Figure 1.

Intronic deletions in VANGL1 associate with kidney disease

(A) Association of copy number variation in VANGL1 detected by qPCR with the presence or absence of nephritis in SLE (n = 177); χ² 2d.f., p < 0.0001 (LN = lupus nephritis).

(B) Comparison of MAF of VANGL1 CNV in esv3587290 in gnomAD global and Tiwi Islander populations (n = 120); Fisher’s exact, p < 0.0001).

(C) Representative whole genome sequencing reads of intronic deletion in VANGL1 of the maximum length reported for the CNV.

(D) Comparison of relative VANGL1 expression in PBMCs from (i) SLE patients with 0 or 2 copies of VANGL1, (ii) Healthy controls or SLE patients with or without lupus nephritis.

e) RNaseq read alignment demonstrating skipping of exon 2 in a patient homozygous for the VANGL1 CNV with read covering exon 1 and exon 3 highlighted in yellow.