Table 1.

Combined rare damaging variants among Wnt/PCP genes in human NTD samples

Sample	Gene	Variant	Chr.	Positiona	Minor/major allele	Sex	Phenotypeb	SIFTc	PP2d	MAF in ExACe
NTD_27	CELSR2	p.Thr2026Met	1	109,810,233	T/C	M	SB	D	D	0.000009415
	DVL3	p.Asp403Asn	3	183,885,376	A/G			D	P	NAf
NTD_39	CELSR2	p.Arg2480Cys	1	109,813,177	T/C	M	SB	D	D	0.00003766
	FZD7	p.Leu383Gln	2	202,900,518	A/T			D	D	NA
NTD_122	CELSR2	p.Arg1990His	1	109,808,784	A/G	M	EC	D	P	0.0001318
	CELSR3	p.Arg1194His	3	48,696,487	T/C			D	D	0.00002825
NTD_15	LRP6	p.Arg386Cys	12	12,334,194	A/G	F	AE,SB	D	D	0.000273
	CELSR1	p.Arg714His	22	46,930,927	T/C			D	D	NA
NTD_56	CELSR2	p.Arg2626Cys	1	109,814,294	T/C	NA	SB	D	P	0.0004425
	FZD5	p.Trp242Leu	2	208,632,739	A/C			D	D	NA
NTD_19	VANGL1	p.Arg207His	1	116,206,697	A/G	F	SB	D	D	0.00001883
	CELSR1	p.Thr1086Met	22	46,929,811	A/G			D	D	0.0001318

^aPositions are given in bp from GRCh37

^bSB, spinabifida; EC, encephalocele; AE, anencephaly

^cSIFT predictions: D, deleterious

^dPolyPhen2 (PP2) predictions: D, probably damaging; P, possibly damaging

^eMAF from Exome Aggregation Consortium (ExAC) database

^fNot available