Table 2.

Variants in FOXA2 identified in additional BA patients

Patient No.	Disease Classification	FOXA2						rs1904589
		dbSNP ID	Genomic Position on chr20	cDNA change	Protein Change	MAF (1000G)	Variant Origin	Genotype	G allele Origin
1	Syndromic BA	rs200459003	22562990	c.530C>T	p.Ala291Val	0.0008	Maternal	A/G	Paternal
2	Isolated BA	rs201902165	22563686	c.176G>A	p.Ser59Asn	0.0060	Paternal	A/G	Maternal
3	Isolated BA	-	22562889	c.991A>T	p.Ter325Ser	-	Maternal	A/G	N/A
4	Isolated BA	-	22563564	c.298G>A	p.Ala100Thr	-	Maternal	A/G	N/A
5	Isolated BA	rs200459003	22562990	c.530C>T	p.Ala291Val	0.0008	Maternal	A/G	N/A
6	Isolated BA	rs200459003	22562990	c.530C>T	p.Ala291Val	0.0008	Paternal	G/G	Both
7	Isolated BA	rs200459003	22562990	c.530C>T	p.Ala291Val	0.0008	Maternal	A/G	Paternal

We identified 4 FOXA2 rare missense coding variants in 7 patients. None of these variants were observed in ESP; 2 were observed in the 1000 Genome Project (1000G) with a MAF<0.01, and 2 were not observed in 1000G. One of these variants appeared 3 times in exome sequencing of 100 patients with isolated BA and once through Sanger sequencing of 46 patients with syndromic BA with abdominal heterotaxy. The expression-altering NODAL polymorphism, rs1904589, is also shown with its corresponding inheritance pattern for each patient identified to have a rare, protein-altering FOXA2 variant.