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Table 4 The novel pathogenic phenotypically enriched locus

From: Systematic identification of phenotypically enriched loci using a patient network of genomic disorders

PEL ID Type* Chr Start Length (Kb) Phenotype Cases/Carrier (DGV) P valuea P b
PEL 3 d 3 181296306 175.931 Anophthalmia 6/9 (0) 1.80E-15 100
PEL 5 d 7 95693340 89.973 Ectrodactyly 7/10 (0) 1.70E-14 100
PEL 4 d 3 181296306 175.931 Abnormality of globe size 8/9 (0) 1.90E-14 100
PEL 4 d 3 181296306 175.931 Aplasia/Hypoplasia affecting the eye 8/9 (0) 1.90E-13 100
PEL 71 d 2 200208169 38.268 Abnormality of the palate 11/19 (0) 2.10E-11 100
PEL 31 d 3 181166306 576 Abnormality of globe size 6/9 (0) 4.10E-11 100
PEL 105 d 2 200208169 38.268 Abnormality of the oral cavity 12/19 (0) 2.50E-10 100
PEL 84 d 15 100019051 189.992 Growth delay 13/18 (0) 2.70E-10 100
PEL 31 d 3 181166306 576 Aplasia/Hypoplasia affecting the eye 6/9 (0) 2.70E-10 100
PEL 128 d 2 200208169 38.268 Abnormality of the mouth 14/19 (0) 1.90E-09 100
PEL 131 d 15 100019051 189.992 Growth abnormality 14/18 (0) 6.40E-09 100
PEL 129 d 15 99057570 65.959 Growth delay 11/16 (0) 8.10E-09 100
PEL 69 d 11 31735689 39.768 Aplasia/Hypoplasia affecting the eye 5/8 (0) 1.00E-08 100
PEL 126 d 2 166091754 49.616 Seizures 10/15 (0) 1.00E-08 100
PEL 175 d 7 112349829 160.71 Delayed speech and language development 12/18 (0) 1.00E-08 100
PEL 78 d 14 29904720 411.94 Aplasia/Hypoplasia of the cerebrum 10/12 (0) 1.50E-08 100
PEL 82 d 14 29904720 411.94 Aplasia/Hypoplasia of the cerebrum 10/12 (0) 1.50E-08 100
PEL 141 d 7 114297499 533.997 Delayed speech and language development 11/15 (0) 4.50E-08 100
PEL 166 d 2 166244769 311.476 Seizures 9/14 (0) 6.00E-08 100
PEL 202 d 15 99057570 65.959 Growth abnormality 12/16 (0) 8.80E-08 100
PEL 152 d 14 29904720 411.94 Microcephaly 8/12 (0) 1.60E-07 100
PEL 159 d 14 29904720 411.94 Microcephaly 8/12 (0) 1.60E-07 100
PEL 216 d 2 200208169 38.268 Abnormality of the palate 7/13 (0) 1.60E-07 100
PEL 385 d 2 200246437 0 Abnormality of the face 16/19 (0) 1.60E-07 100
PEL 137 d 6 76509712 359.49 Joint laxity 5/9 (0) 1.60E-07 100
PEL 390 d 7 112349829 160.71 Neurodevelopmental delay 13/18 (0) 1.60E-07 100
PEL 412 d 13 92065689 29.285 Growth delay 9/17 (0) 2.00E-07 100
PEL 419 d 13 92065689 29.285 Growth delay 9/17 (0) 2.00E-07 100
PEL 436 D 16 3831263 32.469 Abnormality of the face 15/18 (0) 4.20E-07 100
PEL 222 d 2 201936560 57.623 Abnormality of the mouth 10/13 (0) 4.80E-07 100
PEL 222 d 2 200208169 38.268 Abnormality of the mouth 10/13 (0) 4.80E-07 100
PEL 242 d 7 114297499 533.997 Neurodevelopmental delay 12/15 (0) 5.20E-07 100
PEL 114 d 13 48557360 146.432 Abnormality of the globe 8/9 (0) 5.90E-07 100
PEL 250 d 7 119973023 238.728 Delayed speech and language development 9/13 (0) 8.80E-07 100
PEL 123 d 12 66224830 22.517 Short stature 7/8 (0) 1.10E-06 100
PEL 184 d 1 28743173 21.263 Deeply set eye 4/7 (0) 1.90E-06 100
PEL 462 d 1 11270844 47.828 Abnormality of the skull 10/14 (0) 1.90E-06 100
PEL 417 d 2 201936560 57.623 Abnormality of the mouth 9/13 (0) 2.00E-06 100
PEL 330 d 14 29781404 230.359 Seizures 7/12 (0) 2.10E-06 100
PEL 227 d 9 77206264 34.573 Seizures 7/10 (0) 2.10E-06 100
PEL 133 D 2 219965169 9.153 Cutaneous finger syndactyly 3/5 (0) 2.30E-06 100
PEL 116 d 3 181296306 6.681 Abnormality of the ocular region 9/9 (0) 2.50E-06 100
PEL 173 D 2 59105866 181.965 Midface retrusion 3/5 (0) 4.00E-06 100
PEL 120 D 2 59105866 181.965 Strabismus 5/5 (0) 4.40E-06 100
PEL 276 d 7 94174003 41.631 Decreased body weight 4/7 (0) 7.20E-06 100
PEL 329 d 7 95693340 89.973 Abnormality of limb bone morphology 8/10 (0) 1.30E-05 100
PEL 304 d X 133530468 102.522 Global developmental delay 6/8 (0) 1.50E-05 100
PEL 388 d 10 28842276 86.821 Abnormality of the eyelid 6/8 (0) 1.70E-05 100
PEL 210 D 2 59105866 181.965 Feeding difficulties in infancy 4/5 (0) 1.70E-05 100
PEL 455 d 10 28842276 86.821 Abnormality of the palpebral fissures 5/8 (0) 2.00E-05 100
PEL 251 d 13 41726952 39.763 Abnormal eye morphology 6/7 (0) 2.00E-05 100
PEL 470 d 10 28842276 86.821 Abnormality of the hair 5/8 (0) 2.20E-05 100
PEL 358 d 1 28743173 21.263 Abnormality of globe location 5/7 (0) 2.90E-05 100
PEL 460 d 3 181648378 93.928 Abnormality of the ocular region 7/9 (0) 3.60E-05 100
PEL 338 d 5 170676605 370.857 Abnormality of the cardiac septa 4/6 (0) 3.90E-05 100
PEL 133 D 2 219965169 9.153 Toe syndactyly 3/5 (0) 4.00E-05 100
PEL 454 d 1 177800358 362.172 Short stature 5/7 (0) 4.40E-05 100
PEL 369 d 14 57423809 185.438 Abnormality of the eye 7/8 (0) 4.50E-05 100
PEL 449 d 7 94174003 41.631 Abnormality of the foot 5/7 (0) 4.90E-05 100
PEL 294 d 1 157149743 12.346 Abnormal hair quantity 3/4 (0) 5.70E-05 100
PEL 213 d 1 157149743 12.346 Abnormality of the lip 4/4 (0) 5.70E-05 100
PEL 327 d 19 10640379 140.937 Abnormal genital system morphology 4/5 (0) 7.00E-05 100
PEL 448 d 14 58205713 144.654 Abnormality of the skull 7/8 (0) 8.00E-05 100
PEL 203 d 13 33963658 138.576 Abnormality of the neck 3/3 (0) 8.20E-05 100
PEL 423 d 3 181692255 50.051 Abnormality of the face 9/9 (0) 1.10E-04 100
PEL 324 d 7 94953990 5.573 Growth abnormality 6/6 (0) 2.20E-04 100
PEL 456 D 2 219965169 9.153 Abnormality of the lower limb 4/5 (0) 5.20E-04 100
PEL 361 D 7 106664270 182.398 Strabismus 3/3 (0) 5.40E-04 100
PEL 404 D 7 107527586 136.426 Abnormality of eye movement 3/3 (0) 8.20E-04 100
PEL 407 D 1 113036203 122.933 Abnormality of the palate 3/3 (0) 1.00E-03 100
  1. *Duplication (D) and deletion (d). a Adjusted P-values from the Fisher’s Exact test of the case–control analysis. b This table show only those PELs with a penetrance higher than 100 %. The penetrance was calculated as described by Cooper et al. [8, 28]
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