. Author manuscript; available in PMC: 2014 Oct 1.

Published in final edited form as: Am J Med Genet A. 2014 Jul 31;164(10):2567–2571. doi: 10.1002/ajmg.a.36691

Table 1.

Rare functional Variants in GWAS candidate Genes

Genes	HGVS^a	Amino acid change	Polyphen/SIFT predictions	Cleft details	Nigerian Cases [N=140]	Ethiopian Cases [N=80]	1KG	EVS
ARHGAP29	c.2864G>A	p.Arg955His	Benign/tolerated	CLP	1	0	1	0
ARHGAP29	c.2738C>A	p.Ser913Leu	Stop retained	CL	1	0	3	11
PAX7	c.1396G>A	p.Gly466Ser	Benign/tolerated	CL	0	1	0	0
PAX7	c.952+2T>A^**		Donor splice site variant	CL	0	1	0	0
	c.1282G>A^**	p.Asp428Asn	Possibly damaging/deleterious	CL	1	0	0	0
MAFB	c.493C>G^**	p.His165Asn	Benign/Tolerated	CP	1	0	0	0

1KG = 1000 genomes, EVS= Exome variant server

^**

New variants

Ref Seq [ARHGAP29 NM_004815.3; PAX7 NM_001135254.1; MAFB NM_00546

CL = Cleft lip CP= Cleft palate CLP = Cleft lip and palate