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Table 1 Genotype frequencies for single markers used in both direct and indirect association analysis obtained with the Haploview 3.2 software package. P-values and OR are for allelic analysis.

From: Genetic association study of synphilin-1in idiopathic Parkinson's disease

Exon/Intron Nucleotide change Chromosome location Amino acid change Genotypes Cases 11/12/22 Controls 11/12/22 MAF Cases/controls Allele 1 vs. allele 2 p-value OR (95% CI)
1 g.IVS1-70G>A 121 754 613 ---- 165/115/19 206/176/24 0.26/0.28 0.43 0.90 [0.71–1.15]
4 T131>C 121 786 462 Val44Ala 296/1/0 405/0/0 0.0/0.0 0.42 ND
4 C636>T 121 786 967 Pro212Pro 296/1/0 405/0/0 0.0/0.0 0.42 ND
5 g.IVS4-26G>A 121 788 920 ---- 153/115/32 97/181/34 0.30/0.30 0.91 0.98 [0.78–1.24]
5 C1134>T 121 789 001 Leu378Leu 295/2/0 404/1/0 0.0/0.0 0.58 2.73 [0.36–20.9]
6 g.IVS5+188A>C 121 789 313 ---- 133/118/42 173/181/53 0.34/0.35 0.78 0.97 [0.77–1.21]
6 g.IVS5+235A>G 121 789 360 ---- 151/115/33 196/183/32 0.30/0.30 0.95 1.01 [0.80–1.27]
7 g.IVS6-62G>A 121 804 161 ---- 291/6/0 397/8/0 0.01/0.01 1.00 1.02 [0.37–2.84]
7 g.IVS6-23T>C 121 804 200 ---- 154/118/27 202/179/31 0.29/0.29 0.86 0.98 [0.76–1.23]
10 C1861>T 121 814 302 Arg621Cys 293/4/0 395/10/0 0.01/0.01 0.42 0.54 [0.18–1.64]
10 G2125>C 121 814 565 Glu709Gln 296/1/0 401/4/0 0.0/0.0 0.40 0.34 [0.05–2.27]
  1. One PSP affected (not accounted for here) was found to be homozygous for this variant. OR-Odds ratio. The SNPs used for indirect analysis were highly heterozygous; rs1946649, g.IVS1-70G>A (ObsHet; 0.41); rs2242224, g.IVS4-26G>A (ObsHet; 0.42); rs304383, g.IVS5+188A>C (ObsHet; 0.43); rs2242223, g.IVS5+235A>G (ObsHet; 0.42) and rs22900987, g.IVS6-23T>C (0.42).