Table 1

List of candidate genes prioritised by immune-related function and enrichment in T cell receptor signalling pathway

FamiliesNumber of genesImmune-related genesT cell differentiation and development genesTCR proximal signalling genesTCR interactive genes
pSS
 pSS-00122 CRHR2, ITK ITK ITK
 pSS-00230 CD36, TRIM16 CD36, TRIM16
 pSS-0036 PLCL1, VWA8 PLCL1 PLCL1
 pSS-0041 DUS2
 pSS-0051 CERK CERK CERK (TCR)
 pSS-00626 ADAMTS5, TRIM16 TRIM16
 pSS-0077 VWA8
 pSS-0278 VGLL3
 pSS-03120 PTPRC (CD45) PTPRC (CD45) PTPRC (CD45)
RA
 RA-00814 NFAT5 NFAT5 NFAT5
 RA-00921 CD36, THEMIS,CFHR5 CD36, THEMIS THEMIS
 RA-01022 PTPN3 PTPN3
 RA-01148 CR2, TESPA1 TESPA1
 RA-02823 IRAK3, PTPRC (CD45) PTPRC (CD45) PTPRC (CD45)
 RA-02930 LAX1, IL31RA LAX1 LAX1
SLE
 SLE-01214 P2RX 7 P2RX 7 P2RX7 (ATP and calcium)
 SLE-01328 LAT LAT LAT
 SLE-01422 DGKD, IL12A, SEMA4D DGKD, IL12A, SEMA4D DGKD SEMA4D (CD3)
 SLE-01547 CD276
 SLE-01620 PAK2 PAK2
 SLE-01720 CFHR4
 SLE-01817 RPP21
 SLE-01943 LAG3 LAG3 (TCR)
 SLE-02035 RIPK1
 SLE-02122 TEC TEC TEC
 SLE-03033 VWA8, IL1RL2
Autoimmunity
 Autoimmunity-02244 PRKD1, IRAK4 PRKD1 PRKD1 IRAK4
 Autoimmunity-0237 ASL ASL
 Autoimmunity-02450 DPP4, LCK, RIPK1 DPP4, LCK LCK
 Autoimmunity-02535
 Autoimmunity-02625 ARL14,PTPRC (CD45) PTPRC (CD45) PTPRC (CD45)
  • Number of genes: total number of candidate genes with cosegregated with phenotype, rare and potential pathogenic variants by whole-exome sequencing and filtering.

  • TCR-proximal signalling genes: the core elements of the TCR signalling pathway, which downstream of TCR are responsible for the cascade of events leading to T cell activation.

  • TCR-interactive genes: crosstalk between TCR singling network and other immune pathways.

  • pSS, primary Sjögren’s syndrome; RA, rheumatoid arthritis; SLE, systemic lupus erythematosus; TCR, T cell receptor.