Table 3 Genetic pattern of non-syndromic PIDs among genetically resolved Eastern Iranian patients.
Gene | State (Inheritance) | Variations | Type | Gene (NM_ID) | SNP-ID | MAF | AP1 | exon | Classification (ACMG criteria) | change | Publication No | Associated disease (omim) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
ARHGEF1 | Homo (AR) | c.1480G > T (p.Asp494Tyr) | M | NM_004706.4 | – | N/A | D | 16 | VUS (PM2, PP3) | NO | Novel | IMD62 (618,459) |
BTK | Hem (XLR) | c.37C > T (p.Arg13Ter) | N | NM_000061.3 | rs128620187 | N/A | N/A | 2 | P (PVS1, PM3, PM2, PP5) | NO | 11 | XLA (300,755) |
BTK | Hem (XLR) | c.763C > T (p.Arg255Ter) | N | NM_000061.2 | rs128621193 | N/A | N/A | 8 | P (PVS1, PM2, PM3, PP5) | NO | 16 | IMD1 (300,755) |
C1QA | Homo (AR) | c.159G > T (p.Glu53Asp) | M | NM_015991.4 | rs750646958 | Absent | B | 2 | VUS (PM2, BP4) | NO | Novel | C1QD1 (613,652) |
CARD9 | Homo (AR) | c.883C > T ( p.Gln295*) | N | NM_052813.5 | rs121918338 | Absent | N/A | 6 | P (PVS1, PM3, PM2, PP5) | NO | Novel | IMD103 (212,050) |
CARMIL2 | Homo (AR) | c.871 + 1G > T | S | NM_001013838.3 | – | N/A | D | 11 | P (PVS1, PM2, PM3, PP5) | NO | 1 | IMD58 (618,131) |
CARMIL2 | Homo (AR) | c.871 + 1G > T | S | NM_001013838.3 | rs886041044 | Absent | D | 11 | P (PVS1, PM3, PM2, PP5) | NO | 1 | IMD58 (618,131) |
CD3E | Homo (AR) | c.103 + 1G > A | S | NM_000733.4 | rs201543770 | Absent | D | 5 | LP (PVS1, PM2, PP5) | NO | 2 | IMD18 (615,615) |
CR2 | Homo (AR) | c.1777 T > G (p.Cys593Gly) | M | NM_001006658.3 | –– | N/A | D | 10 | VUS (PM2, PP3) | NO | Novel | CVID7 (614,699) |
CYBB | Hem (XLR) | c.536G > T (p.Gly179Val) | M | NM_000397.4 | – | N/A | N/A | 6 | LP (PVS1, PM2 , PM5) | NO | Novel | CGDX (306,400) |
CYBB | Hem (XLR) | c.1465_1466insC (p.Asn489fs) | Ins | NM_000397.4 | – | N/A | N/A | 12 | LP (PVS1, PM2 ) | NO | Novel | CGDX (306,400) |
ICOS | Homo (AR) | c.334 T > C (p.Ser112Pro) | M | NM_012092.4 | – | N/A | U | 2 | VUS (PM2) | NO | Novel | CVID1 (607,594) |
IFNGR1 | Homo (AR) | c.254G > A (p.Cys85Tyr) | M | NM_000416.2 | – | N/A | D | 3 | VUS (PM2, PP3) | NO | 1 | IMD27A (209,950) |
IFNGR1 | Homo (AR) | c.55dupA (p.met19Asnfs Ter16) | Ins | NM_000416.3 | – | N/A | N/A | 1 | LP (PVS1, PM2) | NO | Novel | IMD27A (209,950) |
IKBKB | Homo (AR) | c.201-1G > A | S | NM_001556.3 | – | N/A | D | 4 | LP (PVS, PM2) | NO | Novel | IMD15B (615,592)* |
IKBKB | Het (AD) | c.1654A > G (p.Met552Val) | M | NM_001556.3 | rs200018957 | Absent | U | 16 | VUS (PM2) | NO | Novel | IMD15A (618,204) |
IKBKB | Homo (AR) | c.201-1G > A | S | NM_001556.3 | – | N/A | D | 4 | LP (PVS, PM2) | NO | Novel | IMD15B (615,592) |
IL12B | Homo (AR) | c.282dupC (p.Glu95ArgfsTer21) | Dup | NM_002187.3 | – | N/A | N/A | 3 | LP (PVS1PM2) | NO | Novel | IMD29 (614,890) |
IL12RB1 | Homo (AR) | c.509 T > A (p.Val170Glu) | M | NM_005535.3 | – | N/A | U | 5 | VUS (PM2, PM3, PP5) | NO | Novel | IMD30 (614,891) |
IL12RB1 | Homo (AR) | c.629 T > A (p.Val210Glu) | M | NM_001290024.1 | – | N/A | U | 5 | VUS (PM2, PM3, PP5) | NO | Novel | IMD30 (614,891) |
IL2RG | Hem (XLR) | c.670C > T (p.Arg224Trp) | M | NM_000206.3 | rs869320658 | N/A | D | 5 | P (PM1,PM2,PM5,PS4,PP3,PS3,PP4,PP5) | NO | 9 | SCIDX1 (300,400)* |
IL2RG | Homo (AR) | c.664C > T (p.Arg222Cys) | M | NM_000206.3 | – | N/A | D | 5 | P (PP1, PM2, PM5, PM1, PP4, PS4, PP3, PP5) | NO | 24 | SCIDX1 (300,400) |
IL7R | Homo (AR) | c.537 + 1G > A | S | NM_002185.5 | rs777878144 | Absent | D | 4 | P (PVS1, PM3, PM2, PP5) | NO | 3 | IMD104 (608,971) |
IL7R | Homo (AR) | c.358delA (p.Ile121fs) | Del | NM_002185.5 | – | N/A | N/A | 3 | LP (PVS1, PM2) | NO | Novel | IMD104 (608,971)* |
JAK3 | Homo (AR) | c.184 + 1G > T | S | NM_000215.4 | – | N/A | D | 2 | LP (PVS1, PM2 ) | NO | Novel | SCID (600,802) |
MALT1 | Homo (AR) | c.571C > T (p.Arg191Ter) | N | NM_006785.4 | rs1266114717 | Absent | N/A | 4 | P (PVS1, PM2 , PP5) | NO | 2 | IMD12 (615,468) |
MALT1 | Homo (AR) | c.1454A > G (p.Asn485Ser) | M | NM_006785.4 | – | N/A | U | 12 | VUS (PM2) | NO | Novel | IMD12 (615,468) |
MSN | Hem (XLR) | c.1141C > T (p.Arg381Cys) | M | NM_002444.3 | rs754305867 | Absent | U | 10 | VUS (PM2) | NO | Novel | IMD50 (300,988) |
NCF1 | Homo (AR) | c.125G > A (p.Arg42Gln) | M | NM_000265.7 | rs119103270 | Absent | D | 2 | P (PM3,PP3,PM2,PM5,PP5) | NO | 2 | CGD1 (233,700) |
RAG1 | Homo (AR) | c.2688G > A (p.Trp896Ter) | N | NM_000448.2 | – | N/A | N/A | 2 | VUS | LP (PVS1PM2) | 1 | SCID (601,457) |
RAG1 | Homo (AR) | c.2210G > A (p.Arg737His) | M | NM_000448.3 | rs104894286 | Absent | D | 2 | P (PM3PM2PM5PM1PP3PP2PS3PP5) | NO | 9 | SCID (601,457)* |
RAG1 | Homo (AR) | c.2893G > C (p.Glu965Gln) | M | NM_000448.3 | – | N/A | U | 2 | VUS (PM2PM1PP2) | NO | Novel | SCID (601,457) |
RAG2 | Homo (AR) | c.130G > A (p.Gly44Arg) | M | NM_000536.4 | – | Absent | D | 2 | VUS (PM1, PM2, PP3, PP2) | NO | Novel | SCID (601,457) |
RAG2 | Homo (AR) | c.200G > T (p.Cys67Phe) | M | NM_000536.4 | – | N/A | D | 2 | VUS (PM2,PP3,PM1,PP2) | NO | Novel | SCID (601,457) |
SH2D1A | Hem (XLR) | c.32 T > A (p.Ile11Asn) | M | NM_002351.5 | – | N/A | N/A | 1 | VUS (PM2,PP3,PM1,PP2) | NO | Novel | XLP2 (308,240) |
TLR3 | Het (AD / AR) | c.2656_2657insTAGG (p.A888Rfs*5) | Ins | NM_003265.3 | – | N/A | N/A | 5 | VUS (PM2) | NO | Novel | IMD83 (613,002) |
TNFRSF13B | Het (AD / AR) | c.704_705delCT (p.Pro235ArgfsTer169) | Del | NM_012452.3 | rs749017984 | < 0.01 | N/A | 5 | VUS | LP (PVS1, PM2) | 2 | CVID2 (240,500) |
