Association of HLA-B Gene Polymorphisms with Type 2 Diabetes in Pashtun Ethnic Population of Khyber Pakhtunkhwa, Pakistan
Table 1
HLA-B variants reported by whole exome sequencing.
SNP ID
Gene
Variant
Chr
cDNA position
Protein position
HGVSc
HGVSp
SIFT score
PolyPhen score
Alternate allele frequency (%)
Read depth
Case
Control
Case
Control
rs2308655
HLA-B
C>C/G
6
1100
349
c.1046G>C
p.Cys349Ser
Del (0.03)
Damaging
87.48
55.22
235
169
rs1051488
HLA-B
C>C/T
6
1039
329
c.985G>A
p.Ala329Thr
Tol (0.05)
Benign
49.07
45
108
80
rs1131500
HLA-B
C>C/T
6
970
306
c.916G>A
p.Val306Ile
Tol (1)
Benign
47.35
49.07
77
54
rs1050341
HLA-B
T>T/C
6
706
218
c.652A>G
p.Ile218Val
Tol (0.51)
Benign
52.16
53.02
301
218
rs1131285
HLA-B
C>C/G
6
664
204
c.610G>C
p.Glu204Gln
Tol (1)
Benign
83.33
85.19
228
257
rs1131275
HLA-B
G>G/C
6
657
201
c.603C>G
p.Asp201Glu
Tol (1)
Benign
85.24
86.05
244
258
rs1050696
HLA-B
A>A/G
6
637
195
c.583T>C
p.Tyr195His
Tol (0.22)
Benign
24.73
29.9
275
291
rs2308466
HLA-B
T>G/A
6 6
614
187
c.560A>C
p.Glu187Ala
Tol (0.57)
Benign
34.67
41.52
349
289
rs2523600
HLA-B
C>T/G
613
187
c.559G>A
p.Glu187Lys
Tol (0.71)
Benign
34.67
41.32
349
288
rs697742
HLA-B
C>C/A
6
593
180
c.539G>T
p.Arg180Leu
Tol (0.66)
Benign
50.99
59.2
402
299
rs9266144
HLA-B
G>G/A
6
592
180
c.538C>T
p.Arg180Trp
Tol (0.2)
Benign
16.34
19.4
410
299
rs151341293
HLA-B
T>T/A
6
581
176
c.527A>T
p.Glu176Val
Tol (0.65)
Benign
25.11
33.04
462
339
rs1050654
HLA-B
G>G/T
6
517
155
c.463C>A
p.Arg155Ser
Tol (0.09)
Benign
37.63
53.15
481
301
rs1140412
HLA-B
G>G/C
6
417
121
c.363C>G
p.Ser121Arg
Tol (0.79)
Benign
61.79
68.91
123
119
rs1071652
HLA-B
C>C/G
6
416
121
c.362G>C
p.Ser121Thr
Tol (0.75)
Benign
61.67
59.02
120
122
rs1050388
HLA-B
C>C/T
6
356
101
c.302G>A
p.Ser101Asn
Tol (1)
Benign
22.08
29.59
240
169
rs1131215
HLA-B
C>C/A
6
346
98
c.292G>T
p.Asp98Tyr
Tol (0.62)
Benign
74.04
72.97
262
185
Abbreviations: SNP: single nucleotide polymorphism; Chr: chromosome; HGVS: human genome association variation; HGVSc: the HGVS coding sequence name; HGVSp: the HGVS protein sequence name; Del: deletion; Tol: tolerated.
