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)

 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)*

 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)*

 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)*

 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)*

 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)*

 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)*

 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)*

 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)*