Genes associated with “hypotonia”

Diagnostic yield calculator →
566 genes foundHPO: Hypotonia
Some sources returned errors (1)

openTargets: Error: OT search: 403

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

16 genes
1
40
score
ClinGen: DefinitiveGTR ↑

Floppy infant

Frequency
38%
n=13
P/LP Variants
4
OT Score
-
2
32
score
ClinGen: DefinitiveP2G #6GTR ↑

Hypotonia

Frequency
33%
n=6
P/LP Variants
4
OT Score
-
3
28
score
ClinGen: DefinitiveP2G #43GTR ↑
Frequency
-
P/LP Variants
10
OT Score
-
4
27
score
ClinGen: DefinitiveGTR ↑

Generalized hypotonia

Frequency
-
P/LP Variants
5
OT Score
-
5
26
score
ClinGen: DefinitiveGTR ↑

Hypotonia

Frequency
76%
n=38
P/LP Variants
3
OT Score
-
6
26
score
GTR ↑

Neonatal hypotonia

Frequency
100%
n=244
P/LP Variants
64
OT Score
-
7
26
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
6
OT Score
-
8
25
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
6
OT Score
-
9
22
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
8
OT Score
-
22KAT6B
Def
21POLR2A
Def
21ATP7A
Def
20ARID2
Def

Generalized hypotonia

20CACNA1C
Def
20GRIN1
Def
20RNU4-2
Str

Consider

114 genes
20GAA
DefSF
19PLA2G6
Def

Hypotonia

19NFIX
Def

Axial hypotonia

19SURF1
Def
19EHMT1
Def
19ASXL3
Def
19CASK
Def
19MED13L
Def
19KANSL1
Def
18PEX6
Def#13
17PEX26
Def
17CSNK2A1
Def
17CSNK2B
Def
17PAFAH1B1

Axial hypotonia

17ATP6V0A2
Def

Hypotonia

16EZH2
Def#10

Hypotonia

16PEX3
Def#7

Appendicular hypotonia

16COX10
Def#9

Generalized hypotonia

16TMEM237
Def#3

Generalized hypotonia

15ALG12
Def
15PPP2R1A
Def
15MKRN3

Neonatal hypotonia

15PLP1
Def

Hypotonia

15SETBP1
Def

Hypotonia

14CTNNB1
Def
14KMT2E
Def
14MECP2
Def
14SETD2
Def
14SLC6A8
Def
14WDR26
Def
14SCO2
Def
14NDUFA10
Mod
14POMGNT1
Def

Generalized hypotonia

14PEX12
Def#15

Generalized hypotonia

14ALDH7A1
Def

Hypotonia

13ARSA
Def
13PEX5
Def#20

Generalized hypotonia

13PEX16
Def

Neonatal hypotonia

13ATRX
Def
13CHD8
Def
13CHEDDA

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

13GRIN2B
Def
13HADDS

HYPOTONIA, ATAXIA, AND DELAYED DEVELOPMENT SYNDROME; HADDS

13HADDTS

HYPOTONIA, ATAXIA, DEVELOPMENTAL DELAY, AND TOOTH ENAMEL DEFECT SYNDROME; HADDTS

13HIDEA

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

13MEF2C
Def
13NDHSAL

NEURODEVELOPMENTAL DISORDER WITH HYPOTONIA, SEIZURES, AND ABSENT LANGUAGE; NDHSAL

13NEDHELS

NEURODEVELOPMENTAL DISORDER WITH HYPOTONIA AND IMPAIRED EXPRESSIVE LANGUAGE AND WITH OR WITHOUT SEIZURES; NEDHELS

13NEDHND

NEURODEVELOPMENTAL DISORDER WITH HYPOTONIA, NEUROPATHY, AND DEAFNESS; NEDHND

13NEDHSIL

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

13NEDIDHA

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

13NMIHBA

NEURODEVELOPMENTAL DISORDER WITH MICROCEPHALY, HYPOTONIA, AND VARIABLE BRAIN ANOMALIES; NMIHBA

13NR2F1
Def
13POGZ
Def
13SLC9A6
Def
13GNB1
Def
13DDC
Def
12DLD
Def

Hypotonia

12FKRP
Def

Neonatal hypotonia

12COL6A3
Def
12FBN2
Def
12GFAP
Def
12NPC1
Def
12COL6A2
Def

Hypotonia

12NFIA
Def

Hypotonia

11MPV17
Def

Axial hypotonia

11ADNP
Def
11AHDC1
Def
11CTCF
Def
11FOXG1
Def
11SATB2
Def
11GLDC
Def
11HECW2
Def
11SCN8A
Def
11SRCAP
Def
11VPS13B
Def
11WAC
Def
11ZBTB20
Def
11HDAC4
11FKTN
Def

Generalized hypotonia

10UBE3B
Def

Generalized hypotonia

10RERE
Def

Hypotonia

10GALC
Def

Axial hypotonia

10TAOK1
Def

Hypotonia

9TMEM70
Def

Hypotonia

9MBOAT7
Def

Generalized hypotonia

9AP4B1
Def
9AP4M1
Def
9ATN1
Def
9ATP1A3
Def
9COL5A2
Def
9CSF1R
Def
9DNMT3A
Def
9HIBCH
Def
9HNRNPU
Def
9KLHL40
Def
9MAGEL2
Def
9PIGN
Def
9SCN3A
Def
9TET3
Def
9D2HGDH
Def

Hypotonia

9ZNF462
Def

Generalized hypotonia

9SLC25A19
Lim

Axial hypotonia

9SLC17A5
Def

Generalized hypotonia

9BCL11A
Def
9CNOT1
Def
9COL5A1
Def
9GATAD2B
Def
9MTM1
Def
9TRIP12
Def
9NGLY1
Def

Facial hypotonia

8MMAA
Def

Generalized hypotonia

8NALCN
8TRMU
Def

Hypotonia

Possible

383 genes — click to expand
8SYNGAP1
Def

Hypotonia

8ST3GAL5
Def

Hypotonia

8NSUN2
Def

Hypotonia

7CLPB
Lim
7PLOD1

Hypotonia

7OPHN1
Def

Generalized hypotonia

7ETHE1
Def

Hypotonia

7LIFR
Def

Hypotonia

7TRAPPC6B
Def

Hypotonia

7GEMIN5
Def

Appendicular hypotonia

7ABCC6
Def
7ACADVL
Def
7AGXT
Def
7B9D1
Def
7BICRA
Def
7COL6A1
Def
7CORO1A
Def
7DPF2
Def
7ECHS1
Def
7FLCN
Def
7GBE1
Def
7GNAI1
Def
7H1-4
Def
7KIF1A
Def
7KPTN
Def
7LAMA2
Def
7LMBRD1
Def
7MERTK
Def
7MLC1
Def
7MTOR
Def
7MTR
Def
7MTRR
Def
7MYH11
DefSF
7MYO15A
Def
7NDE1
Def
7OPN1LW
Def
7PCCB
Def
7PMM2
Def
7PRRT2
Def
7PURA
Def
7RAB3GAP2
Def
7RBCK1
Def
7SERAC1
Def
7SMARCC2
Def
7SOD1
Def
7THOC2
Def
7TNFRSF13B
Def
7TRPM3
Def
7TUBB3
Def
7TUBGCP6
Def
7TYMP
Def
7USP7
Def
7ATAD3A

Hypotonia

7KIFBP
Def

Hypotonia

7STRADA

Hypotonia

7EBP
Def

Axial hypotonia

6PPP2R5C
Def

Hypotonia

6EIF4A2

Hypotonia

6ASH1L
Def

Hypotonia

6SHOC2
Def

Generalized hypotonia

6ANAPC1
Mod
6FLII
Mod
6NARS1
Mod
6SBF1
Mod
6SOX2
6SUCLG1
Mod
6MACF1
Mod

Hypotonia

6AP4S1
Def

Hypotonia

6DST
Def

Hypotonia

6SPINK5
Def

Hypotonia

6SCAF4
Def

Hypotonia

5GOT2
Mod

Neonatal hypotonia

5KCNT1
Def

Generalized hypotonia

5BCKDK
Def

Hypotonia

5ABCC1
Lim
5ARX
Def

Generalized hypotonia

5ATPAF2
Lim
5BUB1
Lim
5CLIFAHDD

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

5GRAP
Lim
5IHPRF1

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

5MCAHS2

MULTIPLE CONGENITAL ANOMALIES-HYPOTONIA-SEIZURES SYNDROME 2; MCAHS2

5MIEF2
Lim
5NEDHCS

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

5NEDHSF

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

5NEDRIHF

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

5PDCD1
Lim
5PMP22
Def

Hypotonia

5SMS
Def

Generalized hypotonia

5SOX10
Def

Neonatal hypotonia

5RFXAP
Def

Hypotonia

5EDEM3
Str

Hypotonia

5CDK13
Def

Hypotonia

5IQSEC1
Lim

Generalized hypotonia

5BRAT1
Def

Axial hypotonia

5DCC
Def

Hypotonia

5DNM1L
Def

Axial hypotonia

5NDUFV2
Def

Axial hypotonia

5OSTM1
Def

Axial hypotonia

5SCN4A
Def

Hypotonia

5ZIC1
Def

Hypotonia

5LAMB1
Mod

Hypotonia

5GRIK2
Def

Axial hypotonia

5VPS41

Hypotonia

5MYO5A
Def

Hypotonia

4PNPT1
Mod

Severe muscular hypotonia

4TRMT10C
Mod

Hypotonia

4HCFC1
Def

Hypotonia

4MICOS13
Def

Axial hypotonia

4MYO18B
Def

Generalized hypotonia

4NDUFB11
Def

Axial hypotonia

4ACKR3
4ACOXL
4ADM2
4AGAP1
4AKAP10
4ALDH3A1
4ALDH3A2
4ALDOA
4ALKBH5
4ANKMY1
4ANO7
4AQP12A
4AQP12B
4ASB1
4ASB18
4ASPHD1
4ATG4B
4BCL2L11
4BMERB1
4BRD1
4C16ORF54
4CAPN10
4CAPN10-DT
4CDIPT
4CDIPTOSP
4CDK8
4CDPF1
4CELSR1
4CEP20
4CHKB-CPT1B
4CHKB-DT
4CIMAP1B
4COPS3
4COPS8
4COPS8-DT
4COPS9
4CPT1B
No
4CRELD2
4CROCC2
4CYFIP1
4DCLRE1B
4DENND6B
4DOC2A
4DRC11
4DRC3
4DRG2
4DTYMK
4DUSP28
4EEF1D
4EIPR1
4EPIC1
4EPN2
4EPN2-IT1
4ESPNL
4EVPLL
4FAM106A
4FAM106B
4FAM240C
4FARP2
4FBLN7
4FBXO36
4FBXW10
4FIMP1
4FOXO3B
4GAL3ST2
4GBX2
4GDPD3
4GID4
4GPC1
4GPR35
4GRAMD4
4GRAPL
4GRM7
4GTSE1
4GTSE1-DT
4HDAC10
4HDLBP
4HES6
4HHATL
4HIRIP3
4IFT54
4IL17REL
4ILKAP
4ING5
4INO80E
4KCTD13
4KCTD13-DT
4KIF22
4KLHDC7B
4KLHDC7B-DT
4KLHL30
4LGALS9B
4LGALS9C
4LLGL1
4LMF2
4LRRFIP1
4LY6G5B
4MAB21L4
4MAPK11
4MAPK12
4MAPK3
4MAPK7
4MAPK8IP2
4MARF1
4MED9
4MFAP4
4MIRLET7A3
4MIRLET7B
4MIRLET7BHG
4MOV10L1
4MPRIP
4MPV17L
4MPV17L-BMERB1
4MTERF4
4MVP-DT
4NCAM1
4NCAPH2
4NEU4
4NIPA1
4NIPA2
4NOMO3
4NPIPA5
4NPIPA6
4NPIPA7
4NT5M
4NTAN1
4ODC1
4OPSIN-LCR
4OR6B2
4OR6B3
4PAGR1
4PANX2
4PDXDC1
4PER2
4PIM3
4PKDREJ
4PLD6
4PLXNB2
4PPARA
4PPP1R7
4PPP4C
4PPP6R2
4PRPSAP2
4PRR21
4PRR34
4PRUNE1
4PWAR6
4RAB17
4RAB17-DT
4RAB9B
4RABL2B
4RALGAPA1
4RAMP1
4RASD1
4RBM44
4RGPD6
4RGPD8
4RNF112
4RNPEPL1
4RPGRIP1
4RRN3
4RTP5
4SACK1G
4SELENOO
4SEPSECS
4SEPTIN2
4SEZ6L2
4SHMT1
4SIRT4
4SLC12A6
4SLC47A1
4SLC47A2
4SLC5A10
4SMCR2
4SMCR5
4SMCR8
4SNED1
4SNORA59B
4SNRPN
4SNURF
4SOCAR
4SOD1-DT
4SOX2-OT
4SOX4
4SPECC1
4SPECC1-DT
4SREBF1
4STK25
4SUPT16H
4SYCE3
4SYT1
4TAFA5
4TANAR
4TANGO2
4TAOK2
4TBC1D20
4TBC1D22A
4TBC1D28
4TBX6
4TECPR2
4THAP4
4TLCD3B
4TMEM219
4TMEM63A
4TMEM87B
4TNPO2
4TOM1L2
4TOP3A
4TRABD
4TRCR1
4TRG-CCC3-1
4TRIM16L
4TRW-CCA2-1
4TTC38
4TTLL8
4TUBGCP5
4TVP23B
4TWIST2
4UBE2F
4UBE2F-SCLY
4UICLM
4ULK2
4WNT7B
4YPEL3
4YPEL3-DT
4ZBED4
4ZC3H6
4ZC3H8
4ZG16
4METTL23
Def

Hypotonia

4ATXN7L3

Hypotonia

4GUF1
Lim

Hypotonia

4TIMM50
Def

Hypotonia

4SLC4A10
Str

Hypotonia

4DNAJC12
Def

Axial hypotonia

4NEXMIF
Def

Axial hypotonia

4CHRNA7
Ref

Hypotonia

4NAA20
Mod

Generalized hypotonia

3PRMT7

Hypotonia

3FCSK
Lim

Hypotonia

3GLUL
Mod

Hypotonia

3MRAS
Mod

Hypotonia

3SUZ12

Generalized hypotonia

3OXR1

Hypotonia

3ACTN2
Def

Generalized hypotonia

3ARFGEF2
Def

Generalized hypotonia

3ARMC9
Def

Hypotonia

3BCL11B
Def

Generalized hypotonia

3CASR
Def

Hypotonia

3CDC42
Def

Generalized hypotonia

3CHRNA1
Def

Hypotonia

3CHRNB1
Def

Hypotonia

3CYP27B1
Def

Hypotonia

3DPAGT1
Def

Hypotonia

3ETFB
Def

Hypotonia

3FARS2
Def

Hypotonia

3FBP1
Def

Hypotonia

3IQSEC2
Def

Generalized hypotonia

3ITGA3
Def

Hypotonia

3LARGE1
Def

Generalized hypotonia

3MCOLN1
Def

Hypotonia

3MRPS22
Def

Hypotonia

3MTFMT
Def

Hypotonia

3NAA10
Def

Hypotonia

3PRF1
Def

Generalized hypotonia

3RMND1
Def

Severe muscular hypotonia

3RNASEH2C
Def

Hypotonia

3SLC25A26
Def

Generalized hypotonia

3SLC25A46
Def

Hypotonia

3TBC1D24
Def

Generalized hypotonia

3TREX1
Def

Axial hypotonia

3TUBB4A
Def

Axial hypotonia

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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.