Table 1.

Rare disruptive variants (MAF ≤ 0.001, CADD phred≥20) in the 26 PD candidate genes identified in the discovery families

CHR	Genomic position (hg19)	dbSNP	Gene	RefSEq	Nucleotide Change	AA Change	Exonic Function	Cl	MAF Max in public data sets	CADD phred	Family
16	723,544	rs143816083	RHOT2	NM_138769	c.G1795T	p.G599W	NSV	N	0.0001	25	1
3	184,039,223	rs746291399	EIF4G1	NM_198241	c.C851G	p.S284C	NSV	N	0.00004	25	2
1	8,022,928	rs142405016	PARK7	NM_007262	c.G83A	p.R28Q	NSV		0.0002	35	5
7	6,062,997	rs749728733	AIMP2	NM_006303	c.T638C	p.I213T	NSV	N	0.00002	27	7
2	86,408,450	rs201861204	IMMT	NM_001100169	c.C91T	p.R31C	NSV	N	0.0002	26	7
1	20,971,042	rs74315358	PINK1	NM_032409	c.G836A	p.R279H	NSV	P	0.00004	26	7
16	89,717,990		CHMP1A	NM_002768	c.C92T	p.A31V	NSV	N	NA	23	9
2	74,757,823		HTRA2	NM_013247	c.A586G	p.N196D	NSV	N	NA	23	9
3	132,222,165		DNAJC13	NM_015268	c.C4824G	p.S1608R	NSV	N	NA	20	10
17	42,398,033		SLC25A39	NM_001143780	c.C758A	p.T253N	NSV	N	NA	21	10
2	54,895,594	rs200093475	SPTBN1	NM_003128	c.C6983A	p.T2328N	NSV	N	0.00004	27	12
22	39,078,021	rs200476832	TOMM22	NM_020243	c.C38T	p.P13L	NSV	N	0.0002	25	12
19	14,589,354		GIPC1	NM_202470	c.875dupA	p.K292fs	Fs_ins	N	NA	NA	13
6	162,394,354	rs114974496	PARK2	NM_004562	c.C714G	p.C238W	NSV	P	0.00004	25	13
5	121,787,252	rs751412863	SNCAIP	NM_005460	c.A2710G	p.K904E	NSV	N	0.00004	24	14
12	40,704,237	rs34995376	LRRK2	NM_198578	c.G4322A	p.R1441H	NSV	P	0.00001	27	14
7	99,654,828		ZSCAN21	NM_145914	c.C199T	p.R67W	NSV	N	NA	24	16
9	34,290,328	rs372797268	KIF24	NM_194313	c.T971C	p.I324T	NSV	N	0.0001	26	17
16	10,911,991		TVP23A	NM_001079512	c.G58T	p.E20X	stopgain	N	NA	38	18
1	65,858,474		DNAJC6	NM_001256864	c.C1829T	p.P610L	NSV	N	NA	23	19
15	75,652,021		MAN2C1	NM_001256494	c.1882_1887del	p.628_629del	NFs_del	N	NA	NA	19
15	75,652,016		MAN2C1	NM_001256494	c.1890_1892del	p.630_631del	NFs_del	N	NA	NA	19
22	32,870,999		FBXO7	NM_012179	c.C10T	p.R4W	NSV	N	NA	33	20
16	4,557,822	rs772245870	HMOX2	NM_001286271	c.C226T	p.R76W	NSV	N	0.00001	34	20
1	200,957,957	rs751952433	KIF21B	NM_001252100	c.G3235A	p.A1079T	NSV	N	0.00002	29	21
11	122,931,465		HSPA8	NM_006597	c.G247A	p.V83I	NSV	N	NA	21	24
4	947,062		TMEM175	NM_032326	c.C547T	p.R183X	stopgain	N	NA	34	25
1	200,974,537		KIF21B	NM_001252100	c.C631T	p.R211C	NSV	N	NA	34	26

CHR Chromosome, hg19 human genome build to which these variants are annotated, dbSNP reference number in SNP database, ref. seq reference number of the gene transcript, AA Change Amino acid change, CI Clinical interpretation, P Pathogenic, UP Uncertain pathogenicity, N Novel, PD Parkinson’s disease, IPDGC International Parkinson’s Disease Genetics Consortium, CADD phred Combined Annotation Dependent Depletion, Fs_ins Frame shift insertion, NFs_del Non Frame shift deletion, NSV Non-synonymous variant, MAF Minor Allele Frequency, NA Not Annotated, MAF max in public datasets: highest allelic frequency annotated in public databases including 1000 Genomes Project (AFR. AMR. EAS. EUR. SAS), ExAC browser (NFE. AFR. SAS. EAS and AMR), ESP6500si-v2 (European American and African American population)