Table 3.

Rare missense variants (MAF <0.01) in the coding sequence of PTK7 gene detected in 343 Chinese NTDs

chr6 position	rs#	DNA change	aa change	SIFT	PolyPhen	No. of carriers	Phenotype(num)b	MAF in gnomAD
43096973	rs757907657	c.362G>A	p.Arg121His	Tolerated	Benign	1	SB	3.56E‐05
43096994	rs780174508	c.383A>G	p.Asn128Ser	Deleterious	Probably damaging	1	EX	7.14E‐06
43098060	rs149112329	c.587G>A	p.Arg196Gln	Tolerated	Benign	1	EC	2.20E‐04
43100174	NAa	c.1001C>T	p.Pro334Leu	Tolerated	Benign	1	AE	NA
43109441	rs777499261	c.1678G>A	p.Ala560Thr	Tolerated	Possibly damaging	1	SB	2.39E‐05
43109699	rs762888862	c.1823G>A	p.Arg608His	Tolerated	Benign	1	SB	4.99E‐05
43111200	rs148120569	c.2117C>G	p.Pro706Arg	Deleterious	Probably damaging	5	AE(2), CRS, SB(2)	3.83E‐04
43112206	rs200622454	c.2293G>A	p.Gly765Arg	Deleterious	Probably damaging	2	SB	5.66E‐05
43112236	rs775883985	c.2323G>A	p.Val775Met	Deleterious	Benign	1	SB	4.77E‐05
43112282	rs746367585	c.2369G>T	p.Arg790Leu	Deleterious	Benign	4	SB(2),EC,AE	1.06E‐05
43112285	rs55820547	c.2372A>G	p.His791Arg	Tolerated	Benign	2	AE, SB	1.59E‐04
43128584	rs765317932	c.3202G>A	p.Ala1068Thr	Tolerated	Benign	1	SB	7.98E‐06
Total PTK7 rare missense variant allele in NTDs compared to gnomAD controls						21/343 versus 4,578/138,632
						(p = 0.00899)

^aNot available.

^bAE: anencephaly; CRS: craniorachischisis; EC: encephalocele; EX: Exencephaly; SB: spina bifida.