Table 6.
Haplotype analysis of LRRK2 c.4883G>C (p.Arg1628Pro) and c.4883G>A (p.Arg1628His) carriers
| European p.Arg1628Pro haplotype |
R1628H haplotype |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| SNP ID | Chr12 Position | cDNA | Protein | MAF | A | B | C | D | E | Asian p.Arg1628Pro haplotype* |
| rs10878245 | 38,918,058 | c.457T>C | p.Leu153Leu | 0.406 | T | T | T | T | C | - |
| rs7955902 | 38,931,524 | c.1102-10C>A | - | 0.373 | C | C | C | C | A | - |
| rs11175964 | 38,989,254 | c.4269G>A | p.Lys1423Lys | 0.066 | G | G | G | G | G | G |
| rs1896252 | 39,000,026 | c.4828-31T>C | - | 0.459 | T | T | T | T | C | C |
| rs1427263 | 39,000,101 | c.4872C>A | p.Gly1624Gly | 0.346 | A | A | A | A | A | A |
| rs33949390 | 39,000,112 | c.4883G>C/A | p.Arg1628Pro/His | 0.0004/0.0002 | C | C | C | C | A | C |
| rs11176013 | 39,000,140 | c.4911A>G | p.Lys1637Lys | 0.457 | A | A | A | A | G | G |
| rs11564148 | 39,000,168 | c.4939T>A | p.Ser1647Thr | 0.292 | T | T | T | T | A | A |
| rs7307276 | 39,001,280 | c.5170+23T>A | - | 0.452 | T | T | T | T | A | - |
| rs10878371 | 39,002,527 | c.5457T>C | p.Gly1819Gly | 0.453 | T | T | T | T | C | - |
| rs10878405 | 39,028,521 | c.6324G>A | p.Glu2108Glu | 0.306 | G | G | G | G | A | A |
| rs33962975 | 39,043,597 | c.7155A>G | p.Gly2385Gly | 0.136 | G | G | G | G | A | - |
Haplotypes were inferred using BEAGLE (Li, et al., 2011) for four (A-D) carriers of p.Arg1628Pro, and one carrier (E) of p.Arg1628His, respectively. All four p.Arg1628Pro carriers share a common haplotype, which is distinct from the Asian ancestral haplotype described by Ross et al. (Ross, et al., 2008). “-” indicates no SNP data available. SNP markers delineate a chromosome 12 genomic segment 125.5 kb in length. Haplotypes for all four R1628P carriers extend the entire length (144 kb ) of the LRRK2 gene (data not shown). Chromosome position is relative to NCBI Build 36.3 of the human genome sequence, and cDNA variant positions correspond to transcript NM_198578.3.