Table 1.

Molecular Genetic Testing Used in Shwachman-Diamond Syndrome

Gene 1, 2Proportion of SDS Attributed to Pathogenic Variants in This GeneProportion of Pathogenic Variants 3 Detectable by Test Method
Sequence analysis 4Gene-targeted deletion/duplication analysis 5
EFL1<1%6/6 6Unknown 7
DNAJC21<1%3/4 81/4 8
SBDS~92%>90% 9<2% 10
SRP54<1%3/3 11Unknown 7
Unknown 12<10%NA
1.

Genes are listed in alphabetic order.

2.
3.

See Molecular Genetics for information on allelic variants detected in this gene.

4.

Sequence analysis detects variants that are benign, likely benign, of uncertain significance, likely pathogenic, or pathogenic. 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.

5.

Gene-targeted deletion/duplication analysis detects intragenic deletions or duplications. Methods used may include: quantitative PCR, long-range PCR, and multiplex ligation-dependent probe amplification (MLPA) and a gene-targeted microarray designed to detect single-exon deletions or duplications. Assay design is complicated by the presence of SBDSP.

6.
7.

No data on detection rate of gene-targeted deletion/duplication analysis are available.

8.
9.

Rare pathogenic variants, such as c.297_300delAAGA, are also likely the consequence of gene conversion with SBDSP [Carvalho et al 2014; J Rommens, personal communication].

10.

Rare whole-exon deletions [Costa et al 2007], extended conversions of exon 2 and flanking introns, or gene rearrangements involving exon 2 have been observed.

11.
12.

A limited number (<10%) of persons with clear clinical indications of SDS do not appear to have pathogenic variants in any of the known genes, suggesting that pathogenic variants in another gene(s) may also be causative.

From: Shwachman-Diamond Syndrome

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