Test for Spastic Paraplegia 44 - Clinical Genetic Test - GTR

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Test for Spastic Paraplegia 44

Clinical Genetic Test

offered by

Genome Diagnostics Laboratory

GTR Test Accession: GTR000500041.2

CAP

INHERITED DISEASENERVOUS SYSTEM

Last updated in GTR: 2012-09-27

Last annual review date for the lab: 2022-10-27 Past due

At a Glance

Test purpose:

Diagnosis

Conditions (1):

Hereditary spastic paraplegia

Genes (1):

GJC2 (1q42.13)

Methods (1):

Molecular Genetics - Sequence analysis of the entire coding region: Bi-directional Sanger Sequence Analysis

Target population:

Not provided

Clinical validity:

Not provided

Clinical utility:

Not provided

Ordering Information

Offered by:

Genome Diagnostics Laboratory
View lab's website

Specimen Source:

Peripheral (whole) blood
View specimen requirements

Who can order:

Health Care Provider

Lab contact:

Leslie Steele, MSc, Co-ordinator
leslie.steele@sickkids.ca
416-813-7200 ext 1

Contact Policy:

Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.

How to Order:

Requests are made from the referring health care provider through completion of the Molecular Genetics test requisition
Order URL

Test service:

Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings

Test development:

Test developed by laboratory (no manufacturer test name)

Informed consent required:

Decline to answer

Pre-test genetic counseling required:

Decline to answer

Post-test genetic counseling required:

Decline to answer

Recommended fields not provided:

Test Order Code, Test strategy

Conditions

Total conditions: 1

Condition/Phenotype	Identifier

Test Targets

Genes

Total genes: 1

Gene	Associated Condition	Germline or Somatic	Allele (Lab-provided)	Variant in NCBI

Methodology

Total methods: 1

Method Category

Test method

Instrument *

Sequence analysis of the entire coding region

Bi-directional Sanger Sequence Analysis

* Instrument: Not provided

Clinical Information

Test purpose:

Diagnosis

Variant Interpretation:

What is the protocol for interpreting a variation as a VUS?
Novel variations are evaluated using a variety of algorithms including splice site analysis, sequence conservation within species and isoforms and functional estimation (i.e. SIFT, Polyphen, AlignGVGD & Mutation Taster). If the variation cannot be placed into a pathogenic or non-pathogenic state, further studies including evaluation of family members and/or assessing … View more

Are family members with defined clinical status recruited to assess significance of VUS without charge?
Yes.

Will the lab re-contact the ordering physician if variant interpretation changes?
No. They must contact us and want further information if they act on behalf of the patient

Research:

Is research allowed on the sample after clinical testing is complete?
No

Recommended fields not provided:

Clinical validity, Clinical utility, Target population, Sample negative report, Sample positive report

Technical Information

Test Comments:

Sequence analysis of the entire coding region and intron/exon boundaries is available as part of an Autosomal Recessive Hereditary Spastic Paraplegia panel C.

Availability:

Tests performed
Entire test performed in-house

Analytical Validity:

PCR-based sequencing detects 99% of the reported mutations in the SPG44 gene. The sensitivity of DNA sequencing is over 99% for the detection of nucleotide base changes, small deletions, insertions and indels in the region analyzed.

Proficiency testing (PT):

Is proficiency testing performed for this test?
Yes

Method used for proficiency testing:
Formal PT program

PT Provider:
American College of Medical Genetics / College of American Pathologists, ACMG/CAP

VUS:

Software used to interpret novel variations
SIFT, POLYPHEN2, AlignGVGD, Mutation Taster, Splicing Programs

Laboratory's policy on reporting novel variations
They are reported as such to licensed physicians.

Recommended fields not provided:

Test Confirmation, Assay limitations, Description of internal test validation method, Citations for Analytical validity, Description of PT method, Major CAP category, CAP category, CAP test list

Regulatory Approval

FDA Review:

Category: Not Applicable

Additional Information

Reviews:

Genereviews

PubMed Clinical Queries

Clinical resources:

Consumer resources:

MedlinePlusGenetics (GHR)

NCATS Office of Rare Diseases Research (GARD)

MedlinePlus

IMPORTANT NOTE: NIH does not independently verify information submitted to GTR; it relies on submitters to provide information that is accurate and not misleading. NIH makes no endorsements of tests or laboratories listed in GTR. GTR is not a substitute for medical advice. Patients and consumers with specific questions about a genetic test should contact a health care provider or a genetics professional.