SHOX Deficiency Disorders, Sequencing and Deletion/Duplication - Clinical Genetic Test - GTR

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SHOX Deficiency Disorders, Sequencing and Deletion/Duplication

Clinical Genetic Test

offered by

ARUP Laboratories, Molecular Genetics and Genomics

View lab's test page

GTR Test Accession: GTR000597484.3

INHERITED DISEASEENDOCRINOLOGYSYNDROMIC DISEASE ... View more

Last updated in GTR: 2024-07-23

Last annual review date for the lab: 2024-07-12

At a Glance

Test purpose:

Diagnosis; Mutation Confirmation; Risk Assessment; ...

Conditions (1):

Short stature due to partial GHR deficiency

Genes (1):

SHOX (Xp22.33)

Methods (1):

Molecular Genetics - Sequence analysis of the entire coding region: Next-Generation (NGS)/Massively parallel sequencing (MPS)

Target population:

Not provided

Clinical validity:

Not provided

Clinical utility:

Not provided

Ordering Information

Offered by:

ARUP Laboratories, Molecular Genetics and Genomics
View lab's website
View lab's test page

Test short name:

SHOX NGS

Specimen Source:

Peripheral (whole) blood

Who can order:

Genetic Counselor
Health Care Provider
Licensed Physician
Nurse Practitioner
Physician Assistant

Test Order Code:

3004603

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:

Order URL

Test service:

Custom Deletion/Duplication Testing
Comment: Assess for a large deletion or duplication
OrderCode: 3003144

Informed consent required:

Based on applicable state law

Pre-test genetic counseling required:

Decline to answer

Post-test genetic counseling required:

Decline to answer

Recommended fields not provided:

Lab contact for this test, Test strategy, Test development

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

Next-Generation (NGS)/Massively parallel sequencing (MPS)

* Instrument: Not provided

Clinical Information

Test purpose:

Diagnosis; Mutation Confirmation; Risk Assessment; Screening

Variant Interpretation:

What is the protocol for interpreting a variation as a VUS?
Multiple methodologies are utilized to classify a VUS. General knowledge regarding the gene and types of disease-associated mutations is reviewed. Population frequency is used to determine the incidence in which the variant is present in the general population as well as in specific ethnicities. Computational prediction programs are used to … 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?
Yes. For significant changes to variant classification, an amended report is sent to the ordering facility and ARUP Laboratories will attempt to contact the provider. Clinicians are encouraged to continue to analyze the literature and re-contact the laboratory if a reclassification may be warranted.

Recommended fields not provided:

Clinical validity, Clinical utility, Target population, Is research allowed on the sample after clinical testing is complete?, Sample negative report, Sample positive report

Technical Information

Availability:

Tests performed
Entire test performed in-house

Analytical Validity:

The analytical sensitivity is approximately 99 percent for single nucleotide variants (SNVs) and greater than 93 percent for insertions/duplications/deletions (indels) from 1-10 base pairs in size. Indels greater than 10 base pairs may be detected, but the analytical sensitivity may be reduced. Specificity is greater than 99.9 percent for all … View more

Proficiency testing (PT):

Is proficiency testing performed for this test?
Yes

Method used for proficiency testing:
Intra-Laboratory

VUS:

Software used to interpret novel variations
The software utilized varies depending on the gene and variant type. Some examples of computational prediction programs ARUP Laboratories uses are SIFT, Polyphen2, Mutation Taster, NetGene and NNSplice. The evidence of pathogenicity generated by these computer prediction programs is considered weak.

Laboratory's policy on reporting novel variations
ARUP Laboratories complies with New York regulations for all variants reported. If a VUS is incidentally detected using a mutation panel or in an ACMG-recommended gene via exome sequencing, it will not be reported (in agreement with ACMG recommendations for standards for interpretation and reporting of sequence variations). Please see … View more

Recommended fields not provided:

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

Regulatory Approval

FDA Review:

Not provided

Additional Information

Reviews:

PubMed Clinical Queries

Clinical resources:

Molecular resources:

View GHR variations in ClinVar

RefSeqGene

Coriell Institute for Medical Research

Consumer resources:

Genetic Alliance

MalaCards

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.