Study of the collagen type VI alpha 3 (COL6A3) gene in Parkinson’s disease

BMC Neurology

Table 2 Information of probable pathogenic variants identified in our cohort

RefSeq	Variants	Exon	Nucleotide change	Protein change	Population MAF (East Asian)		Frequency in our cohort			In silico prediction
RefSeq	Variants	Exon	Nucleotide change	Protein change	gnomAD	1000 G	PD	control	P value^#	CADD	SIFT	Deleterious vs all algorithms^a
NM_057166.4	rs545819982	36	c.5692G > A	p.G1898R	0	0.0002	1/346	0/400	0.038	20.5	0	18:23
	rs369317566	31	c.5204G > A	p.R1735Q	0	.	1/346	0/400		24.3	0.365	16:23
	rs370862741	29	c.5095C > T	p.R1699C	0.0001	0	1/346	0/400		24.4	0.055	19:23
	rs779508804	27	c.4967G > A	p.R1656Q	0.0001	.	1/346	2/400		24.5	0.053	16:23
	rs770876436	12	c.3707 T > C	p.F1236S	0.0003	.	1/346	0/400		24.6	0.002	16:23
	rs114322958	11	c.3091G > A	p.A1031T	0.0063	0.0008	1/346	9/400		25.5	0.005	20:24
	rs115765346	10	c.2783G > A	p.R928H	0.0001	0	1/346	2/400		27.3	0.002	22:23

^aalgorithms or tools include PolyPhen2_HDIVPolyPhen2_HVAR, LRT, MutationTaster, MutationAssessor, FATHMM, PROVEAN, MetaSVM, MetaLR, VEST3, M-CAP, CADD, GERP++, DANN, fathmm-MKL, Eigen, GenoCanyon, fitCons, PhyloP, PhastCons, SiPhy and REVEL
^#P value calculated via SKAT-O

ISSN: 1471-2377