Table 1.

Genomic Testing Used in the 3q29 Recurrent Deletion

Deletion 1MethodSensitivity
ProbandAt-risk family members
1.6-Mb heterozygous deletion at 3q29
  • ISCN: seq[GRCh37] del(3)(q29) chr3:195,756,054-197,344,665 2
CMA 3100%100%
Targeted deletion analysis 4See footnote 5.100% 6
1.

See Molecular Genetics for details of the deletion and genes of interest.

2.

Standardized ISCN annotation and interpretation for genomic variants from the Clinical Genome Resource (ClinGen) project (formerly the International Standards for Cytogenomic Arrays [ISCA] Consortium). Genomic coordinates represent the minimum deletion size associated with the 3q29 recurrent deletion as designated by ClinGen. Deletion coordinates may vary slightly based on array design used by the testing laboratory. Note that the size of the deletion as calculated from these genomic positions may differ from the expected deletion size due to the presence of segmental duplications near breakpoints. The phenotype of significantly larger or smaller deletions within this region may be clinically distinct from the 3q29 recurrent deletion (see Genetically Related Disorders).

3.

Chromosomal microarray analysis (CMA) using oligonucleotide or SNP arrays. CMA designs in current clinical use target the 3q29 region.

4.

Targeted deletion analysis methods can include FISH, quantitative PCR, and multiplex ligation-dependent probe amplification (MLPA) as well as other targeted quantitative methods.

5.

Not applicable. Targeted deletion analysis is not appropriate for an individual in whom the 3q29 recurrent deletion was not detected by CMA designed to target this region.

6.

Targeted deletion analysis may be used to test at-risk relatives of a proband known to have the 3q29 recurrent deletion.

From: 3q29 Recurrent Deletion

Cover of GeneReviews®
GeneReviews® [Internet].
Adam MP, Feldman J, Mirzaa GM, et al., editors.
Seattle (WA): University of Washington, Seattle; 1993-2024.
Copyright © 1993-2024, University of Washington, Seattle. GeneReviews is a registered trademark of the University of Washington, Seattle. All rights reserved.

GeneReviews® chapters are owned by the University of Washington. Permission is hereby granted to reproduce, distribute, and translate copies of content materials for noncommercial research purposes only, provided that (i) credit for source (http://www.genereviews.org/) and copyright (© 1993-2024 University of Washington) are included with each copy; (ii) a link to the original material is provided whenever the material is published elsewhere on the Web; and (iii) reproducers, distributors, and/or translators comply with the GeneReviews® Copyright Notice and Usage Disclaimer. No further modifications are allowed. For clarity, excerpts of GeneReviews chapters for use in lab reports and clinic notes are a permitted use.

For more information, see the GeneReviews® Copyright Notice and Usage Disclaimer.

For questions regarding permissions or whether a specified use is allowed, contact: ude.wu@tssamda.

NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.