Genes associated with “spasticity”

Diagnostic yield calculator →
314 genes foundHPO: SpasticityOpen Targets: Spasticity
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

27 genes
1
ABCD1 →

ATP binding cassette subfamily D member 1

41
score
ClinGen: DefinitiveP2G #7GTR ↑
Frequency
-
P/LP Variants
12
OT Score
0.59
2
SPAST →

spastin

35
score
GTR ↑

Lower limb spasticity

Frequency
-
P/LP Variants
8
OT Score
0.65
3
L1CAM →

L1 cell adhesion molecule

35
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
4
OT Score
0.57
4
SLC2A1 →

solute carrier family 2 member 1

34
score
ClinGen: DefinitiveGTR ↑

Spastic paraplegia

Frequency
-
P/LP Variants
3
OT Score
0.47
5
FA2H →

fatty acid 2-hydroxylase

31
score
ClinGen: DefinitiveP2G #14GTR ↑
Frequency
-
P/LP Variants
2
OT Score
0.65
6
SPG7 →

SPG7 matrix AAA peptidase subunit, paraplegin

30
score
ClinGen: DefinitiveGTR ↑

Upper limb spasticity

Frequency
0%
n=3
P/LP Variants
4
OT Score
0.58
7
SPG11 →

SPG11 vesicle trafficking associated, spatacsin

30
score
ClinGen: DefinitiveGTR ↑

Lower limb spasticity

Frequency
-
P/LP Variants
7
OT Score
0.55
8
CYP7B1 →

cytochrome P450 family 7 subfamily B member 1

29
score
ClinGen: DefinitiveGTR ↑

Lower limb spasticity

Frequency
100%
n=16
P/LP Variants
4
OT Score
0.56
9
AP4M1 →

adaptor related protein complex 4 subunit mu 1

29
score
ClinGen: DefinitiveGTR ↑

Spastic tetraplegia

Frequency
100%
n=5
P/LP Variants
4
OT Score
0.75
27PLP1
Def#6

Spastic gait

27RTN2

Spastic gait

25SLC16A2
Def#11

Spastic paraplegia

25CYP27A1
Def#8
24SLC17A5
Def#12
23FOXG1
Def

Spasticity

23MED27
Def

mediator complex subunit 27

23ARSA
Def#18
22GALC
Def#20
21DLD
Def
21CTNNB1
Def

Spastic diplegia

21GJC2
Def

Spastic paraparesis

21ALS2
Def

Spastic tetraplegia

20KIF5A
Def

kinesin family member 5A

20SLC25A15
Def

Spastic gait

20GFAP
Def
20EIF2B5
Def
20TNR
Def

Consider

108 genes
20GLB1
Def
19AP4B1
Def

adaptor related protein complex 4 subunit beta 1

19POLR3B
Def

Spasticity

18RAB3GAP1
Def
18CYP2U1
Def

Spastic paraplegia

18PSAP
Def
18ATP13A2
Def

ATPase cation transporting 13A2

18AFG3L2
Def

Spasticity

18HPRT1
Def#3

Spasticity

18ARG1
Def#1

Spastic gait

18EIF2B4
Def

Spasticity

17KDM5C
Def

Spasticity

16EIF2B1
Def
16EIF2B3
Def
16GRIN2B
Def

Spasticity

16GJA1
Lim

Spasticity

16ZFYVE26

Lower limb spasticity

16POLR3A
Def
15KIF1A
Def

kinesin family member 1A

15RAB3GAP2
Def
15ASXL3
Def
15CASK
Def
15CNOT1
Def
15SCO2
Def
14DDX3X
Def
14ARX
Def

Lower limb spasticity

14AMACR
Def

Spasticity

13SLC33A1

Spastic paraplegia

13NDUFV1
Def

Spasticity

13ASPM
Def
13ASS1
Def
13ETHE1
Def
13HEXA
Def
13HEXB
Def
13IKSHD

ICHTHYOTIC KERATODERMA, SPASTICITY, HYPOMYELINATION, AND DYSMORPHIC FACIAL FEATURES; IKSHD

13MLC1
Def
13NDMSBA

NEURODEVELOPMENTAL DISORDER WITH PROGRESSIVE MICROCEPHALY, SPASTICITY, AND BRAIN ANOMALIES; NDMSBA

13NEDCHS

NEURODEVELOPMENTAL DISORDER WITH CEREBELLAR HYPOPLASIA AND SPASTICITY; NEDCHS

13NEDDSBA

NEURODEVELOPMENTAL DISORDER WITH DYSMORPHIC FEATURES, SPASTICITY, AND BRAIN ABNORMALITIES; NEDDSBA

13NEDESBA

NEURODEVELOPMENTAL DISORDER WITH EPILEPSY, SPASTICITY, AND BRAIN ATROPHY; NEDESBA

13NEDMCMS

NEURODEVELOPMENTAL DISORDER WITH MICROCEPHALY, CORTICAL MALFORMATIONS, AND SPASTICITY; NEDMCMS

13NEDMISBA

NEURODEVELOPMENTAL DISORDER WITH PROGRESSIVE MICROCEPHALY, SPASTICITY, AND BRAIN IMAGING ABNORMALITIES; NEDMISBA

13NEDSG

NEURODEVELOPMENTAL DISORDER WITH SPASTICITY AND POOR GROWTH; NEDSG

13NEDSPLB

NEURODEVELOPMENTAL DISORDER WITH SPASTICITY, HYPOMYELINATING LEUKODYSTROPHY, AND BRAIN ABNORMALITIES; NEDSPLB

13PEBAS

ENCEPHALOPATHY, PROGRESSIVE, EARLY-ONSET, WITH BRAIN ATROPHY AND SPASTICITY; PEBAS

13PNSED

PERIPHERAL NEUROPATHY WITH VARIABLE SPASTICITY, EXERCISE INTOLERANCE, AND DEVELOPMENTAL DELAY; PNSED

13SPAHGC

SPASTICITY, CHILDHOOD-ONSET, WITH HYPERGLYCINEMIA; SPAHGC

13WDR62
Def
13ABHD16A

Spastic paraplegia

13CSF1R
Def

Spasticity

13GCH1
Def

GTP cyclohydrolase 1

13KCNC2
Def

Spastic tetraplegia

12GRIN1
Def
12HACE1

HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1

12SYNE1
Def
12SDHA
Def

Spasticity

12NDUFS4
Def

Spasticity

12RAB18
Mod

Lower limb spasticity

12EARS2
Def

Spastic tetraparesis

12NARS1
Mod
12SPTAN1
Def

Spastic gait

11B4GALNT1
Def

beta-1,4-N-acetyl-galactosaminyltransferase 1

11GBA2
Def

glucosylceramidase beta 2

11LIG3
Def

DNA ligase 3

11ADSL
Def

Spasticity

11MTRFR
Def

mitochondrial translation release factor in rescue

11AP4E1
Def

adaptor related protein complex 4 subunit epsilon 1

11AP4S1
Def

adaptor related protein complex 4 subunit sigma 1

11SNAP25
Def

synaptosome associated protein 25

11ERLIN2
Def

ER lipid raft associated 2

11GABBR2
Mod

gamma-aminobutyric acid type B receptor subunit 2

11IRF2BPL
Def
11BCS1L
Def

Spasticity

11LIPT1
Mod

Spastic tetraparesis

11UCHL1
Def

ubiquitin C-terminal hydrolase L1

10SOX10
Def

Spastic paraparesis

10TBC1D20
10PNPLA6
Def

Spastic paraplegia

10TECPR2

tectonin beta-propeller repeat containing 2

10ATXN2
Def

Spasticity

10LYST
Def

lysosomal trafficking regulator

10GAN
Def

Spastic paraplegia

10BSCL2
Def

Spastic paraplegia

10RARS2
Def

Lower limb spasticity

9PLA2G6
Def

Spasticity

9ALDH18A1
Def
9EPM2A
Def
9KMT2B
Def
9SERAC1
Def
9TUBB4A
Def
9HTRA1
9EIPR1
9PI4KA
9NDUFC2
Mod

Spasticity

9GABBR1

gamma-aminobutyric acid type B receptor subunit 1

9VAMP1

Spastic paraplegia

9XPA
Def

Spasticity

9PQBP1
Def

Spasticity

9PSMD6
9RAD50
Ref

Spasticity

8CRLF1

Opisthotonus

8ADRA2A

adrenoceptor alpha 2A

8ADRA2B
Ref

adrenoceptor alpha 2B

8ADRA2C

adrenoceptor alpha 2C

8WWOX
Def

Spasticity

8ATL1
Def

Spastic gait

8RAB9B
8TRAPPC12

Possible

124 genes — click to expand
8MCM7

minichromosome maintenance complex component 7

8PPM1N

protein phosphatase, Mg2+/Mn2+ dependent 1N (putative)

8CREB3

cAMP responsive element binding protein 3

8MINPP1
Def

Spastic tetraplegia

8PCYT2

phosphate cytidylyltransferase 2, ethanolamine

8ERLIN1
Def

Spasticity

7WASHC5
Mod

Lower limb spasticity

7CLPB
Lim
7AFG2A
Def

Spasticity

7BRAT1
Def
7DARS2
Def
7FARS2
Def
7GBE1
Def
7NHLRC1
Def
7TUBGCP6
Def
7TYMP
Def
7HTR2A

5-hydroxytryptamine receptor 2A

7HTR2C

5-hydroxytryptamine receptor 2C

7ATP6AP2
Def

Spasticity

7ATXN8OS

Spasticity

6REEP2

Spastic gait

6ANK3
Mod
6SBF1
Mod
6AARS1
Def

Spasticity

6RETREG1
Def

Scissor gait

6FLVCR1
Def

Spasticity

5AP5Z1
Def

Spastic paraplegia

5DSTYK
Mod

Spastic paraplegia

5DARS1

Lower limb spasticity

5HSPD1

Spastic paraplegia

5GPAA1
Def

Spasticity

5RNF170

Lower limb spasticity

5COQ4
Def

Spasticity

5ADAMTS9
Lim
5HMNR11

NEURONOPATHY, DISTAL HEREDITARY MOTOR, AUTOSOMAL RECESSIVE 11, WITH SPASTICITY; HMNR11

5PRICKLE2
Lim
5SETBP1
Def

Opisthotonus

5ZC4H2
Def

Spasticity

5ALG3
Def

Spastic tetraparesis

5BCKDHB
Def

Opisthotonus

5DNM1
Def

Appendicular spasticity

5FDXR
Def

Spastic gait

5FRMPD4
Def

Spasticity

5KIDINS220
Def

Spastic gait

5NFU1
Def

Progressive spastic paraplegia

5SOD1
Def

Lower limb spasticity

5TUBA4A
Mod

Spasticity

5PPIL1

Spastic tetraplegia

5TMEM63C

Spastic gait

4ADAT3
Mod

Spasticity

4GSX2
Mod

Spastic tetraplegia

4THOC2
Def

Spasticity

4FTH1
Mod

Spasticity

4ATN1
Def

Appendicular spasticity

4SCYL2

Spasticity

4TUBB3
Def

Spasticity

4EXOSC8

Spastic tetraparesis

4ADM2
4ATXN7
4BCAS3
4C1QTNF3-AMACR
4CADPS
4CDK19
4CEP15
4CHKB-CPT1B
4CHKB-DT
4CIMAP1B
4CPT1B
No
4DENND6B
4EEFSEC
4EPM2A-DT
4FEZF2
4HDAC10
4HECTD4
4HNRNPUL2-BSCL2
4KBTBD8
4KLHDC7B
4KLHDC7B-DT
4LMF2
4LRIG1
4MAGI1
4MAPK11
4MAPK12
4MAPK8IP2
4NCAPH2
4PLXNB2
4PPP6R2
4PTPRG
4RECQL
Dis
4SELENOO
4SLC39A14
4SUCLG2
4SYCE3
4SYNPR
4TAFA1
4TAFA4
4THOC7
4TMPPE
4YWHAE
4WDR73

Spasticity

4CYFIP2
Def

Spasticity

4TOE1

Spasticity

4CARS2
Mod

Opisthotonus

4TELO2
Def

Spasticity

4PET100
Def

Spastic tetraplegia

4TPK1
Mod

Spasticity

3APC2
Str

Spastic tetraplegia

3WDR45B

Spastic tetraplegia

3ACBD6

Upper limb spasticity

3GDAP2
Str

Spasticity

3PANK2

Spasticity

3ATAD3A

Spasticity

3C19ORF12
Def

Spasticity

3EIF2S3
Def

Spastic tetraparesis

3GM2A
Def

Spastic tetraparesis

3HEPACAM
Def

Spasticity

3KCNT1
Def

Spasticity

3MCCC2
Def

Opisthotonus

3MOCS1
Def

Spastic tetraplegia

3NACC1
Def

Spasticity

3NDUFAF4
Def

Spastic tetraplegia

3POMGNT1
Def

Spasticity

3SPART
Def

Spastic paraparesis

3UNC80
Def

Spasticity

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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.