Table 1.
GLK gene somatic variants resulting in codon or 3′-UTR changes in patients with SLE of Cohort #1 and Cohort #2
| Cohort | Locus | Type | Ref | GLK coding |
Codon/3′-UTR change |
Patient number | Mutation frequency among reads | SLE ID# | Control number | Association with SLE |
| #1 (SLE, n=101) (control, n=163) |
chr2:39 477 820 | SNV | G | c.2624C>G | p.Thr875Ser | 1 | 0.064 | S5 | 0 | p=0.383 |
| chr2:39 494 337 | SNV | A | c.2025T>G | p.Cys675Trp | 1 | 0.070 | 0 | p=0.383 | ||
| chr2:39 507 491 | SNV | C | c.1635G>A | p.Ala546Thr | 2 | 0.044 | S1 | 0 | p=0.146 | |
| 0.076 | S4 | |||||||||
| chr2:39 552 878 | SNV | A | c.800T>A | p.Leu267Ter | 1 | 0.033 | S7 | 0 | p=0.383 | |
| chr2:39 477 124 | SNV | A | c.3320T>C | 3′-UTR U635C* | 17 | >0.027 | S2, S7, S8, S16, S17, S29, S30, F10-4, F13-1, F14-1, F14-2, F15-1, F15-2, F18-1, F18-2, F19-3, F53-3 | 0 | p<0.0001 | |
| #2 (SLE, n=80) (control, n=87) |
chr2:39 499 454 | INDEL | G | c.1942_1943 insert A |
p.Ala648fs | 1 | 0.016 | B52 | 0 | p=0.479 |
| chr2:39 553 291 | SNV | T | c.658A>G | p.Met220Val | 1 | 0.028 | 0 | p=0.479 | ||
| chr2:39 553 305 | SNV | A | c.644T>C | p.Phe215Ser | 1 | 0.028 | 0 | p=0.479 | ||
| chr2:39 553 354 | SNV | C | c.595G>A | p.Ala199Thr | 1 | 0.029 | 0 | p=0.479 | ||
| chr2:39 492 369 | SNV | G | c.2111C>A | p.Pro704Gln | 1 | 0.026 | B53 | 0 | p=0.479 | |
| chr2:39 499 497 | SNV | C | c.1900G>T | p.Asp634Tyr | 1 | 0.070 | 0 | p=0.479 | ||
| chr2:39 517 440 | SNV | G | c.1307C>T | p.Pro436Leu | 1 | 0.031 | 0 | p=0.479 | ||
| chr2:39 570 569 | SNV | C | c.270G>A | p.Met90Ile | 1 | 0.039 | 0 | p=0.479 | ||
| chr2:39 583 402 | SNV | C | c.233G>T | p.Gly78Val | 1 | 0.026 | 0 | p=0.479 | ||
| chr2:39 477 124 | SNV | A | c.3320T>C | 3′-UTR U635C* | 37 | >0.027 | B14, 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, B79 | 14 | p<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.