Table 2.

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.