Genes associated with “hypotonia”

421 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

15 genes
1
EBF3 →

EBF transcription factor 3

42
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
2
OT Score
0.49
2
POLR2A →

RNA polymerase II subunit A

34
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
1
OT Score
0.37
3
RPS6KA3 →

ribosomal protein S6 kinase A3

33
score
ClinGen: DefinitiveP2G #6GTR ↑
Frequency
-
P/LP Variants
2
OT Score
0.34
4
DHX30 →

DExH-box helicase 30

32
score
ClinGen: DefinitiveGTR ↑

Hypotonia

Frequency
100%
n=12
P/LP Variants
3
OT Score
0.42
5
GNB1 →

G protein subunit beta 1

28
score
ClinGen: DefinitiveGTR ↑

Axial hypotonia

Frequency
15%
n=13
P/LP Variants
1
OT Score
0.54
6
AHDC1 →

AT-hook DNA binding motif containing 1

28
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
5
OT Score
0.51
7
PURA →

purine rich element binding protein A

26
score
ClinGen: DefinitiveGTR ↑

Hypotonia

Frequency
100%
n=11
P/LP Variants
1
OT Score
0.52
8
TNPO2 →

transportin 2

25
score
GTR ↑

Hypotonia

Frequency
73%
n=15
P/LP Variants
1
OT Score
0.50
9
24
score
ClinGen: DefinitiveP2G #43GTR ↑
Frequency
-
P/LP Variants
6
OT Score
-
23EHMT1
Def
23GAMT
Def

Hypotonia

22USP7
Def

ubiquitin specific peptidase 7

21DLD
Def
20CSNK2A1
Def

Hypotonia

20SHANK3
Def

Consider

136 genes
20CTCF
Def

Hypotonia

20GAA
DefSF
19ARSA
Def
19TAMM41

Hypotonia

18CEP290
Def

centrosomal protein 290

18TMEM67
Def

transmembrane protein 67

18MVK
Def
18PEX1
Def#14
18PEX19
Def#1

Hypotonia

18DOCK3

dedicator of cytokinesis 3

17UBE3A
Def#18
17ELN
Def
17TMEM216
Def

Hypotonia

17SURF1
Def
16COX6B1
Def

Generalized hypotonia

16ASCC1

Severe muscular hypotonia

16PPP2CA
Def

protein phosphatase 2 catalytic subunit alpha

15PRPS1
Def

Hypotonia

15KMT2A
Def
15MED13L
Def
15MMADHC
Def

Hypotonia

15KANSL1
Def
15TBCK
Def

Generalized hypotonia

14CEP41
Str

Hypotonia

14ATRX
Def
14CNOT1
Def
14GRIN2B
Def
14DDC
Def

dopa decarboxylase

14MMACHC
Def

Generalized hypotonia

14SCO2
Def
14PEX6
Def#13

Generalized hypotonia

14NDUFS1
Def

Hypotonia

14MED12
Def

Generalized hypotonia

14B3GALNT2
Def

Severe muscular hypotonia

13FOXG1
Def

Hypotonia

13PEX26
Def

Neonatal hypotonia

13ACADVL
Def
13AMT
Def
13ASNS
Def
13CASK
Def
13CHD7
Def
13CHEDDA

CONGENITAL HYPOTONIA, EPILEPSY, DEVELOPMENTAL DELAY, AND DIGITAL ANOMALIES; CHEDDA

13DDX3X
Def
13DLG4
Def
13ETHE1
Def
13GBE1
Def
13GLDC
Def
13HIDEA

HYPOTONIA, HYPOVENTILATION, IMPAIRED INTELLECTUAL DEVELOPMENT, DYSAUTONOMIA, EPILEPSY, AND EYE ABNORMALITIES; HIDEA

13IDDHBA

INTELLECTUAL DEVELOPMENTAL DISORDER WITH HYPOTONIA AND BEHAVIORAL ABNORMALITIES; IDDHBA

13MLC1
Def
13MMAA
Def
13MMAB
Def
13NEDAHM

NEURODEVELOPMENTAL DISORDER WITH ATAXIA, HYPOTONIA, AND MICROCEPHALY; NEDAHM

13NEDBASH

NEURODEVELOPMENTAL DISORDER WITH BEHAVIORAL ABNORMALITIES, ABSENT SPEECH, AND HYPOTONIA; NEDBASH

13NEDHAHM

NEURODEVELOPMENTAL DISORDER WITH HYPOTONIA AND AUTISTIC FEATURES WITH OR WITHOUT HYPERKINETIC MOVEMENTS; NEDHAHM

13NEDHIB

NEURODEVELOPMENTAL DISORDER WITH HYPOTONIA AND VARIABLE INTELLECTUAL AND BEHAVIORAL ABNORMALITIES; NEDHIB

13NEDHRIT

NEURODEVELOPMENTAL DISORDER WITH HYPOTONIA, NEONATAL RESPIRATORY INSUFFICIENCY, AND THERMODYSREGULATION; NEDHRIT

13NEDIDHA

NEURODEVELOPMENTAL DISORDER WITH IMPAIRED INTELLECTUAL DEVELOPMENT, HYPOTONIA, AND ATAXIA; NEDIDHA

13NFIX
Def
13NPC1
Def
13PCCA
Def
13PMM2
Def
13POGZ
Def
13PTS
Def
13STAHP

SPASTIC TETRAPLEGIA AND AXIAL HYPOTONIA, PROGRESSIVE; STAHP

13VPS13B
Def
13ZBTB20
Def

Hypotonia

13PPP2R1A
Def
13VAMP2

Axial hypotonia

13PTEN
DefSF

Hypotonia

13PLOD1

procollagen-lysine,2-oxoglutarate 5-dioxygenase 1

13FKTN
Def

Neonatal hypotonia

12SLC6A8
Def

Neonatal hypotonia

12POMT2
Def

Generalized hypotonia

12TRPM3
Def

Hypotonia

12MECP2
Def

Axial hypotonia

12CHAMP1
Def

Hypotonia

12TCF20
Def

transcription factor 20

11SOX5
Def

Generalized hypotonia

11STXBP1
Def

syntaxin binding protein 1

11SATB2
Def
11ASXL1
Def

Hypotonia

11ASXL3
Def

Hypotonia

11KPTN
Def
11MAGEL2
Def
11TET3
Def
11SLC16A2
Def

Neonatal hypotonia

11MED27
Def

mediator complex subunit 27

11ACSL4
Def

Hypotonia

11MSL3
Def

MSL complex subunit 3

10NUDT2

Hypotonia

10SYNE1
Def

Generalized hypotonia

10SKI
Def

Hypotonia

10PMPCA
Def

Hypotonia

10SMARCA5
Mod

SNF2 related chromatin remodeling ATPase 5

10MCCC2
Def

Generalized hypotonia

10RRM2B
10WBP4

Hypotonia

10CZ1P-ASNS
10ELP1
10MTM1
Def

Severe muscular hypotonia

10SLC12A6
10SLC9A6
Def

Generalized hypotonia

10TECPR2
10SLC52A3
Def

Hypotonia

10AP2M1
Def

adaptor related protein complex 2 subunit mu 1

9SCN3A
Def

Generalized hypotonia

9EFEMP1
Def

EGF-like fibulin extracellular matrix protein 1

9MKS1
Def

MKS transition zone complex subunit 1

9CSNK2B
Def
9DNAJC30
Def
9FBN2
Def
9GNAI1
Def
9IVD
Def
9NPC2
Def
9RAB3GAP1
Def
9RAB3GAP2
Def
9SIL1
Def

SIL1 nucleotide exchange factor

9NDUFAF6
Def

Hypotonia

9ADNP
Def
9CHD8
Def
9COL5A1
Def
9HNRNPK
Def
9KMT2E
Def
9MEF2C
Def
9NFIA
Def
9NR2F1
Def
9SETBP1
Def
9IFIH1
Def

Axial hypotonia

9SMARCC2
Def

Hypotonia

9CACNA1D
Def

calcium voltage-gated channel subunit alpha1 D

9EPG5
Def

Hypotonia

9POU3F3
Def

POU class 3 homeobox 3

8DST
Def

dystonin

8AP4M1
Def

Neonatal hypotonia

8TBX1

Hypotonia

Possible

229 genes — click to expand
8MIPEP
Mod

mitochondrial intermediate peptidase

8CLCN6
Mod

Generalized hypotonia

8DLL1
Def

Hypotonia

8MORC2
Def

Hypotonia

8CTNNB1
Def

Hypotonia

8NEMF
Str

nuclear export mediator factor

8PPM1D
Def

Hypotonia

7CLPB
Lim
7BICRA
Def
7COL6A2
Def
7ECHS1
Def
7GABRB3
Def
7GFAP
Def
7GFER
Def
7GJC2
Def
7KCNT1
Def
7LMBRD1
Def
7MTOR
Def
7MTRR
Def
7OCA2
Def
7PCCB
Def
7SETD1B
Def
7TUBB4A
Def
7TYMP
Def
7WAC
Def
7P4HTM

prolyl 4-hydroxylase, transmembrane

7SMARCD1

SWI/SNF related BAF chromatin remodeling complex subunit D1

7TMEM222

transmembrane protein 222

7ARF3

ARF GTPase 3

7KIF5B

kinesin family member 5B

7PGAP3
Def

Hypotonia

7PACS2
Def

Hypotonia

6AP1S1
Def

Hypotonia

6ABHD11
6BAZ1B
6BCL7B
6BUD23
6CLDN3
6CLDN4
6CLIP2
6EIF4H
6FKBP6
6FZD9
6GTF2I
6GTF2IRD1
6LAT2
6LIMK1
6METTL27
6MLXIPL
6RFC2
6STX1A
6TBL2
6TMEM270
6TTI1
6VPS37D
6WSB2
6RUBCN

rubicon autophagy regulator

6SNX27

sorting nexin 27

6TRIP12
Def

Hypotonia

6GCSH
Def

Hypotonia

6RMND1
Def

Generalized hypotonia

6ANK3
Mod
6CACNA1B
Mod
6NARS1
Mod
6SBF1
Mod
6SLC6A1
6UQCRC2
Mod
6OTUD5
Mod

Hypotonia

6SP9

Sp9 transcription factor

6DNM2
Def

Hypotonia

6GOSR2
Def

Hypotonia

6MAG
Def

Hypotonia

6PIGO
Def

Hypotonia

6RIN2
Def

Hypotonia

6SIX6

Hypotonia

6ACTL6B

Axial hypotonia

6PIGA
Def

Hypotonia

6QARS1
Def

Hypotonia

6DDX6

DEAD-box helicase 6

6SIAH1

siah E3 ubiquitin protein ligase 1

6ZEB2
Def

Hypotonia

5ATP2B3

ATPase plasma membrane Ca2+ transporting 3

5FKBP14

FKBP prolyl isomerase 14

5INPP5K

Hypotonia

5LARGE1
Def

Generalized hypotonia

5SOD1
Def

Axial hypotonia

5TWNK
Def

Hypotonia

5HSPD1

Hypotonia

5TANC2
Def

Generalized hypotonia

5GRM7

glutamate metabotropic receptor 7

5POMGNT2
Def

Hypotonia

5PAX7
Mod

Axial hypotonia

5HERC2

Generalized hypotonia

5KMT2C
Def

Generalized hypotonia

5MCAHS2

MULTIPLE CONGENITAL ANOMALIES-HYPOTONIA-SEIZURES SYNDROME 2; MCAHS2

5MCAHS4

MULTIPLE CONGENITAL ANOMALIES-HYPOTONIA-SEIZURES SYNDROME 4; MCAHS4

5NEDHCS

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

5NEDHILD

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

5NEDHSF

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

5NEDHSIL

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

5PHF6
Def

Generalized hypotonia

5ZBTB18
Def

Hypotonia

5AARS1
Def

Axial hypotonia

5PHKG2
Def

Hypotonia

5AP1G1
Str

Hypotonia

5PAN2
Mod

Hypotonia

5DPYSL5

Hypotonia

5SLC34A1
Def

Hypotonia

5COG4
Def

Axial hypotonia

5ITPR1
Def

Generalized neonatal hypotonia

5NDUFAF2
Def

Hypotonia

5STAG1
Def

Neonatal hypotonia

5COG6
Def

Generalized hypotonia

4SUCLG1
Mod

Generalized neonatal hypotonia

4NEDD4L
Def

Hypotonia

4ZSWIM6
Def

Axial hypotonia

4DNM1
Def

Generalized hypotonia

4RMRP
Def

Hypotonia

4SOX11
Def

Hypotonia

4ADM2
4ARRDC1
4ATP10A
4ATP10A-DT
4BET1
4CDR2
4CERT1
4CHKB-CPT1B
4CHKB-DT
4CIMAP1B
4CPT1B
No
4CTBP1
4DPH7
4EEF2K
4EIF4A2
4ENTPD8
4EXD3
4FAM13A
4FOXP4
4GABRA5
4GABRG3
4GOLGA2
4HECTD4
4KLHDC7B
4KLHDC7B-DT
4LMF2
4MAPK8IP2
4MFSD2A
4MKRN3
4MOSMO
4MRPL41
4NCAPH2
4NELFB
4NOXA1
4NPAP1
4NPIPB4
4NPIPB5
4NRARP
4NSUN5
4ODC1
4PDZD9
4PGM2L1
4PNPLA7
4POLR3E
4POM121
4PPP6R2
4PWAR1
4PWAR4
4PWAR5
4PWAR6
4PWARSN
4PWRN1
4PWRN2
4PWRN3
4PWRN4
4RFC5
4SDR42E2
4SETD6
4SNHG14
4SNRPN
4SNURF
4SYCE3
4TOR4A
4TRE-TTC2-2
4TRIM50
4TRIM74
4VPS41
4VWA3A
4ZMYM2
4ZMYND19
4KIDINS220
Def

Axial hypotonia

4RARS2
Def

Axial hypotonia

4FBXO22

Generalized hypotonia

4UBR7

Hypotonia

4RARS1
Def

Axial hypotonia

4RPL10
Def

Generalized hypotonia

4PLEKHG2

Generalized hypotonia

4HTRA2
Def

Hypotonia

4CARS2
Mod

Hypotonia

4DOCK11
Str

Hypotonia

4TTC5

Hypotonia

3COX4I1
Lim

Generalized hypotonia

3NOTCH3
Lim

Axial hypotonia

3UBAP2L

Hypotonia

3WASF1

Generalized hypotonia

3AASS
Def

Hypotonia

3ACADM
Def

Hypotonia

3AMER1
Def

Generalized hypotonia

3BCKDHA
Def

Generalized hypotonia

3CRPPA
Def

Hypotonia

3DDX11
Def

Generalized hypotonia

3HADH
Def

Generalized hypotonia

3KCNJ10
Def

Generalized hypotonia

3KIF1A
Def

Generalized hypotonia

3MANBA
Def

Hypotonia

3MLYCD
Def

Generalized hypotonia

3NANS
Def

Generalized hypotonia

3NARS2
Def

Hypotonia

3NPHP1
Def

Generalized hypotonia

3PIGN
Def

Generalized hypotonia

3PIGT
Def

Generalized hypotonia

3PNPO
Def

Axial hypotonia

3SERAC1
Def

Hypotonia

3SLC25A1
Def

Severe muscular hypotonia

3SLC25A20
Def

Hypotonia

3SLC25A46
Def

Generalized hypotonia

3SPTAN1
Def

Hypotonia

3SUOX
Def

Floppy infant

3TBC1D24
Def

Hypotonia

3ZMIZ1
Def

Facial 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.