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  • Test code: 03251
  • Turnaround time:
    10–21 calendar days (14 days on average)
  • Preferred specimen:
    3mL whole blood in a purple-top EDTA tube (K2EDTA or K3EDTA)
  • Alternate specimens:
    Saliva, assisted saliva, buccal swab and gDNA
  • Sample requirements
  • Request a sample kit
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Invitae Hereditary Spastic Paraplegia Comprehensive Panel

Test description

The Invitae Hereditary Spastic Paraplegia Comprehensive Panel analyzes genes associated with hereditary spastic paraplegia (HSP), a clinically and genetically heterogeneous group of neurological conditions characterized by lower-extremity spastic weakness. These genes were curated based on currently available evidence to provide a comprehensive test for the genetic causes of HSP. Given that HSPs are a heterogeneous group of conditions, identification of the underlying genetic cause can help confirm a clinical diagnosis, predict disease prognosis and progression, facilitate early detection of symptoms, inform family planning and genetic counseling, or promote enrollment in clinical trials.

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Primary panel (62 genes)

ABCD1 ALDH18A1 ALS2 AP4B1 AP4E1 AP4M1 AP4S1 AP5Z1 ARG1 ARL6IP1 ATL1 ATP13A2 B4GALNT1 BSCL2 C12orf65 CAPN1 CPT1C CYP27A1 CYP2U1 CYP7B1 DDHD1 DDHD2 ENTPD1 ERLIN1 ERLIN2 FA2H FARS2 GBA2 GJC2 HACE1 HEXA HSPD1 KCNA2 KDM5C KIDINS220 KIF1A KIF1C KIF5A L1CAM MAG NIPA1 NKX6-2 NT5C2 PLP1 PNPLA6 RAB3GAP2 REEP1 REEP2 RTN2 SACS SLC16A2 SPART SPAST SPG11 SPG21 SPG7 TECPR2 TFG UCHL1 VAMP1 WASHC5 ZFYVE26

Add-on Preliminary-evidence Genes for Hereditary Spastic Paraplegia (16 genes)

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.

ADGRB2 AMPD2 ARSI ATP2B4 C19orf12 CCT5 DSTYK EXOSC3 IBA57 KLC2 PGAP1 SLC33A1 USP8 VPS37A ZFR ZFYVE27

Alternative tests to consider

Broad disorders tested:

  • Hereditary Spastic Paraplegia

Individual disorders tested:

  • Autosomal Dominant Hereditary Spastic Paraplegia (HSP) Subtypes
  • hereditary spastic paraplegia 10 (SPG10)
  • hereditary spastic paraplegia 12 (SPG12)
  • hereditary spastic paraplegia 13 (SPG13)
  • hereditary spastic paraplegia 17 (SPG17), Silver syndrome
  • hereditary spastic paraplegia 31 (SPG31)
  • hereditary spastic paraplegia 4 (SPG4)
  • hereditary spastic paraplegia 6 (SPG6)
  • hereditary spastic paraplegia 72 (SPG72)
  • hereditary spastic paraplegia 73 (SPG73)
  • hereditary spastic paraplegia 8 (SPG8)
  • hereditary spastic paraplegia 9A (SPG9A)
  • hereditary spastic paraplegia type 3A (SPG3A)
  • KCNA2-related hereditary spastic paraplegia and ataxia

  • Autosomal Recessive Hereditary Spastic Paraplegia (HSP) Subtypes
  • ATL1-related hereditary spastic paraplegia
  • hereditary spastic paraplegia 11 (SPG11)
  • hereditary spastic paraplegia 15 (SPG15)
  • hereditary spastic paraplegia 18 (SPG18)
  • hereditary spastic paraplegia 20 (SPG20), Troyer syndrome
  • hereditary spastic paraplegia 21 (SPG21), Mast syndrome
  • hereditary spastic paraplegia 26 (SPG26)
  • hereditary spastic paraplegia 28 (SPG28)
  • hereditary spastic paraplegia 30 (SPG30)
  • hereditary spastic paraplegia 35 (SPG35), fatty acid hydroxylase-associated neurodegeneration (FAHN)
  • hereditary spastic paraplegia 39 (SPG39)
  • hereditary spastic paraplegia 44 (SPG44), hypomyelinating leukodystrophy 2 (HLD2), Pelizaeus-Merzbacher-like disease
  • hereditary spastic paraplegia 45 (SPG45)
  • hereditary spastic paraplegia 46 (SPG46)
  • hereditary spastic paraplegia 47 (SPG47)
  • hereditary spastic paraplegia 48 (SPG48)
  • hereditary spastic paraplegia 49 (SPG49)
  • hereditary spastic paraplegia 50 (SPG50)
  • hereditary spastic paraplegia 51 (SPG51)
  • hereditary spastic paraplegia 52 (SPG52)
  • hereditary spastic paraplegia 54 (SPG54)
  • hereditary spastic paraplegia 55 (SPG55)
  • hereditary spastic paraplegia 56 (SPG56)
  • hereditary spastic paraplegia 57 (SPG57)
  • hereditary spastic paraplegia 61 (SPG61)
  • hereditary spastic paraplegia 62 (SPG62)
  • hereditary spastic paraplegia 64 (SPG64)
  • hereditary spastic paraplegia 7 (SPG7)
  • hereditary spastic paraplegia 72 (SPG72)
  • hereditary spastic paraplegia 75 (SPG75)
  • hereditary spastic paraplegia 76 (SPG76)
  • hereditary spastic paraplegia 77 (SPG77)
  • hereditary spastic paraplegia 78 (SPG78)
  • hereditary spastic paraplegia 79 (SPG79)
  • hereditary spastic paraplegia 9B (SPG9B)
  • hereditary spastic paraplegia type 5A (SPG5A)
  • infantile-onset ascending hereditary spastic paraplegia (IAHSP)
  • X-linked Hereditary Spastic Paraplegia (HSP) Subtypes
  • hereditary spastic paraplegia 2 (SPG2), Pelizaeus-Merzbacher disease
  • hereditary spastic paraplegia 22 (SPG22), Allan-Herndon-Dudley syndrome (AHDS), SLC16A2-specific thyroid hormone cell transporter deficiency
  • Spastic Ataxias
  • spastic ataxia 1 (SPAX1)
  • spastic ataxia 2 (SPAX2)
  • spastic ataxia of Charlevoix-Saguenay (ARSACS)
  • spastic ataxia with hypomyelinating leukodystrophy (SPAX8)
  • Other Disorders
  • arginase deficiency
  • cerebrotendinous xanthomatosis (CTX)
  • complicated spastic paraplegia and intellectual disability 9 (ID9)
  • hypomyelinating leukodystrophy 4 (HLD4), MitCHAP60 disease
  • intellectual disability, Claes-Jensen type
  • L1 Syndrome
  • spastic paraplegia and psychomotor retardation with or without seizures (SPPRS)
  • spastic paraplegia, intellectual disability, nystagmus, and obesity (SINO)
  • Tay-Sachs disease, beta-hexosaminidase A (HEXA) deficiency
  • Warburg micro syndrome (WARBM)
  • X-linked adrenoleukodystrophy (X-ALD)

To view the complete clinical description of this panel, click here.

Hereditary spastic paraplegia can be inherited in an autosomal dominant, autosomal recessive, or X-linked pattern.

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 and 10 to 20 base pairs of adjacent intronic sequence on either side of the coding exons in the transcript listed below. In addition, the analysis covers the select non-coding variants specifically defined in the table below. Any variants that fall outside these regions are not analyzed. Any limitations in the analysis of these genes will be listed on the report. Contact client services with any questions.

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
ADGRB2 NM_001294336.1
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
ARG1 NM_000045.3
ARL6IP1 NM_015161.2
ARSI NM_001012301.2
ATL1 NM_015915.4
ATP13A2 NM_022089.3
ATP2B4 NM_001001396.2
B4GALNT1 NM_001478.4
BSCL2 NM_032667.6
C12orf65 NM_152269.4
C19orf12* NM_001031726.3
CAPN1 NM_001198868.1
CCT5 NM_012073.4
CPT1C NM_001136052.2
CYP27A1 NM_000784.3
CYP2U1 NM_183075.2
CYP7B1 NM_004820.3
DDHD1 NM_001160147.1
DDHD2 NM_015214.2
DSTYK NM_015375.2
ENTPD1 NM_001776.5
ERLIN1 NM_006459.3
ERLIN2 NM_007175.6
EXOSC3 NM_016042.3
FA2H NM_024306.4
FARS2 NM_006567.3
GBA2 NM_020944.2
GJC2* NM_020435.3
HACE1 NM_020771.3
HEXA NM_000520.4
HSPD1 NM_002156.4
IBA57 NM_001010867.3
KCNA2 NM_004974.3
KDM5C NM_004187.3
KIDINS220 NM_020738.2
KIF1A NM_004321.6
KIF1C NM_006612.5
KIF5A NM_004984.2
KLC2 NM_022822.2
L1CAM NM_000425.4
MAG NM_002361.3
NIPA1 NM_144599.4
NKX6-2 NM_177400.2
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
UCHL1 NM_004181.4
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

C19orf12: Deletion/duplication analysis is not offered for exon 1.
GJC2: Analysis includes the promoter variants NM_020435.3:c.-167A>G and NM_020435.3:c.-170A>G.