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. 2020 Nov 23;16(11):e1008802. doi: 10.1371/journal.pgen.1008802

Table 2. Table of association between sets of associated phenotype–gene pairs after FDR correction (gene level association performed using SKAT test with variants weighted by their CADD score).

N markers P-value SKAT weight CADD
HPO Phenotypes genes Totals Common Rare p-value p.fdr
Marfan syndrome gene
HP0000002 Standing/sitting height ratio FBN1 1962 969 993 7.16E-35 4.28E-32
HP0005117 Diastolic blood pressure FBN1 1962 968 994 1.94E-11 3.17E-09
HP0003758 Subcutaneous adipose tissue FBN1 1962 968 994 1.33E-06 1.19E-04
HP0004421 Systolic blood pressure FBN1 1962 968 994 2.41E-05 1.50E-03
HP0002647 Aortic dissection FBN1 1962 968 994 1.18E-04 5.43E-03
HP0000541 Retinal detachment FBN1 1962 968 994 1.55E-03 3.91E-02
Alagille syndrome genes
HP0005117 Diastolic blood pressure JAG1 580 257 323 1.01E-17 4.51E-15
HP0001518 Small for gestational age JAG1 580 257 323 4.45E-13 1.11E-10
HP0004421 Systolic blood pressure JAG1 580 257 323 3.11E-11 4.65E-09
HP0003758 Subcutaneous adipose tissue JAG1 580 257 323 1.08E-04 5.12E-03
HP0000518 Cataract JAG1 580 257 323 1.93E-04 8.25E-03
HP0003124 Hypercholesterolemia JAG1 580 257 323 1.60E-03 3.95E-02
Noonan syndrome / RAS-opathy genes
HP0000821 Hypothyroidism PTPN11 832 263 569 1.58E-77 2.83E-74
HP0005117 Diastolic blood pressure PTPN11 832 263 569 6.32E-46 5.66E-43
HP0004421 Systolic blood pressure PTPN11 832 263 569 4.48E-16 1.61E-13
HP0000002 Standing/sitting height ratio PTPN11 832 263 569 4.91E-13 1.11E-10
HP0001518 Small for gestational age PTPN11 829 265 564 4.45E-12 8.87E-10
HP0045081 Body mass index PTPN11 832 263 569 3.63E-07 3.43E-05
HP0003758 Subcutaneous adipose tissue PTPN11 832 262 570 3.45E-05 2.06E-03
HP0003081 Increased urinary potassium PTPN11 832 262 570 6.16E-04 1.90E-02
HP0001537 Umbilical hernia PTPN11 832 263 569 1.01E-03 2.85E-02
HP0001081 Cholelithiasis PTPN11 832 263 569 1.24E-03 3.34E-02
HP0003758 Subcutaneous adipose tissue CBL 1295 388 907 2.43E-05 1.50E-03
HP0045081 Body mass index CBL 1295 386 909 7.22E-04 2.16E-02
HP0000646 Amblyopia CBL 1295 386 909 1.61E-03 3.95E-02
HP0045081 Body mass index KAT6B 1923 696 1227 2.26E-04 9.22E-03
HP0000002 Standing/sitting height ratio KAT6B 1923 696 1227 1.98E-03 4.52E-02
HP0003758 Subcutaneous adipose tissue MAP2K1 1555 616 939 3.62E-05 2.10E-03
HP0045081 Body mass index MAP2K1 1555 616 939 6.47E-05 3.62E-03
HP0045081 Body mass index NRAS 246 84 162 4.96E-13 1.11E-10
HP0012603 Urine sodium concentration NRAS 246 84 162 2.47E-10 2.77E-08
HP0003758 Subcutaneous adipose tissue NRAS 246 84 162 1.18E-08 1.24E-06
HP0007018 Attention deficit hyperactivity disorder NRAS 246 84 162 3.65E-04 1.30E-02
HP0000002 Standing/sitting height ratio NRAS 246 84 162 5.05E-04 1.68E-02
HP0005117 Diastolic blood pressure NRAS 246 84 162 7.66E-04 2.25E-02
HP0000002 Standing/sitting height ratio RAF1 1282 497 785 2.11E-10 2.61E-08
HP0003124 Hypercholesterolemia RAF1 1282 497 785 3.16E-06 2.70E-04
HP0007018 Attention deficit hyperactivity disorder RAF1 1282 497 785 8.70E-05 4.45E-03
HP0001256 Intellectual disability, mild RAF1 1281 493 788 3.43E-04 1.26E-02
HP0003758 Subcutaneous adipose tissue RAF1 1282 497 785 3.44E-04 1.26E-02
HP0004421 Systolic blood pressure RAF1 1282 497 785 5.94E-04 1.87E-02
HP0001518 Small for gestational age RAF1 1281 496 785 1.18E-03 3.26E-02
HP0003758 Subcutaneous adipose tissue RASA2 1665 454 1211 1.13E-11 2.03E-09
HP0001507 Growth abnormality RASA2 1665 455 1210 2.18E-10 2.61E-08
HP0000002 Standing/sitting height ratio RASA2 1665 454 1211 2.96E-08 2.95E-06
HP0045081 Body mass index RASA2 1665 454 1211 1.27E-05 8.79E-04
HP0001518 Small for gestational age RASA2 1665 452 1213 9.16E-05 4.45E-03
HP0012603 Urine sodium concentration RASA2 1665 454 1211 3.18E-04 1.21E-02
HP0001518 Small for gestational age RIT1 234 90 144 2.15E-10 2.61E-08
HP0001507 Growth abnormality RIT1 234 90 144 4.25E-06 3.47E-04
HP0045081 Body mass index RIT1 234 90 144 5.98E-06 4.47E-04
HP0003081 Increased urinary potassium RIT1 234 90 144 7.94E-05 4.19E-03
HP0003758 Subcutaneous adipose tissue RIT1 234 90 144 3.16E-04 1.21E-02
HP0000023 Inguinal hernia RIT1 234 90 144 4.20E-04 1.45E-02
HP0000120 Creatinine clearance RIT1 234 90 144 1.33E-03 3.47E-02
HP0004421 Systolic blood pressure RRAS 171 67 104 5.71E-04 1.83E-02
HP0001659 Aortic regurgitation RRAS 171 67 104 1.87E-03 4.36E-02
HP0001518 Small for gestational age SHOC2 1183 421 762 9.18E-05 4.45E-03
HP0001507 Growth abnormality SHOC2 1183 423 760 2.41E-04 9.61E-03
HP0001507 Growth abnormality SOS1 1966 669 1297 1.27E-03 3.35E-02
HP0005117 Diastolic blood pressure SOS2 1792 731 1061 7.19E-04 2.16E-02
DiGeorge syndrome genes
HP0045081 Body mass index COMT 691 275 416 5.62E-06 4.39E-04
HP0004421 Systolic blood pressure COMT 691 275 416 7.05E-06 5.06E-04
HP0002155 Hypertriglyceridemia COMT 691 275 416 1.45E-04 6.49E-03
HP0003124 Hypercholesterolemia COMT 691 275 416 2.24E-04 9.22E-03
HP0003302 Spondylolisthesis COMT 691 275 416 4.73E-04 1.60E-02
HP0007018 Attention deficit hyperactivity disorder DGCR2 1267 628 639 7.50E-05 4.08E-03
HP0012603 Urine sodium concentration DGCR2 1267 628 639 3.70E-04 1.30E-02
HP0045081 Body mass index DGCR8 603 231 372 1.93E-05 1.28E-03
HP0004421 Systolic blood pressure DGCR8 603 231 372 5.63E-04 1.83E-02
HP0000002 Standing/sitting height ratio DGCR8 603 231 372 1.51E-03 3.87E-02