Table 2.
APOBEC 3D, 3F, 3G and 3H nonsynonymous and synonymous changes, genotypes, amino acid position and change in the protein, frequencies and Hardy Weinberg Equilibrium calculations from the study population
| Amino acid change and variant ID | Type of change | Genotypes nt # in CDS | Exon | Frequencies (%) | Hardy Weinberg equilibrium |
|---|---|---|---|---|---|
| APOBEC 3D nonsynonymous changes (n = 168) | |||||
| R6K (NI) | AGA➔AAA Transition | 17G/G 17G/A |
1 | 151 (89.9) 17 (10.1) | P-value = 0.49 X2 = 0.48 |
| R97C (rs75858538) | CGC➔TGC Transition | 289 C/C 289 C/T 289 T/T |
1 | 148 (88.1) 19 (11.3) 1 (0.6) | P-value = 0.65 X2 = 0.20 |
| L221R (NI) | CTG➔CGG Transition | 662 T/T 662 T/G | 5 | 165 (98.2) 3 (1.8) | P-value = 0.91 X2 = 0.01 |
| C224Y (rs772893975) | TGT➔TAT Transition | 671G/G 671G/A | 5 | 161 (95.8) 7 (4.2) | P-value = 0.78 X2 = 0.076 |
| T238A (rs201709403) | ACA➔GCA Transition | 712A/A 712A/G | 5 | 154 (91.7) 14 (8.3) | P-value = 0.57 X2 = 0.32 |
| T238I (NI) | ACA➔ATA Transition | 713C/C 713C/T | 5 | 160(95.2) 8(4.8) | P-value = 0.75 X2 = 0.10 |
| R248K (rs61748819) | AGG➔AAG Transition | 743 G/G 743 G/A 743 A/A | 5 | 133 (79.2) 33 (19.6) 2 (1.2) | P-value = 0.98 X2 = 0.001 |
| C320Y (rs61999342) | TGC➔TAC Transition | 959 G/G 959 G/A | 6 | 167 (99.4) 1 (0.6) | P-value = 0.97 X2 = 0.001 |
| APOBEC3D synonymous changes | |||||
| L221 L (rs769426665) | CTG ➔CTC Transversion | 663G/G 663G/C | 5 | 165 (98.2) 3 (1.8) | P-value = 0.91 X2 = 0.01 |
| T316 T (rs184448269) | ACC➔ACT Transition | 948 C/C 948 C/T | 6 | 161 (95.8) 7 (4.2) | P-value =0.78 X2 = 0.08 |
| APOBEC 3F nonsynonymous changes (n = 154) | |||||
| R48P (rs35053197) (in isoform 201 and 202) | CGT➔CCC Transversion | 143 G/G 143 G/C | 2 | 142 (92.2) 12 (7.8) | P-value = 0.61 X2 = 0.25 |
| A78V (rs5750728) (only in isoform 201) | GCC➔GTC Transition | 233 C/C 233 C/T 233 T/T | 4 | 95 (61.7) 56 (36.4) 3 (1.9) | P-value = 0.10 X2 = 2.64 |
| I87L (rs146543452) (only in isoform 201) | ATC➔CTC Transversion | 259 A/A 259 A/C | 4 | 153 (99.4) 1(0.6) | P-value = 0.97 X2 = 0.002 |
| Q87L (rs114704208) (only in isoform 202) | CAG➔CTG Transversion | 260 A/A 260 A/T | 3 | 145 (94.2) 9 (6.8) | P-value = 0.71 X2 = 0.14 |
| A108S (rs2020390) (only in isoform 201) | GCT➔TCT Transversion | 322 G/G 322 G/T 322 T/T | 4 | 54 (35.1) 84 (54.5) 16 (10.4) | P-value = 0.04 X2 = 4.02 |
| V231I (rs2076101) (only in isoform 201) | GTC➔ATC Transition | 691 G/G 691 G/A 691 A/A | 5 | 122 (79.2) 30 (19.5) 2 (1.3) | P-value = 0.92 X2 = 0.01 |
| Y307C (rs12157816) (only in isoform 201) | TAC➔TGC Transition | 920 A/A 920 A/G | 6 | 139 (90.3) 15 (9.7) | P-value = 0.52 X2 = 0.40 |
| APOBEC3F synonymous changes | |||||
| I117I (NI) (only in isoform 201) | ATC➔ATT Transition | 351 C/C 351 C/T | 4 | 152 (98.7) 2 (1.3) | P-value =0.94 X2 = 0.007 |
| S118S (rs35928287) (only in isoform 201) | TCC➔TCT Transition | 354 C/C 354 C/T | 4 | 113 (73.4) 41 (26.6) | P-value =0.06 X2 = 3.63 |
| R143R (rs4821862) (only in isoform 201) | CGC➔CGT Transition | 429 C/C 429 C/T 429 T/T | 4 | 19 (12.3) 91 (59.1) 44 (28.6) | P-value = 0.01 X2 = 7.04 |
| Y196Y (rs765418322) (only in isoform 201) | TAT➔TAC Transition | 588 T/T 588 T/C 588 C/C | 4 | 126 (81.8) 24 (15.6) 4 (2.6) | P-value = 0.04 X2 = 4.09 |
| S229S (rs549550231) (only in isoform 201) | TCA➔TCG Transition | 687 A/A 687 A/G | 5 | 152 (98.7) 2 (1.3) | P-value = 0.94 X2 = 0.007 |
| E245E (rs113109079) (only in isoform 201) | GAG➔GAA Transition | 735 G/G 735 G/A 735 A/A | 5 | 146 (94.8) 7 (4.5) 1 (0.7) | P-value = 0.01 X2 = 6.09 |
| S327S (rs35895636) (only in isoform 201) | TCC➔TCT Transition | 981 C/C 981 C/T 981 T/T | 5 | 128 (83.2) 23 (14.9) 3 (1.9) | P-value = 0.12 X2 = 2.39 |
| APOBEC 3G nonsynonymous changes (n = 165) | |||||
| H186R (rs8177832) | CAC➔CGC Transition | 557 A/A5 557 A/G 557 G/G | 4 | 63 (38.2) 82 (49.7) 20 (12.1) | P-value = 0.39 X2 = 0.73 |
| R256H (rs17000736) | CGC➔CAC Transition |
767 G/G 767 G/A | 6 | 161(97.6) 4 (2.4) | P-value = 0.87 X2 = 0.02 |
| Q275E (rs17496046) | CAG➔GAG Transversion | 823 C/C 823 C/G 823 G/G | 6 | 111 (67.3) 49 (29.7) 5 (3.0) | P-value = 0.88 X2 = 0.02 |
| G363R (rs148267053) | GGA➔AGA Transition | 1087 G/G 1087 G/A | 7 | 148 (89.7) 17 (10.3) | P-value = 0.49 X2 = 0.49 |
| APOBEC3G synonymous changes | |||||
| S60S (rs112603901) | TCC➔TCT Transition | 180 C/C 180 C/T | 3 | 147 (89.1) 18 (10.9) | P-value =0.46 X2 = 0.55 |
| A109A (rs375760983) | GCC➔GCT Transition | 327 C/C 327 C/T | 3 | 164 (99.4) 1 (0.6) | P-value =0.97 X2 = 0.002 |
| F119F (rs5757465) | TTT➔TTC Transition | 357 T/T 357 T/C | 3 | 164 (99.4) 1 (0.6) | P-value =0.97 X2 = 0.002 |
| L371 L (rs11545130) | CTG➔TTG Transition | 1111 C/C 1111 C/T | 7 | 158 (95.8) 7 (4.2) | P-value =0.78 X2 = 0.08 |
| APOBEC 3H nonsynonymous changes (n = 133) | |||||
| N15Δ (rs140936762) | -CAA Deletion | 45 CAA/CAA 45 CAA/ Δ 45 Δ / Δ | 1 | 29 (21.8) 49 (36.8) 55 (41.4) | P-value = 0.001 X2 = 10.25 |
| R18L (rs139293) | CGC➔CTC Transversion | 53 G/G 53 G/T 53 T/T | 1 | 112 (84.2) 15 (11.3) 6 (4.5) | P-value = 0.00 X2 = 15.9 |
| G105R (rs139297) | GGC➔CGC Transversion | 313 G/G 313 G/C 313 C/C | 2 | 1 (0.8) 4 (3.0) 128 (96.2) | P-value = 0.00 X2 = 13.4 |
| K121E (rs139298) | AAG➔GAG Transition | 361 A/A 361 A/G 361 G/G | 2 | 1 (0.8) 6 (4.5) 126 (94.7) | P-value = 0.01 X2 = 6.9 |
| K140E (rs139300) | AAG➔GAG Transition | 418 A/A 418 G/G | 2 | 0133 (100) | P-value = N/A X2 = N/A |
| E178D (rs139302) | GAG➔GAC Transversion | 534 G/G 534 G/C 534 C/C | 3 | 3 (2.2) 11 (8.3) 119 (89.5) | P-value = 0.00 X2 = 12.7 |
| APOBEC3H synonymous changes | |||||
| T43 T (rs139294) | ACG➔ACC Transversion | 129 G/G 129 G/C 129 C/C | 1 | 6 (4.5) 7 (5.3) 120 (90.2) | P-value =0.00 X2 = 48.4 |
The following Ensembl transcripts were used for aa positions in the CDS:
A3D: APOBEC3D-201 ENST00000216099.12 (386aa)
A3F: APOBEC3F-201 ENST00000308521.9 (373aa) and APOBEC3F-202 ENST00000381565.2 (101aa)
A3G: APOBEC3G-201 ENST00000407997.3 (384aa)
A3H: APOBEC3H-204 ENST00000442487.7 (183aa)
NI = Not Identified Previously;
Nucleotide change in the codon is shown in bold
CDS = coding sequence