Table 4.
Comparison of A3D, A3F, A3G and A3H allele frequencies between our South African population (SA) and populations in the 1000 Genome Project including: East Asian (EAS), European (EUR), African (AFR), Ad Mixed American (AMR), South Asian (SAS), as well as data from the Exome Aggregation Consortium (ExAC)
| Amino acid change and variant ID | Allele (2n) | SA (336) | EAS (1008) | EUR (1006) | AFR (1322) | AMR (694) | SAS (978) | ExAC (121412) |
| APOBEC 3D nonsynonymous allele frequencies (%) | ||||||||
| R6K (NI) | G (R) A (K) | 94.9 5.1 | NI | NI | NI | NI | NI | NI |
| R97C (rs75858538) | C (R) T (C) | 93.8 6.2 | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 96.6 3.4 (P = 0.0395)* | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 99.7 0.3 (P < 0.0001)* |
| L221R (NI) | T (L) G (R) | 99.1 0.9 | NI | NI | NI | NI | NI | NI |
| C224Y (rs772893975) | G (C) A (Y) | 97.9 2.1 | ND | ND | ND | ND | ND | 100 0 (P < 0.0001)* |
| T238A (rs201709403) | A (T) G (A) | 95.8 4.2 | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* |
| T238I (NI) | C (T) T (I) | 97.6 2.4 | NI | NI | NI | NI | NI | NI |
| R248K (rs61748819) | G (R) A (K) | 89.0 11.0 | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 89.0 11.0 (P = 1.0) | 99.0 1.0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 99.0 1.0 (P < 0.0001)* |
| C320Y (rs61999342) | G (C) A (Y) | 99.7 0.3 | ND | ND | ND | ND | ND | 100 0 (P < 0.0001)* |
| APOBEC3D synonymous allele frequencies (%) | ||||||||
| L221 L (rs769426665) | G (L) C (L) | 99.10.9 | ND | ND | ND | ND | ND | 100 0 (P < 0.0001)* |
| T316 T (rs184448269) | C (T) T (T) | 97.9 2.1 | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 98.8 1.2 (P = 0.2917) | 99.6 0.4 (P = 0.0169)* | 100 0 (P < 0.0001)* | 99.9 0.1 (P < 0.0001)* |
| APOBEC 3F nonsynonymous allele frequencies (%) | ||||||||
| R48P (rs35053197) | G (R) C (P) | 96.1 3.9 | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 96.9 3.1 (P = 0.4762) | 99.4 0.6 (P = 0.0003)* | 99.4 0.6 (P = 0.0001)* | 99.7 0.3 (P < 0.0001)* |
| A78V (rs5750728) | C (A) T (V) | 79.9 20.1 | 29 71 (P < 0.0001)* | 51 49 (P < 0.0001)* | 80 20 (P = 0.9371) | 38 62 (P < 0.0001)* | 39 61 (P < 0.0001)* | 52.3 47.8 (P < 0.0001)* |
| I87L (rs146543452) | A (I) C (L) | 99.7 0.3 | 100 0 (P = 0.2340) | 100 0 (P = 0.2344) | 99.0 1.0 (P = 0.4897) | 100 0 (P = 0.3074) | 100 0 (P = 0.2395) | 100 0 (P < 0.0001)* |
| Q87L (rs114704208) | A (Q) T (L) | 97.1 2.9 | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 94.5 5.5 (P = 0.0606) | 99.6 0.4 (P = 0.0019)* | 100 0 (P < 0.0001)* | 99.7 0.3 (P < 0.0001)* |
| A108S (rs2020390) | G (A) T (S) | 62.3 37.7 | 29.0 71.0 (P < 0.0001)* | 51.0 49.0 (P = 0.0005)* | 68.0 32.0 (P = 0.0600) | 37.0 63.0 (P < 0.0001)* | 40.0 60.0 (P = 0.0001)* | 52.4 47.6 (P < 0.0001)* |
| V231I (rs2076101) | G (V) A (I) | 89.0 11.0 | 29.0 71.0 (P < 0.0001)* | 51.0 49.0 (P < 0.0001)* | 81.0 19.0 (P = 0.0008)* | 38.0 62.0 (P < 0.0001)* | 39.0 61.0 (P < 0.0001)* | 48.4 51.6 (P < 0.0001)* |
| Y307C (rs12157816) | A (Y) G (C) | 95.1 4.9 | 100 0 (P < 0.0001)* | 98.0 2.0 (P = 0.0133)* | 97.0 3.0 (P = 0.1148) | 98.0 2.0 (P = 0.0225)* | 100 0 (P < 0.0001)* | 98.7 1.3 (P < 0.0001)* |
| APOBEC3F synonymous allele frequencies (%) | ||||||||
| I117I (NI) | C (I) T (I) | 99.4 0.6 | NI | NI | NI | NI | NI | NI |
| S118S (rs35928287) | C (S) T (S) | 86.7 13.3 | ND | ND | ND | ND | ND | 99.7 0.3 (P < 0.0001)* |
| R143R (rs4821862) | C (R) T (R) | 41.958.1 | 29.0 71.0 (P < 0.0001)* | 51.0 49.0 (P = 0.0040)* | 45.0 55.0 (P = 0.2781) | 36.0 64.0 (P = 0.1038) | 39.0 61.0 (P = 0.4613) | 45.5 54.6 (P = 0.1787) |
| Y196Y (rs765418322) | T (Y) C (Y) | 89.6 10.4 | ND | ND | ND | ND | ND | 100 0 (P < 0.0001)* |
| S229S (rs549550231) | A (S) G (S) | 99.4 0.6 | ND | ND | ND | ND | ND | 100 0 (P < 0.0001)* |
| E245E (rs113109079) | G (E) A (E) | 97.1 3.9 | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 99.0 1.0 (P = 0.0231)* | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* |
| S327S (rs35895636) | C (S) T (S) | 90.6 9.4 | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 98.3 1.7 (P < 0.0001)* | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 99.8 0.2 (P < 0.0001)* |
| APOBEC 3G nonsynonymous allele frequencies (%) | ||||||||
| H186R (rs8177832) | A (H) G (R) | 63.0 37.0 | 92.8 7.2 (P < 0.0001)* | 97.0 3.0 (P < 0.0001)* | 57.0 43.0 (P = 0.0530) | 92.5 7.5 (P < 0.0001)* | 99.2 0.8 (P < 0.0001) | 93.6 6.4 (P < 0.0001)* |
| R256H (rs17000736) | G (R) A (H) | 98.8 1.2 | 100 0 (P = 0.0036)* | 100 0 (P = 0.0037)* | 98.6 1.4 (P = 1.0) | 100 0 (P = 0.0107)* | 100 0 (P = 0.0040)8 | 100 0 (P = 0.0002)* |
| Q275E (rs17496046) | C (Q) G (E) | 82.1 17.9 | 97.3 2.7 (P < 0.0001)* | 94.6 5.4 (P < 0.0001)* | 87.5 12.5 (P = 0.0119)* | 96.0 4.0 (P < 0.0001)* | 98.7 1.3 (P < 0.0001)* | 94.3 5.7 (P < 0.0001)* |
| G363R (rs148267053) | G (G) A (R) | 94.8 5.2 | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 98.6 1.4 (P = 0.3220) | 99.9 0.1 (P = 0.0017)* | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* |
| APOBEC3G synonymous allele frequencies (%) | ||||||||
| S60S (rs112603901) | C (S) T (S) | 94.5 5.5 | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 99.7 0.3 (P < 0.0001)* | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* |
| A109A (rs375760983) | C (A) T (A) | 99.7 0.3 | ND | ND | ND | ND | ND | 100 0 (P < 0.0001)* |
| F119F (rs5757465) | T (F) C (F) | 99.7 0.3 | 77.6 22.4 (P < 0.0001)* | 55.3 44.7 (P < 0.0001)* | 97.1 2.9 (P = 0.0035)* | 60.2 39.8(P < 0.0001)* | 55.5 44.5 (P < 0.0001)* | 62.8 37.2 (P < 0.0001)* |
| L371 L (rs11545130) | C (L) T (L) | 97.9 2.1 | 100 0 (P < 0.0001)* | 100 0 (P < 0.0001)* | 97.0 3.0 (P = 0.4614) | 99.6 0.4 (P = 0.0157)* | 100 0 (P < 0.0001)* | 99.7 0.3 (P < 0.0001)* |
| APOBEC 3H nonsynonymous allele frequencies (%) | ||||||||
| N15Δ (rs140936762) | CAA(N) Δ | 40.2 59.8 | 74 26 (P < 0.0001)* | 66 34 (P < 0.0001)* | 69 31 (P < 0.0001)* | 72 28 (P < 0.0001)* | 60 40 (P < 0.0001)* | 65.7 34.3 (P < 0.0001)* |
| R18L (rs139293) | G (R) T (L) | 89.8 10.2 | 84.1 15.9 (P = 0.0192)* | 70.7 29.3 (P < 0.0001)* | 93.0 7.0 (P = 0.0972) | 75.8 24.2 (P < 0.0001)* | 69.4 30.6 (P < 0.0001)* | 73.2 26.8 (P < 0.0001)* |
| G105R (rs139297) | G (G) C (R) | 2.2 97.8 | 68.5 31.5 (P < 0.0001)* | 53.6 46.4 (P < 0.0001)* | 12.5 87.5 (P < 0.0001)* | 61.7 38.3 (P < 0.0001)* | 57.1 42.9 (P < 0.0001)* | 51.9 48.1 (P < 0.0001)* |
| K121E (rs139298) | A (K) G (E) | 3.0 97.0 | 68.5 31.5 (P < 0.0001)* | 52.3 47.7 (P < 0.0001)* | 12.5 87.5 (P < 0.0001)* | 61.2 38.8 (P < 0.0001)* | 56.1 43.9 (P < 0.0001)* | 51.5 48.5 (P < 0.0001)* |
| 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) |
| E178D (rs139302) | G (E) C (D) | 6.4 93.6 | 67.0 33.0 (P < 0.0001)* | 54.6 45.4 (P < 0.0001)* | 15.3 84.7 (P < 0.0001)* | 65.4 34.6 (P < 0.0001)* | 56.1 43.9 (P < 0.0001)* | 52.3 47.7 (P < 0.0001)* |
| APOBEC3H synonymous allele frequencies (%) | ||||||||
| T43 T (rs139294) | G (T) C (T) | 7.1 92.9 | 66.7 33.3 (P < 0.0001)* | 54.6 45.4 (P < 0.0001)* | 17.2 82.8 (P < 0.0001)* | 62.0 38.0 (P < 0.0001)* | 56.0 44.0 (P < 0.0001)* | 52.4 47.6 (P < 0.0001)* |
Notes:
NI = Not Identified previously
ND = Not Determined in 1000 genomes database
* = Significant (P value ≤0.05) Fisher’ s Exact Test used for EAS, EUR, AFR, AMR, SAS
Chi Squared Test used for ExAC