Table 3.

Selected prioritized candidate genes from CDH-associated CNV regions

Region	Gene	Embryonic diaphragm expression	Lung expression (peak stage)	Constraint (ExAC pLI)	No. sequence variants (in 275 probands)*
dup 1q41	HLX	High	Alveolar	0.56	1
del 17q12	ACACA	Low	Embryonic/alveolar	1.00	0
	DUSP14	High	Alveolar	0.77	0
	GGNBP2	High	—	1.00	1
	HNF1B	Low	Saccular/alveolar	1.00	0
	LHX1	Low	—	0.29	0
	SYNRG	Low	Alveolar	0.97	2

Diaphragm expression indicates whether a gene is expressed above (“high”) or below (“low”) the median normalized hybridization intensities for intronic probes based on expression microarrays from the embryonic mouse diaphragm (11). Lung expression indicates the peak developmental stage of expression levels in mouse lungs, and “—” indicates this gene is not highly expressed in lung (36).

^*Number of sequence variants in each gene that are rare (<0.1% in control populations) and predicted pathogenic (by SIFT, PolyPhen) in a cohort of 275 patients with CDH studied with WES.