Table 4.
Variants identified the RA/PsA cohort through WES. The table displays the variants detected in the patients. All variants were detected at the heterozygous state, except the one detected within the UGT2B17 gene in patient SN4 (c.1158C>A, p.Tyr386*), which is indicated in the table with the asterisk. Genes reported in bold are those in which a variant was found in more than one patient. The MSR1 gene is also reported in bold because, in addition to the frameshift variant carried by subject SP2, a large deletion affecting the gene was identified in patient SN3 through the SNPs-array technique. (AF = allele frequency; NA = not available; D = damaging; T = tolerated).
| Subject | Gene | cDNA | ID | Protein | AF | PaPI Score | PolyPhen-2 | DANN Score | SIFT |
|---|---|---|---|---|---|---|---|---|---|
| SP1 | WNT10A (ENST00000258411) | c.321C>A | rs121908119 | p.Cys107 * | 0.00066 | D | NA | D | NA |
|
DVL1 (ENST00000378888) |
c.780C>G | NA | p.His260Gln | NA | D | T | D | D | |
| SP2 |
ABCB7 (ENST00000253577) |
c.1767T>G | rs150273961 | p.His589Gln | 0.00056 | D | D | D | D |
|
MSR1 (ENST00000350896) |
c.260C>G | NA | p.Ser87 * | NA | D | NA | D | NA | |
| SP3 |
PRKDC (ENST00000314191) |
c.7790G>A | rs55923149 | p.Arg2597Gln | 0.000026 | D | D | D | D |
|
UGT2B17 (ENST00000317746) |
c.1237G>T | NA | p.Ala413Ser | NA | D | NA | D | D | |
| SP4 |
DVL1 (ENST00000378888) |
c.1148C>A | NA | p.Ser383Tyr | NA | D | T | D | D |
|
PRKDC (ENST00000314191) |
c.5983G>A | rs768367219 | p.Val1995Ile | 0.000014 | D | D | D | T | |
|
ORAI1 (ENST00000330079) |
c.144_150dupCGCCGTC | rs1555322554 | p.Pro51fs | 0.000014 | D | NA | NA | NA | |
|
SERPING1 (ENST00000278407) |
c.1198C>T | rs201363394 | p.Arg400Cys | 0.000049 | D | D | D | T | |
| SN1 |
ORAI1 (ENST00000330079) |
c.698C>T | rs369586125 | p.Pro233Leu | 0.000012 | D | T | D | D |
| SN2 |
GNRHR (ENST00000226413) |
c.785G>A | rs104893837 | p.Arg262Gln | 0.0018 | D | D | D | D |
| SN3 |
NCAPD3 (ENST00000534548) |
c.1712A>C | rs199812722 | p.His571Pro | 0.000069 | D | D | D | T |
|
CLCF1 (ENST00000312438) |
c.226C>G | rs765776881 | p.Pro76Ala | 0.0000082 | D | T | D | D | |
| SN4 |
UGT2B17 (ENST00000317746) |
c.1158C>A * | NA | p.Tyr386 * | NA | D | NA | D | NA |
|
HACE1 (ENST00000262903) |
c.217G>A | rs946488994 | p.Ala73Thr | NA | D | T | D | D | |
| SN5 |
NCAPD2 (ENST00000315579) |
c.860C>G | NA | p.Pro287Arg | NA | D | D | D | D |
|
ESR1 (ENST00000440973) |
c.715G>T | NA | p.Ala239Ser | NA | D | D | D | D | |
| SN6 |
SAMHD1 (ENST00000262878) |
c.997C>T | rs770005027 | p.Arg333Cys | 0.000024 | D | D | D | D |
|
CYP27A1 (ENST00000258415) |
c.1435C>T | rs72551322 | p.Arg479Cys | 0.0043 | D | D | D | D | |
|
CCDC88C (ENST00000389857) |
c.5102G>T | NA | p.Arg1701Leu | NA | D | D | D | D |