Publications about genetic testing for neurological disorders
  1. NGS Panel – Genetic Testing for Spastic Paraplegia

Spastic Paraplegia

June 15, 2017

Disease synonyms

Hereditary Spastic Paraplegia (HSP), Spastic paraplegia, SPG, Familial Spastic Paraplegia, Hereditary Spastic Paraparesis, Strumpell-Lorrain Syndrome

Hereditary Spastic Paraplegia (HSP) autosomal recessive, Spastic paraplegia autosomal recessive, ARSPG, Spastic paraplegia, SPG, Familial spastic paraplegia, Hereditary spastic paraparesis, Strumpell-Lorrain Syndrome

Inheritance pattern

Autosomal recessive, autosomal dominant

Clinical features

Hereditary Spastic Paraplegia (HSP), also known as SPG (Spastic Paraplegia) is a group of inherited neurological diseases whose main feature is progressive spasticity in the lower limbs as a result of neuronal dysfunction 1, 2. The condition sometimes also affects the optic nerve and retina or causes cataracts, ataxia, epilepsy, cognitive impairment, peripheral neuropathy, and deafness 1, 2. The prevalence of HSP/SPG has been estimated to range from 1.3 in 100,000 affected patients in Ireland 3 to 9.6 in 100,000 patients in Spain 4.

The major neuropathological feature of SPG is axonal degeneration that is maximal in the terminal portions of the longest descending and ascending tracts. These include the crossed and uncrossed corticospinal tracts to the legs and fasciculus gracilis. The spinocerebellar tract is also involved to a lesser extent. Neuronal cell bodies of degenerating fibers are preserved and there is no evidence of primary demyelination.

Spasticity in the lower limbs alone is described as pure SPG. However, SPG is classified as complex or complicated when it is associated with other neurological signs, including ataxia, mental retardation, dementia, extrapyramidal signs, visual dysfunction, or epilepsy, or with extra neurological signs. Complicated forms are diagnosed as SPGs when pyramidal signs are the predominant neurological characteristic.

Genetic types of SPG can be inherited in an autosomal dominant, autosomal recessive, X-linked, or maternally inherited (mitochondrial) manner 1, 2. Different genetic types of SPG usually cannot be distinguished by clinical and neuroimaging parameters alone, therefore molecular genetic testing is imperative. Genetic mapping has identified at least 60 different SPG loci, designated as SPG (Spastic Paraplegia) in order of their discovery (SPG1, SPG2 etc.) 1, 2, 5.

Diagnosis of SPG is established by the following clinical features 1, 2:

  • Typical clinical symptoms of spastic gait impairment and neurologic findings of spastic weakness, hyperreflexia, typically associated with bilateral extensor plantar responses
  • A family history of similarly affected first-degree relatives
  • Autosomal dominant, autosomal recessive, or X-linked inheritance or maternal (mitochondrial) inheritance
  • The exclusion of other disorders.

The molecular genetic testing strategy for the SPGs is based on the following features 1, 2:

  • Mode of inheritance
  • Clinical findings (e.g., age at onset, additional clinical features, MRI findings)
  • Prevalence of the disorder (e.g., mutations of SPG4 (encoding spastin), the single most common cause of dominantly inherited SPG, accounts for approximately 30-40% of affected individuals)
  • Patient’s ethnicit.

Autosomal dominant SPG has been associated with following genes: ALDH18A1, ATL1, ATP2B4, BICD2, BSCL2, HSPD1, KIAA0196, KIF5A, NIPA1, REEP1, RTN2, SLC33A1, SPAST, TTR, VAMP1, ZFYVE27. The rational for selection of these particular genes in CENTOGENE´s Spastic paraplegia autosomal dominant panel is illustrated in Table 1.

Homozygous ALDH18A1 mutations were identified as segregating in three independent families with autosomal dominant hereditary spastic paraplegia, as well as in two sporadic patients 5. All affected patients showed decreased levels of plasma ornithine, citrulline, arginine and proline 5.

ATL1 mutations have been confirmed as the most common cause of early-onset SPG (SPG3A), accounting for approximately 30%-50% of all AD SPG with onset before age of ten 6. SPG3A accounts for approximately 10%-15% of all AD SPG cases 6. ATL1 gene encodes atlastin protein, a member of the dynamin family of large GTPases that contains conserved motifs for GTPase binding site and hydrolysis. Atlastin play essential roles in a wide variety of vesicle trafficking events: regulation of neurotrophic factors, recycling of synaptic vesicles, maintenance and distribution of mitochondria, maintenance of the cytoskeleton, and others 6. Thus, there are many possibilities by which atlastin mutations could cause axonal degeneration.

Recently a novel mutation c.803G>A, p.R268Q was identified in plasma membrane calcium ATPase (ATP2B4) gene in a Chinese family with autosomal dominant SPG 7. This mutation co-segregated with the phenotype in the six family members studied and is predicted to be pathogenic when multiple deleteriousness predictions were combined.

Mutations in BICD2 cause a complex neurological phenotype consisting of major features of congenital spinal muscular atrophy and hereditary spastic paraplegia 8. Missense mutation c.320C>T; p.Ser107Leu was identified in several affected families worldwide.

Mutations in the BSCL2 gene are reported to cause an autosomal dominant disorder characterized by amyotrophy of predominantly upper limb muscles and mild pyramidal features 9. The phenotypic spectrum of BSCL2-related neurologic disorders includes Silver syndrome and variants of Charcot-Marie-Tooth disease type 2, distal hereditary motor neuropathy (dHMN) type V, and spastic paraplegia 17 (SPG17). Most common mutation are identified within the exon 3 (p.Asn88Ser and p.Ser90Leu are the only two mutations associated with BSCL2-related neurologic disorders to date) 9.

Spastic paraplegia 13, autosomal dominant (SPG13) is caused by mutations in the HSPD1 gene 10. The HSPD1 gene encodes the heat shock 60kDa protein 1 (chaperonin), a member of the chaperonin family, that has a function as a signaling molecule in the innate immune system. It is also essential for the folding and assembly of newly imported proteins in the mitochondria. Only three missense mutations have been reported so far 10.

Mutations in the KIAA0196 gene have been found to cause spastic paraplegia type 8 (SPG8) 11. The gene KIAA0196 encodes synthesis of the membrane protein strumpellin. Five point mutations that cause spastic paraplegia have been reported so far.

Mutations in the gene KIF5A cause the disease spastic paraplegia type 10 (SPG10) 12. The gene KIF5A encodes kinesin family member 5A, a member of the protein complex that functions as a microtubule motor in intracellular organelle transport. Subjects with KIF5A mutations exhibit either uncomplicated SPG or SPG associated with distal muscle atrophy 12.

The NIPA1 gene mutations are causing autosomal dominant hereditary spastic paraplegia 6 (SPG6). The NIPA1 gene (non-imprinted in Prader-Willi/Angelman syndrome 1) is highly expressed in neuronal tissues and encodes a putative membrane transporter or receptor 13. This gene encodes a magnesium transporter that associates with early endosomes and the cell surface in a variety of neuronal and epithelial cells. The mutations on the NIPA1 gene appear to act through a dominant negative gain of function. Ten mutations have been reported thus far, half of them related to SPG and half to the ALS phenotype 13.

Mutations in the REEP1 gene, encoding receptor accessory protein 1, a mitochondrial protein that functions to enhance the cell surface expression of odorant receptors 14, have been linked with the spastic paraplegia autosomal dominant type 31 and distal hereditary motor neuropathy type 5B (HMN5B). More than 40 mutations have been reported in the REEP1 gene, and only one of them was associated with HMN5B. All the other mutations are mostly missense and small deletions associated with SPG31 14.

Mutations in the ER-shaping protein reticulon 2, encoded by the gene RTN2, are the cause of the axon-degenerative disorder hereditary spastic paraplegia type 12 (SPG12) 15. The RTN2 protein was found to interact with spastin, and this interaction implicates a reticulon protein in axonopathy, showing that this protein participates in a network of interactions among SPG proteins involved in ER shaping, and further support the hypothesis that abnormal ER morphogenesis is a pathogenic mechanism in SPG.

Mutations in the SLC33A1 gene cause spastic paraplegia type 42 (SPG42), as well as a lethal autosomal-recessive disorder with congenital cataracts, hearing loss, and low serum copper and ceruloplasmin 16. SLC33A1 is encoding solute carrier family 33, the protein that belongs to the family of the acetyl-CoA transporters.

Spastic paraplegia 4 (SPG4) is caused by mutations in the SPAST gene, which encodes spastin protein 17. SPG4 (SPAST-associated HSP) is the most frequently occurring form of autosomal dominant hereditary spastic paraplegia, accounting for an estimated 15%-40% of the pure dominant forms of hereditary spastic paraplegia 17. SPG4 is characterized by insidiously progressive bilateral lower-limb gait spasticity. More than 50% of affected individuals have some weakness in the legs and an impaired sense of vibration at the ankles. About one third of those affected have sphincter disturbances. Onset is insidious, mostly in young adulthood, although symptoms may start as early as one year of age and as late as age 75 17. The SPAST gene encodes the protein spastin, a putative nuclear member of the AAA (ATPases associated with diverse cellular activities) protein family. SPAST is ubiquitously expressed in adult and fetal human tissues, showing slightly higher expression in the fetal brain.

Mutations in gene TTR have been associated with SPG phenotypes in families with primary diagnosis of amyloidosis 18. Familial transthyretin amyloidosis is characterized by a slowly progressive peripheral sensorimotor neuropathy and autonomic neuropathy as well as non-neuropathic changes of cardiomyopathy, nephropathy, vitreous opacities, and CNS amyloidosis. Several missense mutations have been reported so far.

Mutations in VAMP1 gene are causing spastic ataxia 1 (SPAX1), a rare neurodegenerative disorder characterized by lower-limb spasticity and ataxia in the form of head jerks, ocular movement abnormalities, dysphagia, dysarthria, and gait disturbance 19. VAMP1 encodes a vesicle-associated membrane protein 1, a critical protein for synaptic exocytosis.

The ZFYVE27 gene encodes the protein protruding (zinc finger, FYVE domain containing 27). Mutations in this gene have been related to the spastic paraplegia type 33, classified as a pure spastic paraplegia 20.

Hereditary autosomal recessive SPG is diagnosed based on the following 1, 2:

  • Typical clinical symptoms of spastic gait impairment and neurological findings of spasticity and weakness of the lower limbs
  • Positive family history of autosomal recessive disease
  • Exclusion of other disorders.

Mutations in the following genes have been associated with autosomal recessive SPG: ALS2, AMPD2, AP4B1, AP4E1, AP4M1, AP4S1, AP5Z1, ARL6IP1, ARSI, B4GALNT1, C12ORF65, C19orf12, CCT5, CYP2U1, CYP7B1, DDHD1, DDHD2, ENTPD1, ERLIN1, ERLIN2, EXOSC3, FA2H, FLRT1, GBA2, GJC2, KIF1A, KIF1C, L1CAM, MAG, NT5C2, PLP1, PNPLA6, REEP2, SACS, SLC16A2, SPG11, SPG20, SPG21, SPG7, TECPR2, TFG, USP8, VPS37A, WDR48, ZFYVE26 (Table 2). Among the autosomal recessive SPGs, approximately 20% of the patients carry mutations in the SPG11 (KIAA1840) gene 21, whereas >15 other genes are rarely mutated and account for rare cases of SPGs, for example in single families 21-42 (Table 2).

Treatment of SPG is exclusively symptomatic. Spasticity benefits from daily physical therapy, baclofen or tizanidine. Long-term intrathecal baclofen therapy can be administered via a surgically implanted programmable pump. Hypertonic bladder benefits from anticholinergic drugs and neuropathic pain from gabapentin or pregabalin. Parkinsonism, dementia, and epilepsy are treated according to the respective guidelines.

CENTOGENE offers sequencing and deletion/duplication analysis for the Spastic paraplegia panel, autosomal dominant (ALDH18A1, ATL1, ATP2B4, BICD2, BSCL2, HSPD1, KIAA0196, KIF5A, NIPA1, REEP1, RTN2, SLC33A1, SPAST, TTR, VAMP1, ZFYVE27) and Spastic paraplegia panel, autosomal recessive (ALS2, AMPD2, AP4B1, AP4E1, AP4M1, AP4S1, AP5Z1, ARL6IP1, ARSI, B4GALNT1, C12ORF65, C19orf12, CCT5, CYP2U1, CYP7B1, DDHD1, DDHD2, ENTPD1, ERLIN1, ERLIN2, EXOSC3, FA2H, FLRT1, GBA2, GJC2, KIF1A, KIF1C, L1CAM, MAG, NT5C2, PLP1, PNPLA6, REEP2, SACS, SLC16A2, SPG11, SPG20, SPG21, SPG7, TECPR2, TFG, USP8, VPS37A, WDR48, ZFYVE26).

Differential diagnosis

The differential diagnosis of SPG-related disorders – depending on the major symptoms in the initial case – includes the following diseases:

  • Structural abnormalities involving the brain or spinal cord (e.g., tethered cord syndrome and spinal cord compression)
  • Motor neuron disorders such as slowly progressive amyotrophic lateral sclerosis (ALS) or primary lateral sclerosis (PLS)
  • Leukodystrophies such as steadily progressive multiple sclerosis, B12 deficiency, Krabbe disease, metachromatic leukodystrophy, and adrenomyeloneuropathy
  • Spinocerebellar ataxias (SCAs), Friedreich ataxia, spastic ataxia of Charlevoix-Saguenay, etc.
  • Infection (e.g., human immunodeficiency virus [HIV AIDs], tropical spastic paraplegia and neurosyphilis)
  • Metabolic disorders
  • Dopa-responsive dystonia.

Testing strategy

CENTOGENE offers advanced, fast and cost-effective strategy to test large NGS panels and diagnose complex phenotypes based on the PCR-free Whole Genome Sequencing and NGS technology. This approach offers an unparalleled advantage by reducing amplification/capture biases and provides sequencing of entire gene at a more uniform coverage.

To confirm/establish the diagnosis, CENTOGENE offers the following testing strategy for hereditary spastic paraplegia using NGS Panel Genomic targeted towards this specific phenotype:

Step 1: Whole genome sequencing from a single filter card. The sequencing covers the entire genic region (coding region, exon/intron boundaries, intronic and promoter) for all the genes included in the Spastic paraplegia panels. Copy Number Variants analysis derived from NGS data is also included.

Step 2: If no mutation is identified after analysis of the Spastic paraplegia panels, based on the approval and consent, we further recommend to continue the bioinformatics analysis of the data obtained by whole genome sequencing to cover genes that are either implicated in an overlapping phenotype or could be involved in a similar pathway but not strongly clinically implicated based on the current information in literature.

Referral reasons

The following individuals are candidates for spastic paraplegia-related gene testing:

  • Individuals with a family history of hereditary spastic paraplegia and presentation of lower extremity spasticity and weakness and other common symptoms
  • Individuals without a positive family history, but with symptoms resembling hereditary spastic paraplegia
  • Individuals with a negative but suspected family history, in order to perform proper genetic counseling (prenatal analyses are recommended in families with affected individuals).

Test utility

Sequencing, deletion/duplication of hereditary spastic paraplegia-related genes should be performed in all individuals suspected of having hereditary spastic paraplegias and suspected phenotypes. In parallel, other genes reported to be related with this clinical phenotype should also be analyzed for the presence of mutations, due to the overlap in many clinical features caused by those particular genes.

Confirmation of a clinical diagnosis through genetic testing can allow for genetic counseling and may direct medical management. Genetic counseling can provide a patient and/or family with the natural history of the hereditary spastic paraplegias and related disorders, identify at-risk family members, provide reproductive risks as well as preconception/prenatal options, and allow for appropriate referral for patient support and/or resources.