Table 5 Comparison of A3D, A3F, A3G and A3H allele frequencies between our South African population (SA) and other African populations in the 1000 Genome Project including: the African Caribbeans in Barbados (ACB), Americans of African Ancestry in USA (ASW), Esan in Nigeria (ESN), Gambian in the Western Gambia (GWD), Luhya in Webuye, Kenya (LWK), Mende in Sierra Leone (MSL) and Yoruba in Ibadan, Nigeria (YRI)
Amino acid change and variant ID | Allele (2n) | SA (336) | ACB (192) | ASW (122) | ESN (198) | GWD (226) | LWK (198) | MSL (170) | YRI (216) |
APOBEC 3D nonsynonymous allele frequencies (%) | |||||||||
R6K (NI) | G (R) A (K) | 94.9 5.1 | NI | NI | NI | NI | NI | NI | NI |
R97C (rs75858538) | C (R) T (C) | 93.8 6.2 | 97 3 (P = 0.1506) | 94 6 (P = 1.0) | 97 3 (P = 0.0614) | 98 2 (P = 0.0253)* | 94 6 (P = 1.0) | 98 2 (P = 0.0262)* | 97 3 (P = 0.1631) |
L221R (NI) | T (L) G (R) | 99.1 0.9 | NI | NI | NI | NI | NI | NI | NI |
C224Y (rs772893975) | G (C) A (Y) | 97.9 2.1 | ND | ND | ND | ND | ND | ND | ND |
T238A (rs201709403) | A (T) G (A) | 95.8 4.2 | 100 0 (P = 0.0030)* | 99 1 (P = 0.1322) | 100 0 (P = 0.0016)* | 100 0 (P = 0.0012)* | 100 0 (P = 0.0016)* | 100 0 (P = 0.0036)* | 100 0 (P = 0.0013)* |
T238I (NI) | C (T) T (I) | 97.6 2.4 | NI | NI | NI | NI | NI | NI | NI |
R248K (rs61748819) | G (R) A (K) | 89.0 11.0 | 91 9 (P = 0.4596) | 96 4 (P = 0.0267)* | 86 14 (P = 0.3375) | 92 8 (P = 0.3890) | 87 13 (P = 0.5785) | 86 14 (P = 0.4668) | 87 13 (P = 0.5018) |
C320Y (rs61999542) | G (C) A (Y) | 99.7 0.3 | ND | ND | ND | ND | ND | ND | ND |
APOBEC3D synonymous allele frequencies (%) | |||||||||
L221 L (rs769426665) | G (L) C (L) | 99.1 0.9 | ND | ND | ND | ND | ND | ND | ND |
T316 T (rs184448269) | C (T) T (T) | 97.9 2.1 | 99 1 (P = 0.3657) | 99 1 (P = 0.3657) | 98 2 (P = 0.3657) | 99 1 (P = 0.3657) | 99 1 (P = 0.3657) | 98 2 (P = 0.3657) | 99 1 (P = 0.3657) |
APOBEC 3F nonsynonymous allele frequencies (%) | |||||||||
R48P (rs35053197) | G (R) C (P) | 96.1 3.9 | 98 2 (P = 0.3074) | 98 2 (P = 0.3670) | 95 5 (P = 0.8202) | 99 1 (P = 0.1100) | 95 5 (P = 0.6559) | 98 2 (P = 0.2763) | 95 5 (P = 0.6663) |
A78V (rs5750728) | C (A) T (V) | 79.9 20.1 | 78 22 (P = 0.6518) | 73 27 (P = 0.1236) | 82 18 (P = 0.6453) | 77 23 (P = 0.3943) | 76 24 (0.3756) | 85 15 (P = 0.2183) | 86 14 (P = 0.0798) |
I87L (rs146543452) | A (I) C (L) | 99.7 0.3 | 100 0 (P = 1) | 100 0 (P = 1) | 100 0 (P = 1) | 98 2 (P = 0.0878) | 99 1 (P = 1) | 99 1 (P = 1) | 100 0 (P = 1) |
Q87L (rs114704208) | A (Q) T (L) | 97.1 2.9 | 92.2 7.8 (P = 0.0171)* | 93.4 6.6 (P = 0.0994) | 96.5 3.5 (P = 0.7961) | 96.0 4.0 (P = 0.6287) | 93.0 7.0 (P = 0.0718) | 94.7 5.3 (P = 2141) | 94.4 5.6 (P = 0.1738) |
A108S (rs2020390) | G (A) T (S) | 62.3 37.7 | 67 33 (P = 0.2922) | 66 34 (P = 0.5796) | 69 31 (P = 0.1268) | 62 38 (P = 0.8572) | 65 35 (P = 0.6371) | 76 24 (P = 0.0031)* | 70 30 (P = 0.0619) |
V231I (rs2076101) | G (V) A (I) | 89.0 11.0 | 79 21 (P = 0.0041)* | 73 27 (P = 0.0001)* | 84 16 (P = 0.1053) | 78 22 (P = 0.0007)* | 80 20 (P = 0.0092)* | 85 15 (P = 0.2485) | 87 13 (P = 0.5829) |
Y307C (rs12157816) | A (Y) G (C) | 95.1 4.9 | 95 5 (P = 0.8368) | 98 2 (P = 0.1703) | 96 4 (P = 0.5129) | 98 2 (P = 0.1649) | 98 2 (P = 0.1489) | 96 4 (P = 0.8218) | 95 5(P = 1.0) |
APOBEC3F synonymous allele frequencies (%) | |||||||||
I117I (NI) | C (I) T (I) | 99.4 0.6 | NI | NI | NI | NI | NI | NI | NI |
S118S (rs35928287) | C (S) T (S) | 86.7 13.3 | ND | ND | ND | ND | ND | ND | ND |
R143R (rs4821862) | C (R) T (R) | 41.9 58.1 | 45 55 (P = 0.5775) | 45 55 (P = 5892) | 39 61 (P = 0.6433) | 50 50 (P = 0.0794) | 45 55 (P = 0.4624) | 46 54 (P = 0.3372) | 47 53 (P = 0.2840) |
Y196Y (rs765418322) | T (Y) C (Y) | 89.6 10.4 | ND | ND | ND | ND | ND | ND | ND |
S229S (rs549550231) | A (S) G (S) | 99.4 0.6 | ND | ND | ND | ND | ND | ND | ND |
E245E (rs113109079) | G (E) A (E) | 97.1 2.9 | 99 1 (P = 0.2175) | 98 2 (P = 0.7356) | 100 0 (P = 0.0139)* | 98 2 (P = 0.5717) | 99 1 (P = 0.0971) | 98 2 (P = 0.5517) | 98 2 (P = 0.1350) |
S327S (rs35895636) | C (S) T (S) | 90.6 9.4 | 98 2 (P = 0.0013)* | 99 1 (P = 0.0006)* | 96 4 (P = 0.0126)* | 100 0 (P = 0.0001)* | 97 3 (P = 0.0064)* | 100 0 (P = 0.0001)* | 98 2 (P = 0.0004)* |
APOBEC 3G nonsynonymous allele frequencies (%) | |||||||||
H186R (rs8177832) | A (H) G (R) | 63.037.0 | 56 44 (P = 0.1147) | 75 25 (P = 0.0249)* | 49 51 (P = 0.0026)* | 57 43 (P = 0.1344) | 68 32 (P = 0.3013) | 49 51 (P = 0.0030)* | 52 48 (P = 0.0101)* |
R256H (rs17000736) | G (R) A (H) | 98.8 1.2 | 98 2 (P = 0.7118) | 98 2 (P = 0.6631) | 99 1 (P = 0.6550) | 97 3 (P = 0.1316) | 98 2 (P = 1.0) | 99 1 (P = 0.6660) | 99 1 (P = 1.0) |
Q275E (rs17496046) | C (Q) G (E) | 82.117.9 | 90 10 (P = 0.0026)* | 91 9 (P = 0.0064)* | 86 14 (P = 0.0725) | 87 13 (P = 0.0482)* | 83 17 (P = 0.3526) | 91 9 (P = 0.0027)* | 87 13 (P = 0.0473)* |
G363R (rs148267053) | G (G) A (R) | 94.8 5.2 | 98 2 (P = 0.1066) | 99 1(P = 0.0532) | 100 0 (P = 0.0005)* | 98 2(P = 0.0429)* | 99 1(P = 0.0142)* | 98 2 (P = 0.0902) | 98 2 (P = 0.1209) |
APOBEC3G synonymous allele frequencies (%) | |||||||||
S60S (rs112603901) | C (S) T (S) | 94.5 5.5 | 99 1 (P = 0.0027)* | 98 2(P = 0.1191) | 100 0 (P = 0.0002)* | 100 0 (P = 0.0001)* | 99 1 (P = 0.0026)* | 100 0 (P = 0.0006)* | 100 0 (P = 0.0001)* |
A109A (rs375760983) | C (A) T (A) | 99.7 0.3 | ND | ND | ND | ND | ND | ND | ND |
F119F (rs5757465) | T (F) C (F) | 99.7 0.3 | 93 7 (P = 0.0001)* | 89 11 (P = 0.0001)* | 100 0(P = 1.0) | 98 2 (P = 0.1639) | 98 2 (P = 0.1507) | 99 1 (P = 1.0) | 99 1 (P = 0.5654) |
L371 L (rs11545130) | C (L) T (L) | 97.9 2.1 | 98 2 (P = 0.7523) | 98 2 (P = 1.0) | 97 3 (P = 0.7698) | 98 2 (P = 1.0) | 95 5 (P = 0.1239) | 98 2 (P = 1.0) | 95 5 (P = 0.1299) |
APOBEC 3H nonsynonymous allele frequencies (%) | |||||||||
N15Δ (rs140936762) | CAA(N) Δ | 40.2 59.8 | 71 29 (P < 0.0001)* | 70 30 (P < 0.0001)* | 61 39 (P = 0.0004)* | 78 22 (P < 0.0001)* | 62 38 (P = 0.0002)* | 75 25 (P < 0.0001)* | 68 32 (P < 0.0001)* |
R18L (rs139293) | G (R) T (L) | 89.8 10.2 | 93 7 (P = 0.3230) | 87 13 (P = 0.3885) | 93 7 (P = 0.3212) | 94 6 (P = 0.0972) | 94 6 (P = 0.0873) | 93 7 (P = 0.3053) | 96 4 (P = 0.0076)* |
G105R (rs139297) | G (G) C (R) | 2.2 97.8 | 15 85 (P < 0.0001)* | 25 75 (P < 0.0001)* | 10 90 (P = 0.0007)* | 13 87 (P < 0.0001)* | 9 91 (P = 0.0012)* | 11 89 (P < 0.0002)* | 9 91 (P < 0.0016)* |
K121E (rs139298) | A (K) G (E) | 3.0 97.0 | 15 85 (P < 0.0001)* | 25 75 (P < 0.0001)* | 10 90 (P = 0.0025)* | 13 87 (P < 0.0001)* | 9 91 (P = 0.0070)* | 11 89 (P = 0.0008)* | 9 91 (P = 0.0086)* |
K140E (rs139300) | A (K) G (E) | 0100 | 0100 (P = 1.0) | 0100 (P = 1.0) | 0100 (P = 1.0) | 0100 (P = 1.0) | 0100 (P = 1.0) | 0100 (P = 1.0) | 0100 (P = 1.0) |
E178D (rs139302) | G (E) C (D) | 6.4 93.6 | 17 83 (P = 0.0004)* | 29 71 (P < 0.0001)* | 11 89 (P = 0.0900) | 16 84 (P = 0.0007)* | 16 84 (P = 0.0018)* | 13 87 (P = 0.0248)* | 11 89 (P = 0.0991) |
APOBEC3H synonymous allele frequencies (%) | |||||||||
T43 T (rs139294) | G (T) C (T) | 7.1 92.9 | 22 78 (P < 0.0001)* | 30 70 (P < 0.0001)* | 16 84 (P = 0.0026)* | 16 84 (P = 0.0024)* | 13 87 (P = 0.0545) | 17 83 (P = 0.0016)* | 13 87 (P = 0.0439)* |