Table 1.
Frequency of the LRRK2 p.A419V variant across ancestries
| Dataset | Ancestry | PD, n (%) breakdown in cohort | Control, n (%) breakdown in cohort | N Total Carriers | AF Total (AC) | N PD Carriers | AF PD cases (AC) | N Control Carriers | AF controls (AC) | AF gnomAD |
|---|---|---|---|---|---|---|---|---|---|---|
| GP2 25,699 cases; 13,652 controls | AAC | 338 (29.01) | 827 (70.99) | 0 | 0 (0/2330) | 0 | 0 (0/676) | 0 | 0 (0/1654) | NA |
| AFR | 983 (37.09) | 1667 (62.91) | 0 | 0 (0/5300) | 0 | 0 (0/1966) | 0 | 0 (0/3334) | 0.00001334 | |
| AJ | 1709 (67.47) | 824 (32.53) | 1 | 0.00020 (1/5066) | 1 | 0.00029 (1/3418) | 0 | 0 (0/1648) | 0 | |
| AMR | 2005 (58.4) | 1428 (41.6) | 0 | 0 (0/6866) | 0 | 0 (0/4010) | 0 | 0 (0/2856) | 0.00006669 | |
| CAH | 644 (67.51) | 310 (32.49) | 14 | 0.0073 (14/1908) | 14 | 0.011 (14/1288) | 0 | 0 (0/620) | NA | |
| CAS | 661 (66.77) | 329 (33.23) | 17 | 0.0086 (17/1980) | 13 | 0.0098 (13/1322) | 4 | 0.006 (4/658) | NA | |
| EAS | 3192 (57.3) | 2379 (42.7) | 97 | 0.0089 (99/11,142) | 81* | 0.013 (82/6384) | 16* | 0.0036 (17/4758) | 0.01028 | |
| EUR | 15,332 (73.63) | 5492 (26.37) | 37 | 0.00094 (39/41,648) | 35 ^# | 0.0012 (37/30,664) | 2 | 0.00018 (2/10,984) | 0.0001493 | |
| MDE | 481 (70.94) | 197 (29.06) | 0 | 0 (0/1356) | 0 | 0 (0/962) | 0 | 0 (0/394) | 0.0008267 | |
| SAS | 354 (64.01) | 199 (35.99) | 0 | 0 (0/1106) | 0 | 0 (0/708) | 0 | 0 (0/398) | 0.0001977 | |
| AMP-PD 2835 cases; 2.251 controls | EUR | 2251 (44.26) | 2835 (55.74) | 1 | 0.000098 (1/10,172) | 0 | 0 (0/4502) | 1 | 0.00018 (1/5670) | 0.0001493 |
| UKB 2954 cases; 56,256 controls | AAC | 3 (2.21) | 133 (97.79) | 0 | 0 (0/272) | 0 | 0 (0/6) | 0 | 0 (0/266) | NA |
| AFR | 19 (4.11) | 443 (95.89) | 0 | 0 (0/924) | 0 | 0 (0/38) | 0 | 0 (0/886) | 0.00001334 | |
| AJ | 33 (7.42) | 412 (92.58) | 0 | 0 (0/890) | 0 | 0 (0/66) | 0 | 0 (0/824) | 0 | |
| AMR | 2 (4) | 48 (96) | 0 | 0 (0/100) | 0 | 0 (0/4) | 0 | 0 (0/96) | 0.00006669 | |
| CAH | 9 (5.08) | 168 (94.92) | 0 | 0 (0/354) | 0 | 0 (0/18) | 0 | 0 (0/336) | NA | |
| CAS | 7 (3.32) | 204 (96.68) | 0 | 0 (0/422) | 0 | 0 (0/14) | 0 | 0 (0/408) | NA | |
| EAS | 3 (1.91) | 154 (98.09) | 2 | 0.0064 (2/314) | 0 | 0 (0/6) | 2 | 0.0065 (2/308) | 0.01028 | |
| EUR | 2827 (4.98) | 53963 (95.02) | 10 | 0.000088 (10/113,580) | 1 | 0.00018 (1/5654) | 9 | 0.000083 (9/107,926) | 0.0001493 | |
| MDE | 6 (8.82) | 62 (91.18) | 0 | 0 (0/136) | 0 | 0 (0/12) | 0 | 0 (0/124) | 0.0008267 | |
| SAS | 45 (6.3) | 669 (93.7) | 2 | 0.0014 (2/1428) | 1 | 0.011 (1/90) | 1 | 0.00075 (1/1338) | 0.0001977 | |
| AOU 2103 cases; 29,733 controls | AFR | 144 (6.8) | 5884 (19.8) | 0 | 0 (0/12,052) | 0 | 0 (0/288) | 0 | 0 (0/11,764) | 0.00001334 |
| AMR | 231 (11) | 3877 (13) | 1 | 1.22E-04 (1/8216) | 0 | 0 (0/462) | 1 | 0.0001 (1/7754) | 0.00006669 | |
| EAS | 15 (0.7) | 748 (2.5) | 8 | 0.005 (8/1526) | 2 | 0.066 (2/30) | 6 | 0.004 (6/1496) | 0.01028 | |
| EUR | 1692 (80.4) | 18,926 (63.7) | 13 | 3.15E-04 (13/41,236) | 1 | 2.96E-04 (1/3384) | 12 | 3.17E-04 (12/37,852) | 0.0001493 | |
| MDE | 5 (0.2) | 70 (0.2) | 0 | 0 (0/150) | 0 | 0 (0/10) | 0 | 0 (0/140) | 0.0008267 | |
| SAS | 16 (0.8) | 228 (0.8) | 0 | 0 (0/488) | 0 | 0 (0/32) | 0 | 0 (0/456) | 0.0001977 | |
| Singapore EAS-WES 3967 cases; 5457 controls | EAS | 3967 (42.09) | 5457 (57.91) | 177 | 0.0058 (180/18,848) | 107” | 0.0139 (110/7934) | 70 | 0.0064 (70/10,914) | 0.01028 |
| JPN 2729 cases; 61,332 controls | EAS | 2729 (4.26) | 61,332 (95.74) | 2086 | 0.0165 (2,107/128,112) | 167‘ | 0.0321 (175/5458) | 1915“ | 0.0158 (1,932/122,664) | 0.01028 |
*Include 1 homozygous carrier.
^Include 2 homozygous carriers.
“Include 3 homozygous carriers.
'Include 8 homozygous carriers.
"Include 17 homozygous carriers.
#22 out of 35 of these patients were submitted from Central Asia.
AC Allele Counts, AF Allele Frequency, AF gnomAD Population specific allele frequency in gnomAD 4.1, AAC African American or Caribbean, AFR Sub-Saharan African, AJ Ashkenazi Jewish, AMR Admixed American, CAH Complex Admixture History, CAS Central Asian, EAS East Asian populations, EUR European, MDE Middle Eastern, SAS South Asian.