Genes associated with “hereditary spastic paraplegia

102 genes foundHPO: Spastic paraplegiaOpen Targets: hereditary spastic paraplegia4829 ClinVar P/LP variants3 PanelApp panels
Some sources returned errors (2)

omim: Error: OMIM search: 429

omimClinSyn: Error: OMIM CS: 429

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

58 genes
1
DDHD1

DDHD domain containing 1

59
score
ClinGen: DefinitivePanel: Green (3)P2G #34GTR ↑

hereditary spastic paraplegia 28

Frequency
33%
n=3
P/LP Variants
6
OT Score
0.76
2
GBA2

glucosylceramidase beta 2

57
score
ClinGen: DefinitivePanel: Green (3)P2G #48GTR ↑

hereditary spastic paraplegia 46

Frequency
100%
n=5
P/LP Variants
5
OT Score
0.78
3
SPG11

SPG11 vesicle trafficking associated, spatacsin

56
score
ClinGen: DefinitivePanel: Green (3)P2G #4GTR ↑

hereditary spastic paraplegia 11

Frequency
-
P/LP Variants
83
OT Score
0.79
4
FA2H

fatty acid 2-hydroxylase

54
score
ClinGen: DefinitivePanel: Green (3)GTR ↑

hereditary spastic paraplegia 35

Frequency
-
P/LP Variants
7
OT Score
0.85
5
NT5C2

5'-nucleotidase, cytosolic II

54
score
ClinGen: DefinitivePanel: Green (3)GTR ↑

hereditary spastic paraplegia 45

Frequency
100%
n=9
P/LP Variants
4
OT Score
0.74
6
SPAST

spastin

54
score

hereditary spastic paraplegia 4

Frequency
-
P/LP Variants
71
OT Score
0.84
7
ENTPD1

ectonucleoside triphosphate diphosphohydrolase 1

53
score
ClinGen: DefinitivePanel: Green (3)P2G #47GTR ↑

hereditary spastic paraplegia 64

Frequency
100%
n=4
P/LP Variants
5
OT Score
0.73
8
AP5Z1

adaptor related protein complex 5 subunit zeta 1

52
score
ClinGen: DefinitivePanel: Green (3)GTR ↑

hereditary spastic paraplegia 48

Frequency
100%
n=2
P/LP Variants
15
OT Score
0.75
9
CYP2U1

cytochrome P450 family 2 subfamily U member 1

52
score
ClinGen: DefinitivePanel: Green (3)P2G #29GTR ↑

hereditary spastic paraplegia 56

Frequency
-
P/LP Variants
7
OT Score
0.83
51L1CAM
DefP:G×3#8

X-linked hydrocephalus with stenosis of the aqueduct of Sylvius

50B4GALNT1
DefP:G×3

hereditary spastic paraplegia 26

49PLP1
DefP:G×3#10

Pelizeaus-Merzbacher spectrum disorder

47ERLIN2
DefP:G×3

Spastic paraplegia

47WASHC5
ModP:G×3

hereditary spastic paraplegia 8

47ARL6IP1
DefP:G×3

hereditary spastic paraplegia 61

46KIF1A
DefP:G×3

Spastic paraplegia

44SPG7
P:G×3#5

hereditary spastic paraplegia 7

43ATL1
DefP:G×3

hereditary spastic paraplegia 3A

42TECPR2
P:G×3

hereditary spastic paraplegia 49

40ERLIN1
DefP:G×3

ER lipid raft associated 1

40PNPLA6
DefP:G×3

trichomegaly-retina pigmentary degeneration-dwarfism syndrome

40CPT1C
LimP:G×2

hereditary spastic paraplegia 73

40BSCL2
DefP:G×3

hereditary spastic paraplegia 17

40DDHD2
P:G×3

hereditary spastic paraplegia 54

39UCHL1
DefP:G×2

early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome

39CYP7B1
DefP:G×3

hereditary spastic paraplegia 5A

39REEP1
P:G×3

hereditary spastic paraplegia 31

38ZFYVE26
P:G×3

hereditary spastic paraplegia 15

36MAG
DefP:G×3
35KIDINS220
DefP:G×3

spastic paraplegia, intellectual disability, nystagmus, and obesity

35AP4E1
DefP:G×3

hereditary spastic paraplegia 51

34ALS2
DefP:G×3#11

infantile-onset ascending hereditary spastic paralysis

33GJC2
DefP:A×3

hereditary spastic paraplegia 44

33KIF5A
DefP:G×3

hereditary spastic paraplegia 10

33ATP13A2
DefP:G×3

autosomal recessive spastic paraplegia type 78

33ALDH18A1
DefP:G×3

autosomal recessive complex spastic paraplegia type 9B

32IBA57
DefP:A×3

hereditary spastic paraplegia 74

31FARS2
DefP:G×3

hereditary spastic paraplegia 77

30SPART
DefP:G×3

Troyer syndrome

30AP4S1
DefP:G×3

hereditary spastic paraplegia 52

29REEP2
P:G×3

hereditary spastic paraplegia 72

28AP4B1
DefP:G×3

hereditary spastic paraplegia 47

27ABCD1
DefP:G×3#1

adrenoleukodystrophy

26SLC16A2
DefP:G×3#2

Allan-Herndon-Dudley syndrome

26HPDL
ModP:G

neurodevelopmental disorder with progressive spasticity and brain white matter abnormalities

25AP4M1
DefP:G×3
24UBAP1
P:G×3

spastic paraplegia 80, autosomal dominant

24SPG21
P:G×3

mast syndrome

24NIPA1
P:G×3

hereditary spastic paraplegia 6

24KIF1C
P:G×3

kinesin family member 1C

24RTN2
P:G×3

hereditary spastic paraplegia 12

23HACE1
P:G×3

HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1

23GPT2
DefP:G

glutamic--pyruvic transaminase 2

22SERAC1
DefP:G×3
22AMPD2
P:A×3

hereditary spastic paraplegia 63

21CAPN1
P:G×3

autosomal recessive spastic paraplegia type 76

21PCYT2
P:G×3

phosphate cytidylyltransferase 2, ethanolamine

20DSTYK
ModP:A×3

hereditary spastic paraplegia 23

Consider

23 genes
20C19ORF12
DefP:G×3

hereditary spastic paraplegia 43

19RNASEH2B
DefP:G×2

Aicardi-Goutieres syndrome 2

18SPTAN1
DefP:G×2

spastic paraplegia 91, autosomal dominant, with or without cerebellar ataxia

18RNF170
P:G

spastic paraplegia 85, autosomal recessive

17PI4KA
P:A

spastic paraplegia 84, autosomal recessive

17HSPD1
P:G×3

hypomyelinating leukodystrophy 4

17SLC2A1
DefP:G×2#13

dystonia 9

17KDM5C
DefP:G×3

syndromic X-linked intellectual disability Claes-Jensen type

17SLC25A15
DefP:G×2

ornithine translocase deficiency

16GBE1
DefP:G

adult polyglucosan body disease

16TUBB4A
DefP:G×3
16WDR45B
P:G×3

neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures

16VPS37A
LimP:A×3

hereditary spastic paraplegia 53

12CCT5
P:R×3

hereditary sensory and autonomic neuropathy with spastic paraplegia

12SLC33A1
P:A×3#14

hereditary spastic paraplegia 42

11ABHD16A
P:G×2

spastic paraplegia 86, autosomal recessive

11PAX3
Def#9

Waardenburg syndrome type 3

11VAMP1
P:A×3

spastic ataxia 1

11GAN
Def#6

giant axonal neuropathy 1

11PDHX
Def#7

pyruvate dehydrogenase E3-binding protein deficiency

8ELOVL1
P:G

ichthyotic keratoderma, spasticity, hypomyelination, and dysmorphic facial features

Possible

15 genes — click to expand
8STXBP1
Def

developmental and epileptic encephalopathy, 4

7MECP2
Def

X-linked intellectual disability-psychosis-macroorchidism syndrome

7PEX3
Def

peroxisome biogenesis disorder 10B

7CNNM2
Def
7ITPR1
Def
5MTRFR
Def

hereditary spastic paraplegia 55

5KLC2
P:R

spastic paraplegia, optic atropy, and neuropathy

leukodystrophy, hypomyelinating, 23, with ataxia, deafness, liver dysfunction, and dilated cardiomyopathy

5LAMB1
Mod

cobblestone lissencephaly without muscular or ocular involvement

5NFU1
Def

spastic paraplegia 93, autosomal recessive

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