Table 1. [Molecular Genetic Testing Used in CASK Disorders]. - GeneReviews® - NCBI Bookshelf

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Table 1.

Molecular Genetic Testing Used in CASK Disorders

Gene ¹	Method	Proportion of Probands with a Pathogenic Variant ² Detectable by Method
CASK	Sequence analysis ³	~70% ^4, 5
	Gene-targeted deletion/duplication analysis ⁶	~30% ^4, 5, 6
	CMA ⁷	~28% ^4, 7
	Karyotype	Rare ⁸

1.: See Table A. Genes and Databases for chromosome locus and protein.
2.: See Molecular Genetics for information on allelic variants detected in this gene.
3.: Sequence analysis detects variants that are benign, likely benign, of uncertain significance, likely pathogenic, or pathogenic. Variants may include small intragenic deletions/insertions and missense, nonsense, and splice site variants; typically, exon or whole-gene deletions/duplications are not detected. For issues to consider in interpretation of sequence analysis results, click here.
4.: Data derived from the subscription-based professional view of Human Gene Mutation Database [Stenson et al 2020]
5.: Percentages are based on female probands. Surviving male probands are more likely to have a variant detected by sequence analysis (see Genotype-Phenotype Correlations).
6.: Gene-targeted deletion/duplication analysis detects intragenic deletions or duplications. Methods used may include a range of techniques such as quantitative PCR, long-range PCR, multiplex ligation-dependent probe amplification (MLPA), and a gene-targeted microarray designed to detect single-exon deletions or duplications. Gene-targeted deletion/duplication testing will detect deletions ranging from a single exon to the whole gene; however, breakpoints of large deletions and/or deletion of adjacent genes (e.g., those described by Moog et al [2011], Burglen et al [2012], Hayashi et al [2012], Hayashi et al [2017]) may not be detected by these methods.
7.: Chromosomal microarray analysis (CMA) uses oligonucleotide or SNP arrays to detect genome-wide large deletions/duplications (including CASK) that cannot be detected by sequence analysis. Most reported deletions/duplications in CASK are large enough to be detected by CMA. The ability to determine the size of the deletion/duplication depends on the type of microarray used and the density of probes in the Xp11.4 region. CMA designs in current clinical use target the Xp11.4 region.
8.: Two females with a balanced Xp inversion disrupting CASK have been observed [Najm et al 2008; K Kutsche, unpublished].

From: CASK Disorders

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