GLK gene germline variants* resulting in codon or 3′-UTR change in patients with SLE of Cohort #1 and Cohort #2
| Locus | Ref | GLK coding | Codon/3′-UTR change | Annotated SNP | Cohort | Patient number | SLE ID# | Allele frequency in SLE | Allele frequency in control | Allele frequency in world |
| chr2:39 477 115 | T | c.3329A>C | 3′-UTR (A644C) | rs191224999 | #1 | 1 | F52-01 | 1/172 (0.005814) | 1†/136 (0.007353) | 0.000050 |
| #2 | 2 | B24 B71 | 2/160 (0.012500) | 0 | ||||||
| chr2:39 519 957 | C | c.1228G>A | p.Ala410Thr | rs148167737 | #1 | 3 | S10, F7-01 F7-04 | 2/172 (0.01163) | 0 | 0.000601 |
| #2 | 2 | B33 B45 | 2/160 (0.012500) | 1‡/174 (0.005747) | ||||||
| chr2:39 499 448 | T | c.1949A>G | p.Lys650Arg | rs200566214 | #1 | 2 | F26-01 F26-02 | 1/172 (0.001581) | 0 | 0.000231 |
| #2 | 0 | none | 0 | 0 | ||||||
| chr2:39 505 607 | C | c.1735G>A | p.Ala579Thr | ND | #2 | 1 | B19 | 1/160 (0.006250) | 0 | ND |
GLK coding, GLK variant coding that is a reverse sequence on chromosome 2.
Cohort #1, SLE, n=101 (24 patients with sporadic SLE and 77 patients with SLE from 62 families); non-SLE, n=163 (6 healthy controls and 157 family members without SLE from 62 families).
Cohort #2, SLE, n=80 (patients with sporadic SLE); healthy control, n=87 (non-familial healthy controls).
Allele frequencies were calculated using unrelated patients and controls; if from individual families, only one patient with SLE and one member without SLE from each family are included.
‘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.
*Single nucleotide variants.
†One male family member without SLE control (F52-02) from Cohort #1 harboured this variant.
‡One male non-familial healthy control from Cohort #2 harboured this variant.
Ref, DNA coding from the human genome hg19 reference; SLE, systemic lupus erythematosus; UTR, untranslated region.