Rett Syndrome exon 4 hotspot mutations - Clinical Genetic Test - GTR

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Rett Syndrome exon 4 hotspot mutations

Clinical Genetic Test

offered by

Molecular Genetics Laboratory

View lab's test page

GTR Test Accession: GTR000613205.1

INHERITED DISEASENERVOUS SYSTEMPSYCHIATRIC ... View more

Registered in GTR: 2024-04-15

Last annual review date for the lab: 2025-04-16

At a Glance

Test purpose:

Diagnosis

Conditions (2):

Rett syndrome; Severe neonatal-onset encephalopathy with microcephaly

Genes (1):

MECP2 (Xq28)

Methods (1):

Molecular Genetics - Mutation scanning of select exons: Bi-directional Sanger Sequence Analysis

Target population:

Partial or complete loss of acquired purposeful hand skills; Partial …

Clinical validity:

Not provided

Clinical utility:

Establish or confirm diagnosis

Ordering Information

Offered by:

Molecular Genetics Laboratory
View lab's website
View lab's test page

Test short name:

Rett Syndrome

Specimen Source:

Buffy coat
View specimen requirements

Who can order:

Health Care Provider

Test Order Code:

BM003

Lab contact:

Atanu Dutta, MD, Medical Director
atanu.biochem@aiimskalyani.edu.in
+918967369455

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:

Clinicians from the All India Institute of Medical Sciences Kalyani can order the test using the test request form.
Order URL

Test service:

Sanger Sequencing by primer designing for one variant for one p
Comment: Requires 2 ml EDTA blood
OrderCode: BM002

Test development:

Test developed by laboratory (no manufacturer test name)

Informed consent required:

Yes

Test strategy:

Rett syndrome-causing missense mutations cluster in two regions of MECP2. One of these regions - the methyl-CpG binding domain (MBD) - has been extensively characterized and helps MeCP2 bind DNA. The other region is called the NCoR/SMRT interaction domain (NID) and recruits a gene-silencing complex, but its function has remained … View more

View citations (1)

https://www.pnas.org/doi/full/10.1073/pnas.1505909112

Pre-test genetic counseling required:

Yes

Post-test genetic counseling required:

Yes

Conditions

Total conditions: 2

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

Mutation scanning of select exons

Bi-directional Sanger Sequence Analysis

Applied Biosystems 3500 capillary sequencing instrument

Clinical Information

Test purpose:

Diagnosis

Clinical utility:

Establish or confirm diagnosis

View citations (1)

Kaur S, Christodoulou J. MECP2 Disorders. 2001 Oct 3 [Updated 2019 Sep 19]. In: Adam MP, Feldman J, Mirzaa GM, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1497/

Target population:

Partial or complete loss of acquired purposeful hand skills; Partial or complete loss of acquired spoken language or language skill (e.g., babble); Gait abnormalities: impaired (dyspraxic) or absence of ability; Stereotypic hand movements including hand wringing/squeezing, clapping/tapping, mouthing, and washing/rubbing automatisms

Variant Interpretation:

What is the protocol for interpreting a variation as a VUS?
As per ACMG criteria.

Are family members with defined clinical status recruited to assess significance of VUS without charge?
No.

Will the lab re-contact the ordering physician if variant interpretation changes?
Yes. The laboratory will re-contact ordering physician at least once in 2 years regarding the change the variant classification status over email.

Sample reports:

Sample Negative Report
Sample Negative Report

Sample Positive Report
Sample Positive Report

Sample VUS Report
Sample VUS Report

Recommended fields not provided:

Clinical validity, Is research allowed on the sample after clinical testing is complete?

Technical Information

Test Procedure:

PCR amplification of selected exons followed by Sanger sequencing.

Availability:

Tests performed
Entire test performed in-house

Test performance comments
Biochemistry Special Laboratory

Analytical Validity:

The diagnostic sensitivity of Sanger sequencing was 98%

Proficiency testing (PT):

Is proficiency testing performed for this test?
No

Method used for proficiency testing:
Alternative Assessment

Description of internal test validation method: Help
Assay of positive samples.

VUS:

Software used to interpret novel variations
Varsome; Franklin Genoox

Laboratory's policy on reporting novel variations
As per ACMG criteria.

Recommended fields not provided:

Test Confirmation, Assay limitations, Citations to support 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:

Category: Not Applicable

Additional Information

Reviews:

Genereviews

PubMed Clinical Queries

Clinical resources:

Molecular resources:

View MECP2 variations in ClinVar

RefSeqGene

Coriell Institute for Medical Research

Consumer resources:

MalaCards

MedlinePlusGenetics (GHR)

NCATS Office of Rare Diseases Research (GARD)

MedlinePlus

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