Table 1

GLK gene somatic variants resulting in codon or 3′-UTR changes in patients with SLE of Cohort #1 and Cohort #2

CohortLocusTypeRefGLK
coding
Codon/3′-UTR
change
Patient numberMutation frequency among readsSLE ID#Control numberAssociation with SLE
#1
(SLE, n=101)
(control, n=163)
chr2:39 477 820SNVGc.2624C>Gp.Thr875Ser10.064S50p=0.383
chr2:39 494 337SNVAc.2025T>Gp.Cys675Trp10.0700p=0.383
chr2:39 507 491SNVCc.1635G>Ap.Ala546Thr20.044S10p=0.146
0.076S4
chr2:39 552 878SNVAc.800T>Ap.Leu267Ter10.033S70p=0.383
chr2:39 477 124SNVAc.3320T>C3′-UTR U635C*17>0.027S2, S7, S8, S16, S17, S29, S30, F10-4, F13-1, F14-1, F14-2, F15-1, F15-2, F18-1, F18-2, F19-3, F53-30p<0.0001
#2
(SLE, n=80)
(control, n=87)
chr2:39 499 454INDELGc.1942_1943
insert A
p.Ala648fs10.016B520p=0.479
chr2:39 553 291SNVTc.658A>Gp.Met220Val10.0280p=0.479
chr2:39 553 305SNVAc.644T>Cp.Phe215Ser10.0280p=0.479
chr2:39 553 354SNVCc.595G>Ap.Ala199Thr10.0290p=0.479
chr2:39 492 369SNVGc.2111C>Ap.Pro704Gln10.026B530p=0.479
chr2:39 499 497SNVCc.1900G>Tp.Asp634Tyr10.0700p=0.479
chr2:39 517 440SNVGc.1307C>Tp.Pro436Leu10.0310p=0.479
chr2:39 570 569SNVCc.270G>Ap.Met90Ile10.0390p=0.479
chr2:39 583 402SNVCc.233G>Tp.Gly78Val10.0260p=0.479
chr2:39 477 124SNVAc.3320T>C3′-UTR U635C* 37>0.027B14, B15, B16, B21, B22, B23, B24, B26, B29, B30, B31, B32, B37, B38, B39, B40, B41, B42, B47, B48, B53, B54, B55, B58, B61, B63, B64, B65, B67, B69, B70, B71, B73, B75, B76, B77, B7914p<0.0001
  • GLK coding, GLK variant coding that is a reverse sequence on chromosome 2.

  • Association of GLK somatic variants with SLE was determined by Fisher’s exact test (two-tailed).

  • ‘F’ denotes family member in Cohort #1; ‘S’ denotes patient with sporadic SLE in Cohort #1; ‘B’ indicates patient with sporadic SLE in Cohort #2.

  • Ref, DNA coding from the human genome hg19 reference.

  • *Variant occurs in both Cohort #1 and Cohort #2.

  • .fs, frameship; INDEL, insertion/deletion; SLE, systemic lupus erythematosus; SNV, single nucleotide variant; UTR, untranslated region.