Resequencing analysis of five Mendelian genes and the top genes from genome-wide association studies in Parkinson’s Disease

Benitez, Bruno A.; Davis, Albert A.; Jin, Sheng Chih; Ibanez, Laura; Ortega-Cubero, Sara; Pastor, Pau; Choi, Jiyoon; Cooper, Breanna; Perlmutter, Joel S.; Cruchaga, Carlos

doi:10.1186/s13024-016-0097-0

Molecular Neurodegeneration

Table 2 Summary of the variants found in the European-American case-control sample

From: Resequencing analysis of five Mendelian genes and the top genes from genome-wide association studies in Parkinson’s Disease

Gene	AA change	Cases (478)	MAF	Controls (337)	MAF	p value	Clinical interpretation PD mutation database	Notes
LRRK2	R50H	0	0	1	0.001	n.s.	Unknown	Autosomal Dominant
	R521G	0	0	1	0.001	n.s.	Unknown
	R793M	0	0	2	0.003	0.09	Pathogenic nature unclear
	S885C	1	0.001	0	0	n.s.	Novel
	L119P	2	0.002	1	0.001	n.s.	Non-pathogenic
	P1262A	1	0.001	0	0	n.s.	Non-pathogenic
	I1371V	2	0.002	0	0	n.s.	Pathogenic nature unclear
	V1389I	1	0.001	0	0	n.s.	Unknown
	V1450I	0	0	1	0.001	n.s.	Not pathogenic
	R1514Q	7	0.007	4	0.006	n.s.	Not pathogenic
	M1646T	21	0.022	9	0.013	n.s.	Not pathogenic/Risk
	L1795F	1	0.001	0	0	n.s.	Pathogenic nature unclear
	D1887N	1	0.001	0	0	n.s.	Novel
	G2019S	8	0.008	0	0	0.02	Pathogenic
	N2081D	17	0.018	15	0.022	n.s.	Non-pathogenic
	Y2189C	0	0	1	0.001	n.s.	Pathogenic nature unclear
	A2461V	0	0	1	0.001	n.s.	Unknown
Total		62		36
DJ-1	A179T	1	0.0010	0	0	n.s.	Pathogenic nature unclear	Autosomal Recessive
Total		1		0
PARKIN	D53X	1	0.001	0	0	n.s.	Pathogenic	Autosomal Recessive
	R65C	1	0.001	1	0.001	n.s.	Pathogenic nature unclear
	A82E	1	0.001	1	0.001	n.s.	Pathogenic nature unclear
	R275W	2	0.002	2	0.003	n.s.	Pathogenic nature unclear
	E310D	0	0	1	0.001	n.s.	Pathogenic nature unclear
	R402C	5	0.005	1	0.001	n.s.	Pathogenic nature unclear
	R402H	0	0	1	0.001	n.s.	Unknown
	P437L	3	0.003	2	0.003	n.s.	Pathogenic nature unclear
Total		13		9
PINK1	R147C	0	0	1	0.001	n.s.	Novel	Autosomal Recessive
	R207Q	1	0.001	0	0	n.s.	Unknown
	M318L	0	0	1	0.001	n.s.	Pathogenic nature unclear
	A339S	2	0.002	1	0.001	n.s.	Pathogenic nature unclear
	N367S	2	0.002	0	0	n.s.	Pathogenic nature unclear
	G411S	1	0.001	0	0	n.s.	Pathogenic nature unclear
	R492X	0	0	1	0.001	n.s.	Pathogenic
Total		6		4
GBA^c	R83C	2	0.002	0	0	n.s.	Unknown	PD GWAS Hit
	H294Q	2	0.002	0	0	n.s.	Pathogenic
	T336S	1	0.001	0	0	n.s.	Novel
	E365K	19	0.020	11	0.02	n.s.	Polymorphism, Risk PD
	T408M	17	0.018	0	0	0.0005	Polymorphism
	N409S	7	0.007	1	0.001	0.09	Pathogenic, Risk PD
	E427K	1	0.001	0	0	n.s.	Unknown
	D448H	1	0.001	1	0.001	n.s.	Pathogenic^a
	L483P	7	0.007	2	0.003	n.s.	Pathogenic^a, Risk PD
	A495P	17	0.018	10	0.015	n.s.	Pathogenic^b
Total		74		25		0.001
MAPT	A152T	4	0.004	0	0	0.09	Risk AD, FTD	PD GWAS Hit
	S427F	0	0	2	0.003	0.09	Unknown
	A495T	0	0	1	0.001	n.s.	Non-pathogenic
	A556T	1	0.001	0	0	n.s.	Unknown
Total		5		3

Gene: official Symbol provide by HGNC; AA Change: amino acid change resulting from the observed variant; MAF: Minor allele frequency; Clinical Interpretation: Clinical interpretation is based on PD mutation database [22] and published papers. ^aGBA variants found in pseudo gene. ^b Variant also known as p.A485P ^c Amino acid designations are based on the primary GBA translation product, including the 39-residue signal peptide

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ISSN: 1750-1326

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