Skip to main content

Table 1 Rare disruptive variants (MAF ≤ 0.001, CADD phred≥20) in the 26 PD candidate genes identified in the discovery families

From: Identification of sixteen novel candidate genes for late onset Parkinson’s disease

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
  1. 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)