Table 4.

Annotation of identified SNVs of planar cell polarity genes in human neural tube defects cases.

Gene	RNA accession	Exon	Nucleotide change	Amino acid change	rs ID	Ref allele	Alt allele	Chrs	Position	SIFT	polyphen	Mutation Taster	1000g_chbs	1000g_all	ExAC03	Alt Allele Freq
CELSR1	NM_014246	exon33	c.8772G > C	p.Q2924H	rs200116798	C	G	22	46,760,416	0.13	0.96	0.97	0.0025	0.0006	0.0003	0.00491
CELSR1	NM_014246	exon1	c.3364G > A	p.G1122S	rs200363699	C	T	22	46,929,704	0	0.99	0.66	0.0025	0.0002	0.00002	0.00196
CELSR1	NM_014246	exon1	c.3169C > T	p.R1057C	rs148349145	G	A	22	46,929,899	0.03	0.88	0.75	0	0.0006	0.0001	0.00196
CELSR1	NM_014246	exon1	c.2305C > T	p.R769W	rs201601181	G	A	22	46,930,763	0.03	1	0.77	–	–	0.0002	0.00098
DVL3	NM_004423	exon4	c.443G > A	p.R148Q	rs764021343	G	A	3	183,882,369	0.05	0.98	0.99	–	–	0.00001	0.00098
PTK7	NM_152882	exon13	c.1925C > G	p.P642R	rs148120569	C	G	6	43,111,200	0.01	0.91	1	0.0051	0.0012	0.0004	0.00594
SCRIB	NM_015356	exon23	c.3323G > A	p.G1108E	rs529610993	C	T	8	144,885,908	0.02	1	0.99	–	0.0006	0.00006	0.00295
SCRIB	NM_015356	exon23	c.3131G > A	p.R1044Q	rs782787420	C	T	8	144,886,100	0.26	1	0	–	–	0.0001	0.00197
SCRIB	NM_015356	exon15	c.1931G > T	p.G644 V	rs201104891	C	A	8	144,890,963	0.02	1	0.38	0.0051	0.0008	0.0002	0.00492
SCRIB	NM_015356	exon15	c.1853A > G	p.K618R	novel	T	C	8	144,891,041	0.1	0.92	0.86	–	–	–	0.00098

SIFT, PolyPhen, and Mutation Taster are algorithms for predicting possible impact of an amino acid substitution on the structure and function of a human protein.

Non-synonymous SNVs with SIFT score of < 0.05, Polyphen-2 score of > 0.85 or MutationTaster score of > 0.85 were considered as significant of not being benign.

1000g_all, minor allele frequency of all population in the 1000 genomes.

1000g_chbs, minor allele frequency of the Chinese Han population in the 1000 genomes.

ExAC03, minor allele frequency in the Exome Aggregation Consortium database.

Alt Allele Freq, frequency of variant allele in the population of the present study.