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. Author manuscript; available in PMC: 2018 Jun 1.
Published in final edited form as: Hum Genet. 2017 Mar 16;136(6):679–691. doi: 10.1007/s00439-017-1774-y

Table 2.

De novo sequence variants in the CDH cohort

ID Cohort Ph Gene symbol Dia ExAC
Chr Pos Ref. Alt. cDNA Protein Category
pLI mis_z lof_z
T2 BOSTON C GRB10 3.4 0.367 1.854 3.918 7 50737473 - CT NM_001001549: c.449_450insAG p.S150fs LGD
T33 BOSTON C HSPD1 3.5 0.976 2.711 3.638 2 198362109 G A NM_002156:c.C182T p.T61I D-mis
01-0215 DHREAMS C PTPN12 7.5 0.999 −0.054 5.084 7 77221548 C T NM_001131009:c.C77T p.T26M D-mis
T3 BOSTON C ACTG1 7.6 0.219 5.131 2.413 17 79478517 C T NM_001199954:c.G499A p.E167K D-mis
01-0761 DHREAMS C CDO1 9.4 0.020 −0.088 1.586 5 115147001 C - NM_001801:c.259delG p.D87fs LGD
T15 BOSTON C ADD1 12.0 0.611 0.586 3.906 4 2906653 C T NM_001119:c.C1324T p.R442W D-mis
T38 BOSTON I NAA15 14.0 0.996 3.088 4.805 4 140258100 AT - NM_057175:c.239_240del p.H80fs LGD
T57 BOSTON C POGZ 14.7 1.000 3.284 6.213 1 151378872 GGAA - NM_145796:c.2350_2353del p.F784fs LGD
01-0634 DHREAMS C PRKACB 15.6 0.612 2.547 3.179 1 84649798 C T NM_001242862:c.C277T p.R93X LGD
01-0562 DHREAMS C GATA6 16.8 - - - 18 19761477 C T NM_005257:c.C1366T p.R456C D-mis
01-0147 DHREAMS C STAG2 18.2 1.000 5.111 6.472 X 123197716 C T NM_006603:c.C1840T p.R614X LGD
T49 BOSTON I PLCG1 21.2 0.729 4.359 5.858 20 39797452 G A NM_002660:c.G2425A p.E809K D-mis
T70 BOSTON C FOXP4 22.4 0.672 1.628 3.652 6 41562624 A G NM_001012426:c.A1553G p.N518S D-mis
T35 BOS ON C ARL15 23.2 0.009 0.357 1.081 5 53450409 C T sp - LGD
01-0109 DHREAMS C DLST 23.5 0.950 0.277 3.734 14 75356621 AG - NM_001244883:c.297_298del p.E99fs LGD
T36 BOSTON C GINS3 23.8 0.236 0.613 1.888 16 58437236 G A sp - LGD
01-0136 DHREAMS C PRR14 23.9 0.259 0.655 3.753 16 30667426 C T NM_024031:c.C1552T p.R518W D-mis
01-0083 DHREAMS C TLN1 24.0 1.000 5.133 9.326 9 35725594 C T NM_006289:c.G98A p.R33H D-mis

Chr, chromosome. Ph, phenotype: C, complex; I, isolated CDH. Dia, expression rank in the embryonic mouse diaphragm. Allele: Ref., reference; Alt., alternative. Class: Sp, splice site variant. Category: LGD, likely gene disrupting; D-mis, predicted damaging missense variant by metaSVM, PolyPhen-2, SIFT, or CADD. DHREAMS variants are as reported in Yu et al. (2015). Human reference sequence: GRCh37/hg19.