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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

From: Characterization of APOBEC3 variation in a population of HIV-1 infected individuals in northern South Africa

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
  1. The following Ensembl transcripts were used for aa positions in the CDS:
  2. A3D: APOBEC3D-201 ENST00000216099.12 (386aa)
  3. A3F: APOBEC3F-201 ENST00000308521.9 (373aa) and APOBEC3F-202 ENST00000381565.2 (101aa)
  4. A3G: APOBEC3G-201 ENST00000407997.3 (384aa)
  5. A3H: APOBEC3H-204 ENST00000442487.7 (183aa)
  6. NI = Not Identified Previously;
  7. Nucleotide change in the codon is shown in bold
  8. CDS = coding sequence