
7
OT Score
0.51
4
27
score
ClinGen: DefinitiveP2G #30GTR ↑
Frequency
-
P/LP Variants
8
OT Score
-
5
27
score
ClinGen: DefinitiveP2G #6GTR ↑
Frequency
-
P/LP Variants
5
OT Score
-
6
GNB1 →

G protein subunit beta 1

26
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
1
OT Score
0.54
7
USP7 →

ubiquitin specific peptidase 7

24
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
3
OT Score
0.34
8
24
score
ClinGen: DefinitiveP2G #42GTR ↑
Frequency
-
P/LP Variants
5
OT Score
-
9
24
score
ClinGen: DefinitiveP2G #43GTR ↑
Frequency
-
P/LP Variants
13
OT Score
-
22CASK
Def

Hypotonia

22PURA
Def

purine rich element binding protein A

22GRIN2B
Def
22UNC80
Def
22RAI1
Def
21SPTBN4
Def
21PLA2G6
Def
21SHANK3
Def
21SURF1
Def
20KANSL1
Def

Consider

213 genes
20TNPO2

transportin 2

19ARSA
Def
19SCO2
Def
19ELN
Def
19INPP5E
Def#11

Generalized hypotonia

19FKTN
Def

Hypotonia

19PEX3
Def#7
18UBE3A
Def#18

Generalized hypotonia

18CEP290
Def

centrosomal protein 290

18TMEM67
Def

transmembrane protein 67

18PEX6
Def#13
18PEX1
Def#14
18DOCK3

dedicator of cytokinesis 3

18PLOD1

procollagen-lysine,2-oxoglutarate 5-dioxygenase 1

17TMEM216
Def

Hypotonia

17PEX26
Def
17PEX14
Def
16FGFR3
Def#2

Floppy infant

16ATP6V0A2
Def
16AP4M1
Def

Hypotonia

16PEX10
Def#12

Hypotonia

16PPP2CA
Def

protein phosphatase 2 catalytic subunit alpha

15GALE
Def

Generalized hypotonia

15ALG12
Def
15PPP2R1A
Def
15MED12
Def
15ASXL3
Def
15CHD8
Def
15CNOT1
Def
15CTCF
Def
15KMT2A
Def
15MED13L
Def
15POGZ
Def
15SLC6A8
Def
14SUCLA2
Def

Hypotonia

14CTNNB1
Def
14DDX3X
Def
14FOXG1
Def
14NR2F1
Def
14SATB2
Def
14DDC
Def

dopa decarboxylase

14GRM7

glutamate metabotropic receptor 7

14TBCK
Def

Severe muscular hypotonia

14SLC19A3
Def
14PIGN
Def

Hypotonia

14POMT2
Def

Neonatal hypotonia

14RAB3GAP1
Def

Hypotonia

14GAA
DefSF
13LAMA2
Def

Hypotonia

13ADNP
Def
13ARID2
Def
13ATRX
Def
13CACNA1C
Def
13CHD7
Def
13CLIFAHDD

CONGENITAL CONTRACTURES OF THE LIMBS AND FACE, HYPOTONIA, AND DEVELOPMENTAL DELAY; CLIFAHDD

13COL5A1
Def
13DLG4
Def
13FBN2
Def
13GFAP
Def
13IHPRF1

HYPOTONIA, INFANTILE, WITH PSYCHOMOTOR RETARDATION AND CHARACTERISTIC FACIES 1; IHPRF1

13IHPRF2

HYPOTONIA, INFANTILE, WITH PSYCHOMOTOR RETARDATION AND CHARACTERISTIC FACIES 2; IHPRF2

13KMT2E
Def
13MEF2C
Def
13NEDHCS

NEURODEVELOPMENTAL DISORDER WITH HYPOTONIA, CRANIOFACIAL ABNORMALITIES, AND SEIZURES; NEDHCS

13NEDHILD

NEURODEVELOPMENTAL DISORDER WITH HYPOTONIA, IMPAIRED LANGUAGE, AND DYSMORPHIC FEATURES; NEDHILD

13NEDHSF

NEURODEVELOPMENTAL DISORDER WITH HYPOTONIA, SPEECH DELAY, AND DYSMORPHIC FACIES; NEDHSF

13NEDHSIL

NEURODEVELOPMENTAL DISORDER WITH HYPOTONIA, STEREOTYPIC HAND MOVEMENTS, AND IMPAIRED LANGUAGE; NEDHSIL

13NEDRIHF

NEURODEVELOPMENTAL DISORDER WITH NEONATAL RESPIRATORY INSUFFICIENCY, HYPOTONIA, AND FEEDING DIFFICULTIES; NEDRIHF

13NFIX
Def
13SCN8A
Def
13SLC9A6
Def
13TET3
Def
13MMACHC
Def

Axial hypotonia

12COX6B1
Def

Generalized hypotonia

12CACNA1E
Def

Axial hypotonia

12CSNK2A1
Def
12GRIN1
Def
12MAGEL2
Def
12MTOR
Def
12TYMP
Def
12PRPS1
Def

Neonatal hypotonia

12CEP41
Def

Generalized hypotonia

12NPC1
Def

Generalized hypotonia

12CLPB
Lim

Neonatal hypotonia

12SNX14
Def

Hypotonia

12TCF20
Def

transcription factor 20

12ACOX1
Def

Hypotonia

12KDM6A
Def

Hypotonia

11STXBP1
Def

syntaxin binding protein 1

11BCL11A
Def
11MTM1
Def
11NARS1
Mod
11SBF1
Mod
11RRM2B

Generalized hypotonia

11HDAC4

Hypotonia

11ACADVL
Def
11CSNK2B
Def
11DNAJC30
Def
11HNRNPU
Def
11KPTN
Def
11PCCB
Def
11SRCAP
Def
11SYNE1
Def
11TUBGCP6
Def
11ZBTB20
Def
11MECP2
Def

methyl-CpG binding protein 2

11MED27
Def

mediator complex subunit 27

11LMNA
DefSF

Hypotonia

11BMP4
Def

Severe muscular hypotonia

11MSL3
Def

MSL complex subunit 3

11PDHB
Mod

Generalized hypotonia

10FKBP14

FKBP prolyl isomerase 14

10SOX5
Def

SRY-box transcription factor 5

10POU3F3
Def

Facial hypotonia

10ODC1

Generalized hypotonia

10SMARCA5
Mod

SNF2 related chromatin remodeling ATPase 5

10MCCC2
Def

Hypotonia

10CDKL5
Def

cyclin dependent kinase like 5

10KCNQ2
Def

potassium voltage-gated channel subfamily Q member 2

10CLCN6
Mod
10SLC6A1
10AP2M1
Def

adaptor related protein complex 2 subunit mu 1

10ATAD3A

Hypotonia

10HECW2
Def

Hypotonia

10PDSS2
Mod

Neonatal hypotonia

9EFEMP1
Def

EGF-like fibulin extracellular matrix protein 1

9MKS1
Def

MKS transition zone complex subunit 1

9DHX30
Def

DExH-box helicase 30

9ALDH18A1
Def
9ATP1A3
Def
9BICRA
Def
9COL5A2
Def
9COL6A2
Def
9CSF1R
Def
9DPF2
Def
9IVD
Def
9KCNT1
Def
9MLC1
Def
9MMAA
Def
9MMUT
Def
9MTRR
Def
9PCCA
Def
9RAB3GAP2
Def
9RERE
Def
9ST3GAL5
Def
9TRPM3
Def
9UBE3B
Def
9VPS13B
Def
9WAC
Def
9SIN3A
Def

Hypotonia

9ADM2
9CIMAP1B
9CPT1B
No
9KLHDC7B
9LMF2
9MAPK8IP2
9NCAPH2
9PPP6R2
9SYCE3
9PMPCA
Def

peptidase, mitochondrial processing subunit alpha

9SIL1
Def

SIL1 nucleotide exchange factor

9UBE4A

Hypotonia

9GBE1
Def

Hypotonia

9NDUFAF6
Def

Hypotonia

9SMPD1
Def

Hypotonia

9ANKRD11
Def
9CAMTA1
Def
9FOXC2
Def
9HNRNPK
Def
9KAT6A
Def
9NFIA
Def
9PLP1
Def
9SETBP1
Def
9SYNGAP1
Def
9TBL1XR1
Def
9WDR26
Def
9PDHX
Def

Neonatal hypotonia

9SCO1
Def

Generalized hypotonia

9CACNA1D
Def

calcium voltage-gated channel subunit alpha1 D

8PAX8

Hypotonia

8TAMM41
Mod

TAM41 mitochondrial translocator assembly and maintenance homolog

8SDHB
DefSF

Axial hypotonia

8ABHD11
8BAZ1B
8BCL7B
8BUD23
8CHKB-CPT1B
8CHKB-DT
8CLDN3
8CLDN4
8CLIP2
8DENND6B
8DGCR6

Hypotonia

8EIF4H
8FKBP6
8FZD9
8GTF2I
8GTF2IRD1
8HDAC10
8KLHDC7B-DT
8LAT2
8LIMK1
8MAPK11
8MAPK12
8METTL27
8MLXIPL
8PLXNB2
8RFC2
8SELENOO
8STX1A
8TBL2
8TMEM270
8VPS37D

Possible

485 genes — click to expand
8AUTS2
Def

Generalized hypotonia

8MIPEP
Mod

mitochondrial intermediate peptidase

8SCN1A
Def

Axial hypotonia

8MINPP1
Def

Axial hypotonia

8RCC1

Hypotonia

8SLC4A10
Str

Axial hypotonia

8TRAF7
Def

Hypotonia

8VAMP2

vesicle associated membrane protein 2

8ASCC1

activating signal cointegrator 1 complex subunit 1

8NEMF
Str

nuclear export mediator factor

8COG5
Def

Hypotonia

7SLC12A6

Neonatal hypotonia

7VPS13D
Lim
7GPT2
Def

Hypotonia

7KCNH1
Def

Hypotonia

7RELN
Def

Hypotonia

7KDM6B
Def

Hypotonia

7ACSF3
Def
7ADAMTS18
Def
7AP4B1
Def
7CA5A
Def
7CDT1
Def
7CEP104
Def
7CHAMP1
Def
7COL6A1
Def
7DNAAF1
Def
7DNMT3A
Def
7DRC4
Def
7ECHS1
Def
7ELP1
Mod

Hypotonia

7ESPN
Def
7FANCA
Def
7GABRB3
Def
7GALNS
Def
7GAN
Def
7GCSH
Def
7GFER
Def
7GJC2
Def
7GLDC
Def
7GNAI1
Def
7LMBRD1
Def
7MBTPS1
Def
7MFN2
Def
7MLYCD
Def
7MPV17
Def
7MTHFR
Def
7MYO7A
Def
7NMNAT1
Def
7NPC2
Def
7NPHP4
Def
7OCA2
Def
7PARK7
Def
7PIEZO1
Def
7PIGT
Def
7PIK3CD
Def
7PLEKHG5
Def
7PMM2
Def
7PRRT2
Def
7PTS
Def
7SCN3A
Def
7SERAC1
Def
7SETD1B
Def
7SFXN4
Def
7SLC38A8
Def
7SOD1
Def
7SPG7
Def
7TARDBP
Def
7TNFRSF9
Def
7TUBB3
Def
7TUBB4A
Def
7WWOX
Def
7ZMYM2
Def
7P4HTM

prolyl 4-hydroxylase, transmembrane

7APC2
Str

Hypotonia

7ARF3

ARF GTPase 3

7KIF5B

kinesin family member 5B

7IFT74
Def

Hypotonia

7SMC1A
Def

Axial hypotonia

6EFL1
Def

Hypotonia

6RYR1
DefSF

Hypotonia

6NAXE
Def

Hypotonia

6EEF1D
6MOV10L1
6NSUN5
6PANX2
6PGM2L1
6TRABD
6TRIM50
6TTI1
6VPS41
6WSB2
6RUBCN

rubicon autophagy regulator

6SNX27

sorting nexin 27

6ADSL
Def

Hypotonia

6ASNS
Def

Axial hypotonia

6BRWD3
Def

Hypotonia

6ANK3
Mod
6CACNA1B
Mod
6PRDM16
Str
6SLC7A5
Mod
6TP73
Str
6UQCRC2
Mod
6CERT1

Axial hypotonia

6SP9

Sp9 transcription factor

6AP4S1
Def

Hypotonia

6STIM1
Def

Hypotonia

6AP1G1
Str

Hypotonia

6LRPPRC
Def

Hypotonia

6SLC46A1

Hypotonia

6KLF13
Mod

Hypotonia

6MTR
Def

Hypotonia

6DDX6

DEAD-box helicase 6

6NUDT2

nudix hydrolase 2

6SIAH1

siah E3 ubiquitin protein ligase 1

6SMARCD1

SWI/SNF related BAF chromatin remodeling complex subunit D1

5ATP2B3

ATPase plasma membrane Ca2+ transporting 3

5AIFM1
Def

Hypotonia

5MPZ
Def

Hypotonia

5NOTCH3
Def

Axial hypotonia

5RAP1B
Mod

Hypotonia

5TBC1D24
Def

Hypotonia

5TSFM
Def

Neonatal hypotonia

5HSPD1

Hypotonia

5ADGRL1
Def

Hypotonia

5EXOSC3

exosome component 3

5ARX
Def

Axial hypotonia

5CASZ1
Lim
5COX4I1
Lim
5KIF1B
Lim
5MCAHS1

MULTIPLE CONGENITAL ANOMALIES-HYPOTONIA-SEIZURES SYNDROME 1; MCAHS1

5MCAHS2

MULTIPLE CONGENITAL ANOMALIES-HYPOTONIA-SEIZURES SYNDROME 2; MCAHS2

5MCAHS3

MULTIPLE CONGENITAL ANOMALIES-HYPOTONIA-SEIZURES SYNDROME 3; MCAHS3

5PHF6
Def

Hypotonia

5ZFPM1
Lim
5ABCB7
Mod

Hypotonia

5PIEZO2

Neonatal hypotonia

5DLG3
Def

Hypotonia

5PIGU
Lim

Hypotonia

5ALG13
Def

Hypotonia

5ERCC8
Def

Hypotonia

5GNPAT
Def

Hypotonia

5GOSR2
Def

Appendicular hypotonia

5SDHD
DefSF

Hypotonia

5SLC18A2
Def

Axial hypotonia

5SPTBN2
Def

Hypotonia

5TCTN2
Def

Hypotonia

5YY1
Def

Hypotonia

4CDC42BPB

Hypotonia

4LETM1

Hypotonia

4KDM5A
Lim

Hypotonia

4NDUFB8
Mod

Generalized hypotonia

4EMILIN1
Def

Hypotonia

4LGI1
Def

Axial hypotonia

4ZSWIM6
Def

Axial hypotonia

4POLA1
Mod

Hypotonia

4CFL2
Def

Hypotonia

4DNM1
Def

Generalized hypotonia

4PLG
Def

Generalized hypotonia

4DPH5
Lim

Hypotonia

4AADACL3
4AADACL4
4ACOT7
4ACTRT2
4ADAD2
4AGTRAP
4AJAP1
4ALDOA
4ANGPTL7
4ARHGEF16
4ARLNC1
4ARRDC1
4ASPHD1
4ATAD3B
4ATMIN
4ATP10A
4ATP10A-DT
4ATP2C2
4BCO1
4BET1
4BRD1
4C16ORF46
4C16ORF54
4C16ORF95
4C16ORF95-DT
4C1ORF167
4C1ORF174
4CA6
4CAMTA1-DT
4CAMTA1-IT1
4CBFA2T3
4CCDC27
4CDH13
4CDH15
Dis
4CDIPT
4CDIPTOSP
4CDK10
4CDK8
4CDR2
4CDYL2
4CEDORA
4CENPBD1
4CENPN
4CENPS
4CENPS-CORT
4CFAP107
4CHD5
4CHMP1A
4CIBAR2
4CIROZ
4CLEC3A
4CLSTN1
4CMC2
4COTL1
4CPNE7
4CRELD2
4CRISPLD2
4CTBP1
4CTNNBIP1
4CTU2
4DBNDD1
4DEF8
4DHRS3
4DISP3
4DNAJC11
4DOC2A
4DPEP1
4DPH7
4DRAXIN
4DYNLRB2
4EEF2K
4EIF4A2
4EIPR1
4EMC8
4ENO1
4ENTPD8
4ERRFI1
4ERRFI1-DT
4EXD3
4EXOSC10
4FAM13A
4FAM157C
4FBXO2
4FBXO31
4FBXO44
4FBXO6
4FENDRR
4FIMP1
4FLJ30679
4FOXF1
4FOXL1
Dis
4FOXP4
4GABRA5
4GABRG3
4GDPD3
4GINS2
4GOLGA2
4GPR153
4GPR157
4GSE1
4H6PD
4HECTD4
4HERC2
4HES2
4HES3
4HES5
4HIRIP3
4HNRNPCL1
4HNRNPCL2
4HNRNPCL3
4HNRNPCL4
4HSALR1
4HSBP1
4HSD17B2
4HSDL1
4ICMT-DT
4IL17C
4IL17REL
4INO80E
4IRF8
4JPH3
4KCNAB2
4KCNG4
4KCNK9
4KCTD13
4KCTD13-DT
4KIAA0513
4KIAA2013
4KIF22
4KLHDC4
4KLHL21
4KLHL36
4LNCTAM34A
4LRRC38
4LRRC47
4MAD2L2
4MAFTRR
4MAP1LC3B
4MAPK3
4MASP2
4MBTPS1-DT
4MC1R
4MEAK7
4MEGF6
4MFSD2A
4MKRN3
4MMEL1
4MOSMO
4MPHOSPH6
4MRPL41
4MTHFSD
4MVP-DT
4NALCN
4NECAB2
4NELFB
4NOL9
4NOXA1
4NPAP1
4NPIPB4
4NPIPB5
4NPPA
No
4NRARP
4NUDT7
4OSGIN1
4PABPN1L
4PAGR1
4PANK4
4PDZD9
4PER3
4PHF13
4PIM3
4PKD1L2
4PLCG2
4PLCH2
4PNPLA7
4POLR3E
4POM121
4POU4F1
4PPP4C
4PRAMEF1
4PRAMEF10
4PRAMEF11
4PRAMEF12
4PRAMEF13
4PRAMEF14
4PRAMEF15
4PRAMEF17
4PRAMEF18
4PRAMEF19
4PRAMEF2
4PRAMEF20
4PRAMEF25
4PRAMEF26
4PRAMEF27
4PRAMEF33
4PRAMEF4
4PRAMEF5
4PRAMEF6
4PRAMEF7
4PRAMEF8
4PRAMEF9
4PRDM16-DT
4PRDM2
4PRDM7
4PRXL2B
4PWAR1
4PWAR4
4PWAR5
4PWAR6
4PWARSN
4PWRN1
4PWRN2
4PWRN3
4PWRN4
4RABL2B
4RBP7
4RFC5
4RNF166
4RNF207
4RNU5E-1
4RPL13
4RPL22
4SDR42E1
4SDR42E2
4SEZ6L2
4SLC22A31
4SLC25A33
4SLC2A5
4SLC2A7
4SLC39A14
4SLC45A1
4SMIM1
4SNAI3
4SNORA119
4SNORA59A
4SNRPN
4SNURF
4SOX4
4SPATA2L
4SPATA33
4SPIRE2
4SPSB1
4SYT1
4TAF1C
4TAFA5
4TANGO2
4TAOK2
4TAS1R1
4TBC1D20
4TBX6
4TCF25
4TCP1
4THAP3
4TLCD3B
4TMEM201
4TMEM219
4TNFRSF14
4TNFRSF1B
4TNFRSF25
4TNFRSF8
4TOR4A
4TPRG1L
4TRAPPC2L
4TRE-TTC2-2
4TRIM74
4TRM-CAT6-1
4TTC34
4TTLL8
4UBE4B
4UBIAD1
4USP10
4UTS2
4VAMP3
4VAT1L
4VPS9D1
4VWA3A
4WBP4
4WFDC1
4WRAP73
4YPEL3
4YPEL3-DT
4ZBED4
4ZBTB48
4ZC3H18
4ZC3H18-DT
4ZCCHC14
4ZCCHC14-DT
4ZDHHC7
4ZG16
4ZMYND19
4ZNF276
4ZNF469
4ZNF778
4ZNF778-DT
4KDM4B
Str

Hypotonia

4CEP57
Def

Hypotonia

4FARSB

Hypotonia

4SEL1L

Axial hypotonia

4ZNF526

Axial hypotonia

4SET
Def

Axial hypotonia

4ALAD
Mod

Hypotonia

4SUCLG1
Mod

Floppy infant

4PYROXD1
Def

Neonatal hypotonia

3PIGY
Lim

Axial hypotonia

3FBLN5
Mod

Hypotonia

3GABBR2
Mod

Generalized hypotonia

3NDUFA1
Mod

Axial hypotonia

3RFC4

Hypotonia

3ACADM
Def

Hypotonia

3AGA
Def

Hypotonia

3CANT1
Def

Hypotonia

3CBL
Def

Hypotonia

3CHRNB1
Def

Hypotonia

3DGUOK
Def

Hypotonia

3HEXA
Def

Generalized hypotonia

3HTRA2
Def

Generalized hypotonia

3LARGE1
Def

Generalized hypotonia

3MPC1
Def

Hypotonia

3MYMK
Def

Hypotonia

3NANS
Def

Hypotonia

3SKI
Def

Generalized hypotonia

3SLC25A15
Def

Hypotonia

3SLC6A9
Def

Axial hypotonia

3TLK2
Def

Generalized hypotonia

3TUBA1A
Def

Generalized hypotonia

3VLDLR
Def

Generalized hypotonia

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.