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SPTLC1 - Gene sequencing
Clinical Genetic Test
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offered by
Amsterdam UMC Genome Diagnostics
View lab's test page
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GTR Test Accession: Help GTR000570450.1
INHERITED DISEASEMETABOLIC DISEASENERVOUS SYSTEM ... View more
Registered in GTR: 2020-01-29
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Last annual review date for the lab: 2024-04-16 LinkOut
At a Glance
Test purpose: Help
Diagnosis; Mutation Confirmation; Pre-symptomatic
Conditions (1): Help
Hereditary sensory and autonomic neuropathy type 1
Genes (1): Help
SPTLC1 (9q22.31)
Methods (1): Help
Molecular Genetics - Sequence analysis of the entire coding region: Bi-directional Sanger Sequence Analysis
Target population: Help
Not provided
Clinical validity: Help
Not provided
Clinical utility: Help
Not provided
Ordering Information
Offered by: Help
Amsterdam UMC Genome Diagnostics
View lab's website
View lab's test page
Specimen Source: Help
  • Buccal swab
  • Cell culture
  • Chorionic villi
  • Fibroblasts
  • Isolated DNA
  • Peripheral (whole) blood
Who can order: Help
  • Genetic Counselor
  • Licensed Physician
How to Order: Help
Order URL
Test service: Help
Clinical Testing/Confirmation of Mutations Identified Previously
Custom Sequence Analysis
Informed consent required: Help
No
Test strategy: Help
Simultaneous bi-directional sequencing of all coding/selected exons
Pre-test genetic counseling required: Help
Yes
Post-test genetic counseling required: Help
Yes
Recommended fields not provided:
Test Order Code, Lab contact for this test, Contact policy, Test development
Conditions Help
Total conditions: 1
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 1
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Methodology
Total methods: 1
Method Category Help
Test method Help
Instrument
Sequence analysis of the entire coding region
Bi-directional Sanger Sequence Analysis
Applied Biosystems 3730 capillary sequencing instrument
Clinical Information
Test purpose: Help
Diagnosis; Mutation Confirmation; Pre-symptomatic
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
The 5-classes classification method (Alamut)

Will the lab re-contact the ordering physician if variant interpretation changes? Help
Yes.
Recommended fields not provided:
Clinical validity, Clinical utility, Target population, Are family members with defined clinical status recruited to assess significance of VUS without charge?, Is research allowed on the sample after clinical testing is complete?, Sample negative report, Sample positive report
Technical Information
Test Procedure: Help
DNA is extracted from the patient specimen, PCR amplification and sequence analysis of the entire coding region/ or indicated exons plus additional flanking intronic or other non-coding sequence. Sanger sequencing is carried out and the sequence is visualised on a capillary sequencer. Sequencing is performed separately in both the forward … View more
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
This test detects >99% of described mutations
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Formal PT program

PT Provider: Help
European Molecular Genetics Quality Network, EMQN

Description of PT method: Help
DNA sequencing - Sanger (Full version)
VUS:
Software used to interpret novel variations Help
Alamut (Interactive Biosoftware), including AGVGD, PolyPhen-2, SIFT and MutationTaster for missense predictions and MAXEntScan, NNSPLICE, GeneSplicer and Human Splicing Finder for splice predictions
Recommended fields not provided:
Test Confirmation, Assay limitations, Description of internal test validation method, Citations for Analytical validity, Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review: Help
Not provided
Additional Information

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.