Repository Table E1 - Disease-associated, potentially causative and contributory variants in the PIDD cohort

WESa
aff/
unaff / Sb / Pat# / Sex / Agec / Ethnicity / Status / PIDD sub-groupe / Gene / Inh. / Zyg. / SNV or CNV / Variant / Type of mutation / Variant classg / OMIM# / Year first reported / Ref.
1/0 / 4 / 1.1 / Male / 30y / Norway / Living / I / IKZF1 / AD / Het / CNV / del7p12.2, g.(Chr7: 50435853-50451072)x1 (hg19) / Deletion / 5 / 603023 / Novel / E1
1/0 / 1 / 2.1 / Male / 20y / Norway / Living / I / BTK f* / XL / Hemi / SNV / BTK:NM_000061:exon15:c.1511A>T:p.D504V (HGMD) (maternal) / Missense / 4 / 300755 / 1993 / E2
ELF4 fp / XL / Hemi / SNV / ELF4:NM_001421:exon6:c.560C>A:p.T187N (maternal) / Missense / 3 / 300775 / 2005 / E3
1/2 / 3 / 3.1 / Male / 2,5y / Ecuador / Living / I / CD40LG f* / XL / Hemi / SNV / CD40LG:NM_000074:exon2:c.233_234delinsAA:p.S78* / Frameshift indel / 5 / 308230 / 1993 / E4
PSTPIP1 fn / AD / Het / SNV / PSTPIP1:NM_003978:exon14:c.1115C>T:p.A372V (paternal) / Missense / 3 / 604416 / 2002 / E5
1/0 / 3 / 5.1 / Female / 7y / Turkey / Living / I / AICDA / AR / Hom / SNV / AICDA:NM_020661.2:exon2:c.71G>A:p.R24Q (~HGMD) / Missense / 4 / 605258 / 2000 / E6
1/0 / 3 / 6.1 / Male / 20y / Norway / Living / I / CD40LG / XL / Hemi / SNV / CD40LG:NM_000074:exon5:c.495delA:p.R165Sfs*26 (HGMD) / Frameshift deletion / 4 / 308230 / 1993 / E4
1/0 / 3 / 7.1 / Female / NA / USA-European ancestry / Living / I / SKIV2L / AR / Het / SNV / SKIV2L:NM_006929.4:exon11:c.1120C>T:p.R374* / Nonsense / 5 / 614602 / 2012 / E7
SKIV2L / AR / Het / SNV / SKIV2L:NM_006929.4:exon27:c.3416G>C:p.R1139P / Missense / 3
1/0 / 3 / 8.1 / Male / NA / USA / Deceased / I / SP110 / AR / Hom / SNV / SP110:NM_004509:exon6:c.586dupT:p.Q231fs / Frameshift insertion / 5 / 235550 / 2006 / E8
1/1 / 2 / 9.1 / Male / 6y / USA-European ancestry / Living / II / FOXP3 f* / XL / Hemi / SNV / FOXP3:NM_014009:exon8:c.737T>C:p.L246P (maternal) / Missense / 3 / 304790 / 2001 / E9
RUNX1 fp / AD / Het / SNV / RUNX1:NM_001754:exon9:c.1381A>G:p.N461D / Missense / 3 / 601626 / 1999 / E10
1/0 / 16 / 10.1 / Female / 20y / USA-European ancestry / Living / II / COPA / AD / Het / SNV / COPA:NM_001098398:exon9:c.728A>G:p.D243G (parental) / Missense / 5 / 601924 / 2015 / E11
2/0 / 9 / 11.1 / Female / 20y / USA-European ancestry / Living / II / COPA / AD / Het / SNV / COPA:NM_001098398:exon8:c.698G>A:p.R233H (parental) / Missense / 5 / 601924 / 2015 / E11
1/0 / 3 / 12.1 / Female / 14y / USA-European ancestry / Living / II / COPA / AD / Het / SNV / COPA:NM_001098398:exon9:c.718T>C:p.W240R (paternal) / Missense / 4 / 601924 / 2015 / E11
1/4 / 5 / 13.1 / Female / 8y / USA-European ancestry / Living / II / CBL / AD/ de novo / Het / SNV / CBL:NM_005188:exon8:c.1111T>C:p.Y371H (HGMD) (de novo) / Missense / 5 / 613563 / 2010 / E12
1/0 / 3 / 14.1 / Male / 6y / USA-European ancestry / Deceasedd / II / CTLA4 / AD / Het / SNV / CTLA4:NM_005214:exon2:c.410C>A:p.P137Q (paternal) / Missense / 3 / 616100 / 2014 / E13, E14
1/0 / 4 / 15.1 / Female / 20y / Norway / Living / II / CTLA4 / AD / Het / SNV / CTLA4:NM_005214:exon1: c.94_101delinsTTCTCTTCATCA: p.P32Ffs*29 (maternal) / Frameshift indel / 5 / 616100 / 2014 / E13, E14
1/2 / 3 / 16.1 / Female / 21y / Ecuador / Living / II / CASP10 / AD / Het / SNV / CASP10:NM_032977.3:exon 9:c.1202_1208del:p.C401Lfs*15 (paternal) / Frameshift deletion / 5 / 603909 / 1999 / E15
1/0 / 2 / 17.1 / Female / NA / USA-European ancestry / Living / II / PLCG2 / AD / Het / SNV / PLCG2:NM_002661:exon21:c.2300C>T:p.P767L / Missense / 3 / 614468 / 2012 / E16
1/1 / 3 / 19.1 / Male / 12y / Ecuador / Living / II / FOXP3 f* / XL / Hemi / SNV / FOXP3:NM_014009:exon12:c.1208G>A:p.G403E / Missense / 3 / 304790 / 2001 / E9
NRAS fn / AD/ de novo / Het / SNV / NRAS:NM_002524:exon4:c.379A>G:p.T127A, outside hot spot region / Missense / 3 / 614470 / 2007 / E17
1/0 / 3 / 20.1 / Female / 12y / Norway / Living / II / FASLG / AD / Het / SNV / FASLG:NM_000639.1:exon2:c.394G>C:p.G132R (paternal) / Missense / 3 / 601859 / 1996 / E18
1/2 / 4 / 22.1 / Female / 6y / USA-European ancestry / Living / III / COPA / AD / Het / SNV / COPA:NM_001098398:exon9:c.772C>T:p.H258Y (de novo) / Missense / 4 / 601924 / 2015 / E11
1/0 / 2 / 23.1 / Male / 9y / Norway / Living / III / PIK3CD / AD / Het / SNV / PIK3CD:NM_005026:exon15:c.1821G>T:p.E607D / Missense / 3 / 615513 / 2013 / E19
1/2 / 3 / 24.1 / Female / 13y / USA-Hispanic/ latino ancestry / Living / V / Potential novel gene3 / AR / Hom / SNV / Potential novel gene3:exon15:c.1315A>G:p.M439V / Missense / 3 / Novel
2/0 / 4 / 26.1 / Male / 9y / USA-European ancestry / Living / V / CORO1A / AR / Het / SNV / CORO1A:NM_001193333:exon11:c.1078delC: p.Q360Rfs*45 / Frameshift deletion / 5 / 615401 / 2013, similar phenotype / E20
CORO1A / AR / Het / SNV / CORO1A:NM_001193333:exon4:c.248_249delCT: p.P83Rfs*1 / Frameshift deletion / 5
1/0 / 5 / 27.1 / Female / 28y / USA-Hispanic/ latino ancestry / Living / V / RNF168 fp / AR / Hom / SNV / RNF168: NM_152617:exon2:c.307G>A:p.D103N / Missense / 3 / 611943 / 2009 / E21
ZAP70 f* / AR / Het / SNV / ZAP70: NM_001079:exon12:c.1505C>T:p.P502L / Missense / 3 / 269840 / 1994 / E22
ZAP70 f* / AR / Het / SNV / ZAP70: NM_001079:exon6:c.733G>A:p.G245R / Missense / 3
2/0 / 3 / 28.1 / Male / 16y / Norway / Living / V / BTK fn / XL / Hemi / SNV / BTK:NM_000061.2:intron2:c.141+11C>T (HGMD) / Splicing / 3 / 300755 / 2003 / E23
MAGT1 f* / XL / Hemi / CNV / delXq21.1, g.(chrX:77096742-77112995)x0 (hg19) (maternal) / Deletion / 5 / 300853 / 2011 / E24
2/0 / 4 / 30.1 / Male / NA / Turkey / Deceasedd / V / DOCK8 / AR / Hom / CNV / del9p24.3, g.(Chr9:24850-379936)x0 (hg19) / Deletion / 5 / 243700 / 2009 / E25
1/4 / 5 / 31.1 / Female / 13Y / Turkey / Living / V / DCLRE1C / AR / Hom / SNV / DCLRE1C:NM_001033855:exon3:c.194C>T:p.T65I / Missense / 3 / 602450 / 2001 / E26
1/2 / 3 / 32.1 / Male / 6m / USA-European ancestry / Living / V / Potential novel gene6 / AR / Het / SNV / Potential novel gene6:exon8:c.914C>T:p.P305L (paternal) / Missense / 3 / Novel
Potential novel gene6 / AR / Het / SNV / Potential novel gene6:exon4:c.364G>C:p.E122Q (maternal) / Missense / 3
2/0 / 3 / 33.1 / Female / 30y / Norway / Living / V / Potential novel gene1 / AR / Hom / SNV / Potential novel gene1:exon20:c.1916T>A:p.L639H / Missense / 4 / 607594 / Novel
1/0 / 3 / 34.1 / Male / 6y / USA-Hispanic/ latino ancestry / Living / V / LYST / AR / Het / SNV / LYST:NM_000081:exon23:c.6782G>A:p.R2261H (paternal) / Missense / 3 / 214500 / 1997 / E27, E28
LYST / AR / Het / SNV / LYST:NM_000081:exon4:c.281C>T:p.T94I (maternal) / Missense / 3
1/1 / 3 / 35.1 / Male / 3y / Ecuador / Living / V / WAS / XL / Hemi / SNV / WAS:NM_000377:exon2:c.208G>A:p.G70R (HGMD) (de novo) / Missense / 4 / 301000 / 1994 / E29
1/0 / 3 / 36.1 / Female / 3y / USA-European ancestry / Living / V / DOCK8 / AR / Hom / SNV / DOCK8:NM_203447:exon47:c.6137T>G:p.L2046R / Missense / 3 / 243700 / 2009 / E25
1/0 / 1 / 37.1 / Male / 4y / Norway / Deceased / V / STAT1 f* / AD/AR / Het / SNV / STAT1:NM_007315:exon19:c.1627T>C:p.C543R / Missense / 3 / 614162 / 2011 / E30
TNFRSF13B fp / AD / Het / SNV / TNFRSF13B:NM_012452:exon4:c.542C>A:p.A181E (HGMD) / Missense / 5 / 240500 / 2005 / E31, E32
1/0 / 3 / 38.1 / Male / 5y / Norway / Living / V / LIG4 / AR / Het / SNV / LIG4:NM_002312.3:exon2:c.1341G>T:p.W447C (maternal) / Missense / 4 / 606593 / 2001 / E33
LIG4 / AR / Het / SNV / LIG4:NM_002312.3:exon2:c.482delC:p.A161Vfs*6 (paternal) / Frameshift deletion / 5
1/2 / 4 / 39.1 / Male / 18y / Norway / Living / V / Potential novel gene1 / AR / Hom / SNV / Potential novel gene1:exon20:c.1916T>A:p.L639H / Missense / 4 / 607594 / Novel
1/0 / 3 / 40.1 / Male / 25y / Turkey / Deceasedd / V / DCLRE1C / AR / Hom / SNV / DCLRE1C:NM_001033855.1:exon10:c.632G>T:p.G211V (HGMD) / Missense / 4 / 602450 / 2001 / E26
1/2 / 3 / 41.1 / Male / 2y / USA-European ancestry / Living / VIII / MX2 / AR / Het / SNV / MX2:NM_002463:exon2:c.166G>A:p.A56T (maternal) / Missense / 3 / 147890 / 2015 / E34, E35
MX2 / AR / Het / SNV / MX2:NM_002463:exon5:c.643T>A:p.S215T (paternal) / Missense / 3
1/0 / 3 / 43.1 / Female / 12y / USA-European ancestry / Living / V / TTC7A / AR / Het / SNV / TTC7A:NM_020458:exon2:c.211G>A:p.E71K (HGMD) (maternal) / Missense / 5 / 243150 / 2013 / E36
TTC7A / AR / Het / SNV / TTC7A:NM_020458:intron8:c.1001+3_1001+6delAAGT (HGMD) (paternal) / Frameshift deletion / 4
4/0 / 4 / 45.1 / Male / adult / Norway / Living / VI / Potential novel gene5 / AD / Het / SNV / Potential novel gene5:exon10:c.1082CT:p.P361L / Missense / 3 / 607594 / Novel
2/0 / 2 / 46.1 / Female / 24y / Norway / Living / VI / CTLA4 / AD / Het / SNV / CTLA4:NM_005214:exon2:c.410C>T:p.P137L (paternal) / Missense / 3 / 616100 / 2014 / E13, E14
1/2 / 3 / 47.1 / Female / 1y / USA-European ancestry / Living / VI / NFKB2 / AD / Het / SNV / NFKB2:NM_001077494:exon22:c.2557C>T:p.R853* (HGMD) (de novo) / Nonsense / 5 / 615577 / 2013 / E37, E38, E39
2/0 / 6 / 48.1 / Male / 55y / Norway / Living / VI / TGFB1 / AD / Het / SNV / TGFB1:exon6:c.1010G>A:p.S337N (in both affected) / Missense / 3 / 131300 / Not reported with PIDD
1/1 / 5 / 49.1 / Male / 18y / USA-European ancestry / Living / VI / JAK3 f* / AR / Het / SNV / JAK3:NM_000215:exon15:c.1924G>C:p.G642R / Missense / 3 / 600802 / 1995 / E40
JAK3 f* / AR / Het / SNV / JAK3:NM_000215:exon5:c.452C>G:p.P151R (HGMD) / Missense / 3
TNFRSF13B fp / AD / Het / SNV / TNFRSF13B:NM_012452:exon3:c.310T>C:p.C104R (HGMD) (maternal) / Missense / 5 / 240500 / 2005 / E31, E32
1/0 / 1 / 50.1 / Male / 13y / USA-European ancestry / Living / VI / STAT1 / AD/AR / Het / SNV / STAT1:NM_007315:exon14:c.1154C>T:p.T385M (HGMD) / Missense / 5 / 614162 / 2011 / E30
1/0 / 3 / 53.1 / Male / 16y / Norway / Living / VI / IL10 / AR / Hom / SNV / IL10:NM_000572.2:exon5:c.482T>C:p.F161S / Missense / 3 / 124092 / 2012 / E41
1/0 / 3 / 54.1 / Male / 6y / Norway / Living / VI / SH2D1A / XL / Hemi / SNV / SH2D1A:NM_002351:intron1:c.137+1G>A (HGMD) (de novo) / Splicing / 5 / 308240 / 1998 / E42
1/0 / 3 / 56.1 / Female / 6y / Ecuador / Living / VII / IL12RB1 / AR / Hom / SNV / IL12RB1:NM_005535:exon16:c.1791+2T>G (HGMD) / Splicing / 5 / 614891 / 1998 / E43, E44
1/0 / 3 / 57.1 / Male / 5y / Norway / Living / VII / CFP / XL / Hemi / SNV / CFP:NM_002621.2:exon8:c.962G>A:p.W321* (HGMD) (maternal) / Nonsense / 5 / 312060 / 1995 / E45
1/0 / 2 / 58.1 / Female / 40y / Norway / Living / VII / IFNGR2 / AR / Hom / SNV / IFNGR2:NM_005534:exon4:c.421G>A:p.G141R (HGMD) / Missense / 5 / 614889 / 2005 / E46
1/2 / 3 / 59.1 / Male / 6m / Turkey / Living / VII / IKBKG / XL / Hemi / SNV / IKBKG:NM_001099857:exon10:c.1167dupC:p.E390Rfs*5
In only 55 out of 159 reads (revertant mosaicism) (HGMD) / Frameshift insertion / 5 / 300291 / 2000 / E47
1/0 / 1 / 60.1 / Female / 3y / Mexico / Living / VII / STAT3 / AD / Het / SNV / STAT3:NM_139276:exon15:c.1309C>T:p.H437Y (HGMD) / Missense / 5 / 147060 / 2007 / E48
1/0 / 2 / 61.1 / Male / 4y / Norway / Living / VII / STAT1 / AD/AR / Het / SNV / STAT1:NM_007315:exon14:c.1163A>G:p.K388R (~HGMD) / Missense / 4 / 614892 / 2001 / E49
1/0 / 3 / 62.1 / Female / 12y / Norway / Living / VII / STAT1 / AD/AR / Het / SNV / STAT1:NM_007315:exon23:c.2113G>C:p.G705Q (de novo) / Missense / 4 / 614892 / 2001 / E49
1/0 / 4 / 63.1 / Male / 49y / Norway / Living / IX / TERC / AD / Het / CNV / del3q26.2, g.(Chr3:169482168_169483029-169485768_169486206)x1 (hg19) / Deletion / 5 / 127550 / 2001 / E50
1/0 / 3 / 64.1 / Female / NA / Qatar / NA / VII / IFNGR2 / AR / Hom / SNV / IFNGR2:NM_005534:exon4:c.421G>A:p.G141R (HGMD) / Missense / 5 / 614889 / 2005 / E46
1/0 / 3 / 65.1 / Female / 4y / Norway / Deceased / VIII / KRAS / AD/ de novo / Het / SNV / KRAS:NM_004985:exon2:c.37G>T:p.G13C
In 15/110 reads (somatic mosaicism) (de novo) / Missense / 5 / 614470 / 2011 / E51
1/0 / 2 / 66.1 / Female / 3y / USA-European ancestry / Living / VIII / STAT3 (GOF) / AD / Het / SNV / STAT3:NM_139276:exon10:c.1032G>C:p.Q344H / Missense / 5 / 615952 / 2014 / E52, E53
3/4 / 7 / 67.1 / Male / 12y / Middle East / Living / VIII / PIK3CD / AD / Het / SNV / PIK3CD:NM_005026:exon13:c.1573G>A:p.E525K (paternal) (HGMD) in 20/53, 37/68, and 87/204 reads in all 3 affected siblings. Only in 6/38 reads in the father, who likely was mosaic for the variant, and mildly affected. / Missense / 5 / 615513 / 2013 / E19
1/1 / 4 / 68.1 / Male / 12m / UK / Deceased / VIII / Potential novel gene2 / AR / Het / SNV / Potential novel gene2:exon10:c.1276C>T:p.R426C / Missense / 3 / Novel
Potential novel gene2 / AR / Het / SNV / Potential novel gene2:exon13:c.1744C>T:p.R582* / Nonsense / 5
1/0 / 3 / 69.1 / Female / 5m / NA / NA / VIII / PRF1 / AR / Het / SNV / PRF1:NM_005041:exon2:c.445G>A:p.G149S (HGMD) / Missense / 5 / 603553 / 1999 / E54
PRF1 / AR / Het / SNV / PRF1:NM_005041:exon3:c.1081A>T:p.R361W (HGMD) / Missense / 5
1/0 / 4 / 70.1 / Male / 8y / USA-Asian ancestry / Living / II / CCDC40 / AR / Hom / SNV / CCDC40:NM_017950:exon20:c.3181-2A>G / Splicing / 4 / 613808 / 2011 / E55
1/0 / 1 / 71.1 / Female / 13y / Canada-Native American / Living / VIII / ATP6V0A2 f* / AR / Hom / SNV / ATP6V0A2:NM_012463:intron12:c.1514+1G>A (HGMD) / Splicing / 4 / 611716, 219200 / 2008, but
not PIDD / E56, E57
FBN1 fp / AD / Het / SNV / FBN1:NM_000138: exon27:c.3336G>A:p.M1112I / Missense / 3 / 154700 / 1991 / E58, E59
1/4 / 5 / 72.1 / Male / adult / USA-European ancestry / Deceased / VIII / IRF8 / AR / Het / SNV / IRF8: exon7:c.602C>T:p.A201V (maternal) / Missense / 3 / 614894 / 2012 / E60