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Invitae Hereditary Spastic Paraplegia Comprehensive Panel

Test description

The Invitae Hereditary Spastic Paraplegia Comprehensive Panel analyzes up to 65 genes associated with hereditary spastic paraplegia (HSP). These genes include the most common causes of autosomal dominant, autosomal recessive, and X-linked HSP.

The clinical presentation of HSP is variable, and the Invitae Hereditary Spastic Paraplegia Comprehensive Panel may confirm a clinical diagnosis and identify a causative gene while avoiding costly and time-consuming sequential testing. This test is Invitae’s broadest HSP panel. Because this panel covers genes with dominant, recessive, and X-linked inheritance patterns, it is particularly helpful if the inheritance pattern is unclear based on the individual’s family history.

Genes tested

Primary panel

ABCD1 ALDH18A1 ALS2 AP4B1 AP4E1 AP4M1 AP4S1 AP5Z1 ATL1 B4GALNT1 BSCL2 C12orf65 CYP2U1 CYP7B1 DDHD1 DDHD2 ERLIN2 FA2H GBA2 GJC2 HEXA HSPD1 KDM5C KIF1A KIF1C KIF5A L1CAM NIPA1 NT5C2 PLP1 PNPLA6 REEP1 REEP2 RTN2 SACS SLC16A2 SPART SPAST SPG11 SPG21 SPG7 TECPR2 VAMP1 WASHC5 ZFYVE26

Add-on Preliminary-evidence Genes for Hereditary Spastic Paraplegia

AMPD2 ARL6IP1 ARSI ATP13A2 C19orf12 CCT5 CPT1C ENTPD1 ERLIN1 EXOSC3 IBA57 MAG PGAP1 RAB3GAP2 SLC33A1 TFG USP8 VPS37A ZFR ZFYVE27

Preliminary-evidence genes currently have early evidence of a clinical association with the specific disease covered by this test. Some clinicians may wish to include genes which do not currently have a definitive clinical association, but which may prove to be clinically significant in the future. These genes can be added at no additional charge. Visit our Preliminary-evidence genes page to learn more.

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Primary panel (45 genes)

Panel details and technical assay limitations

Add-on Preliminary-evidence Genes for Hereditary Spastic Paraplegia (20 genes)

AMPD2 ARL6IP1 ARSI ATP13A2 C19orf12 CCT5 CPT1C ENTPD1 ERLIN1 EXOSC3 IBA57 MAG PGAP1 RAB3GAP2 SLC33A1 TFG USP8 VPS37A ZFR ZFYVE27

Panel details and technical assay limitations

Alternative tests to consider

Hereditary spastic paraplegia may have overlapping features with other neurological disorders, in which case clinicians may consider Invitae’s Comprehensive Neuropathy panel, which additionally includes genes associated with Charcot-Marie-Tooth disease, Distal Hereditary Motor Neuropathy, and Hereditary Sensory and Autonomic Neuropathy.

Invitae Comprehensive Neuropathies panel

Clinical information

Clinical description

Hereditary spastic paraplegia (HSP) is a clinically and genetically heterogeneous group of neurological disorders that is subdivided into complicated (i.e., syndromic) and uncomplicated forms. All forms of HSP, complicated and uncomplicated, share the primary symptom of lower-extremity spastic weakness. Individuals with complicated HSP exhibit additional neurologic features such as intellectual disability, seizures, ataxia, peripheral neuropathy, deafness, cataracts, retinal degeneration, or muscle atrophy, depending on which gene is causative. Both types of HSP are caused by the dysfunction of axons in the corticospinal tract that carry signals to the lower extremities, and both types can be inherited in an autosomal dominant, autosomal recessive, or X-linked pattern.

Gene	Subtype	Inheritance			Clinical form		Associated syndromes and other related disorders
Gene	Subtype	Autosomal dominant	Autosomal recessive	X-linked	Uncomplicated	Complicated	Associated syndromes and other related disorders
ABCD1				✓		✓	adrenoleukodystrophy
ALDH18A1	SPG9A, SPG9B	✓	✓			✓	congenital cataracts, hearing loss, and neurodegeneration
ALS2	IAHSP		✓			✓	amyotrophic lateral sclerosis, juvenile; Primary lateral sclerosis, juvenile
AMPD2^*	SPG63		✓			✓	pontocerebellar hypoplasia
AP4B1	SPG47		✓			✓
AP4E1	SPG51		✓			✓
AP4M1	SPG50		✓			✓
AP4S1	SPG52		✓			✓
AP5Z1	SPG48		✓		✓
ARL6IP1^*	SPG61		✓			✓
ARSI^*	SPG66		✓			✓
ATL1	SPG3A	✓			✓		hereditary sensory neuropathy
ATP13A2^*	SPG78		✓			✓	Kufor-Rakeb syndrome
B4GALNT1	SPG26		✓			✓
BSCL2	SPG17	✓				✓	silver syndrome, type-V; distal hereditary motor neuropathy; Charcot-Marie-Tooth disease, type-2; Berardinelli-Seip congenital lipodystrophy
C12ORF65	SPG55		✓			✓
C19orf12^*	SPG43		✓			✓	neurodegeneration with brain iron accumulation type 4
CCT5^*			✓			✓	hereditary sensory neruopathy with spastic paraplegia
CPT1C^*	SPG73	✓			✓
CYP2U1	SPG56		✓			✓
CYP7B1	SPG5		✓		✓	✓
DDHD1	SPG28		✓		✓	✓
DDHD2	SPG54		✓			✓
ENTPD1^*	SPG64		✓			✓
ERLIN1^*	SPG62		✓			✓
ERLIN2	SPG18		✓			✓
EXOSC3^*			✓			✓	pontocerebellar hypoplasia
FA2H	SPG35		✓			✓
GBA2	SPG46		✓			✓
GJC2	SPG44		✓			✓	hypomyelinating leukodystrophy; hereditary lymphedema
HEXA			✓			✓	Hexosaminidase A deficiency
HSPD1	SPG13	✓			✓		MitCHAP-60 disease (hypomyelinating leukodystrophy)
IBA57^*	SPG74		✓			✓
KDM5C	MRXSCJ			✓		✓	X-linked Intellectual disability, Claes-Jensen type
KIF1A	SPG30	✓	✓		✓	✓
KIF1C	SPAX2		✓			✓	spastic ataxia 2
KIF5A	SPG10	✓			✓	✓
L1CAM	SPG11			✓		✓	L1 syndrome
MAG^*	SPG75		✓			✓
NIPA1	SPG6	✓			✓	✓
NT5C2	SPG45		✓			✓
PGAP1^*			✓			✓	intellectual disability
PLP1	SPG2			✓		✓	Pelizaeus-Merzbacher disease
PNPLA6	SPG39		✓			✓	Boucher-Neuhäuser syndrome, Oliver-McFarlane/Laurence-Moon syndrome
RAB3GAP2^*			✓			✓	Warburg Micro syndrome-2, Martsolf syndrome
REEP1	SPG31	✓			✓	✓	distal hereditary motor neuropathy
REEP2	SPG72	✓	✓		✓
RTN2	SPG12	✓			✓
SACS	ARSACS		✓			✓	autosomal recessive spastic ataxia of Charlevoix-Saguenay
SLC16A2				✓		✓	MCT8-specific thyroid hormone cell transporter deficiency (Allan-Herndon-Dudley syndrome)
SLC33A1^*	SPG42	✓			✓		congenital cataracts, hearing loss, and neurodegeneration
SPART (formerly known as SPG20)	SPG20		✓			✓	Troyer syndrome
SPAST	SPG4	✓			✓	✓
SPG7	SPG7		✓		✓	✓	primary lateral sclerosis
SPG11	SPG11		✓			✓	Charcot-Marie-Tooth disease, type-2; amyotrophic lateral sclerosis
SPG21	SPG21		✓			✓
TECPR2	SPG49		✓			✓
TFG^*	SPF57		✓			✓	hereditary motor and sensory neuropathy, Okinawa type
USP8^*			✓		✓
VAMP1	SPAX1	✓				✓
VPS37A^*	SPG53		✓			✓
WASHC5 (formerly known as KIAA0196)	SPG8	✓			✓		Ritscher-Schinzel syndrome 1
ZFR^*	SPG71		✓			✓
ZFYVE26	SPG15		✓			✓	Kjellin syndrome
ZFYVE27^*	SPG33	✓			✓

^*Preliminary-evidence gene

Clinical sensitivity

This multi-gene panel analyzes up to 65 genes, including the most common genetic causes of HSP: ATL1, CYP7B1, K1F5A, REEP1, SPAST, SPG11, and SPG7. Other rare genes are also included on this panel, which increases the clinical sensitivity of this test, though the exact contribution of these additional genes to HSP is not known. In previous studies, the percent of families who received a genetic diagnosis after systematic testing ranged from 33% to 55% in autosomal dominant HSP and 18% to 29% in autosomal recessive HSP.

Inheritance

HSP can be inherited in an autosomal dominant, autosomal recessive, or X-linked pattern.

Penetrance

The penetrance of HSP varies depending on the causative gene and the specific pathogenic variant. Certain genes, such as HSPD1, REEP1, and SPAST, are known to have reduced penetrance and variable expression within a family. Average age of onset also varies by gene and can occur at any time from early childhood to age 70.

Prevalence/Incidence

The prevalence of HSP has been estimated at 1 in 10,000 to 1 in 100,000 people. Approximately 90% of these cases are uncomplicated and 10% present as complicated HSP.

Considerations for testing

The clinical presentation of HSP can be variable. Genetic testing may confirm a suspected diagnosis or rule out disorders with similar symptoms. A genetic diagnosis may also help predict disease progression or inform family planning.

References

Assay

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons, +/- 10 base pairs of adjacent intronic sequence in the transcript listed below. In addition, analysis covers the select non-coding variants specifically defined in the table below. Any variants that fall outside these regions are not analyzed. Any specific limitations in the analysis of these genes are also listed in the table below.

Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for single nucleotide variants, insertions and deletions <15bp in length, and exon-level deletions and duplications. Invitae's methods also detect insertions and deletions larger than 15bp but smaller than a full exon but sensitivity for these may be marginally reduced. Invitae’s deletion/duplication analysis determines copy number at a single exon resolution at virtually all targeted exons. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. Certain types of variants, such as structural rearrangements (e.g. inversions, gene conversion events, translocations, etc.) or variants embedded in sequence with complex architecture (e.g. short tandem repeats or segmental duplications), may not be detected. Additionally, it may not be possible to fully resolve certain details about variants, such as mosaicism, phasing, or mapping ambiguity. Unless explicitly guaranteed, sequence changes in the promoter, non-coding exons, and other non-coding regions are not covered by this assay. Please consult the test definition on our website for details regarding regions or types of variants that are covered or excluded for this test. This report reflects the analysis of an extracted genomic DNA sample. In very rare cases, (circulating hematolymphoid neoplasm, bone marrow transplant, recent blood transfusion) the analyzed DNA may not represent the patient's constitutional genome.

Gene	Transcript reference	Sequencing analysis	Deletion/Duplication analysis
ABCD1	NM_000033.3
ALDH18A1	NM_002860.3
ALS2	NM_020919.3
AMPD2	NM_001257360.1
AP4B1	NM_006594.3
AP4E1	NM_007347.4
AP4M1	NM_004722.3
AP4S1	NM_007077.4
AP5Z1	NM_014855.2
ARL6IP1	NM_015161.1
ARSI	NM_001012301.2
ATL1	NM_015915.4
ATP13A2	NM_022089.3
B4GALNT1	NM_001478.4
BSCL2	NM_032667.6
C12orf65	NM_152269.4
C19orf12	NM_001031726.3
CCT5	NM_012073.3
CPT1C	NM_001136052.2
CYP2U1	NM_183075.2
CYP7B1	NM_004820.3
DDHD1	NM_001160147.1
DDHD2	NM_015214.2
ENTPD1	NM_001776.5
ERLIN1	NM_006459.3
ERLIN2	NM_007175.6
EXOSC3	NM_016042.3
FA2H	NM_024306.4
GBA2	NM_020944.2
GJC2*	NM_020435.3
HEXA	NM_000520.4
HSPD1	NM_002156.4
IBA57	NM_001010867.3
KDM5C	NM_004187.3
KIF1A	NM_004321.6
KIF1C	NM_006612.5
KIF5A	NM_004984.2
L1CAM	NM_000425.4
MAG	NM_002361.3
NIPA1	NM_144599.4
NT5C2	NM_012229.4
PGAP1	NM_024989.3
PLP1	NM_000533.4
PNPLA6	NM_006702.4
RAB3GAP2	NM_012414.3
REEP1	NM_022912.2
REEP2	NM_001271803.1
RTN2	NM_005619.4
SACS	NM_014363.5
SLC16A2	NM_006517.4
SLC33A1	NM_004733.3
SPART	NM_015087.4
SPAST	NM_014946.3
SPG11	NM_025137.3
SPG21	NM_016630.6
SPG7	NM_003119.3
TECPR2	NM_014844.3
TFG	NM_006070.5
USP8	NM_005154.4
VAMP1	NM_014231.3
VPS37A	NM_152415.2
WASHC5	NM_014846.3
ZFR	NM_016107.3
ZFYVE26	NM_015346.3
ZFYVE27	NM_001002261.3

GJC2: Analysis includes the promoter variants NM_020435.3:c.-167A>G and NM_020435.3:c.-170A>G.

Resources

Clinical resources

Invitae brochure Neurology gene list

Patient resources

Patient guide: Genetic testing simplified

Test information

Forms page Specimen requirements page

References

Headquarters | 458 Brannan Street, San Francisco, CA 94107

Laboratory & Shipping | 475 Brannan Street, Suite 230, San Francisco, CA 94107 | www.invitae.com

In the US | clientservices@invitae.com | p: 800-436-3037 | f: 415-276-4164

Outside the US | globalsupport@invitae.com or visit www.invitae.com/contact

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Invitae Hereditary Spastic Paraplegia Comprehensive Panel

Test description

Genes tested

Primary panel

Add-on Preliminary-evidence Genes for Hereditary Spastic Paraplegia

Order test

Primary panel (45 genes)

Customized gene selection (0 included, 0 excluded)

Add-on Preliminary-evidence Genes for Hereditary Spastic Paraplegia (20 genes)

Customized gene selection (0 included, 0 excluded)

Alternative tests to consider

Clinical information

Clinical description

Clinical sensitivity

Inheritance

Penetrance

Prevalence/Incidence

Considerations for testing

References

Assay

Assay and technical information

Resources

Clinical resources

Patient resources

Test information

References

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Invitae Hereditary Spastic Paraplegia Comprehensive Panel

Test description

Genes tested

Primary panel

Add-on Preliminary-evidence Genes for Hereditary Spastic Paraplegia

Order test

Primary panel (45 genes)

Customized gene selection (0 included, 0 excluded)

Add-on Preliminary-evidence Genes for Hereditary Spastic Paraplegia (20 genes)

Customized gene selection (0 included, 0 excluded)

Alternative tests to consider

Clinical information

Clinical description

Clinical sensitivity

Inheritance

Penetrance

Prevalence/Incidence

Considerations for testing

References

Assay

Assay and technical information

Resources

Clinical resources

Patient resources

Test information

References

Cost estimator

Subscriber's Info

Insurance Coverage

Based on the insurance provided, the out-of-pocket cost estimate is