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Table 3 Patients (N = 38) with two or more diagnoses consisting of SNVs detected by ES and PCNVs detected by arrays

From: Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases

Patient ID Findings from arrays Findings from ES
CNVs Size (Mb) Associated disorders Known prior to ES SNVs Associated disorders Inheritance
WD1 1p36.33 del, 8p23.3p22 gain 0.715, 13.753 Unbalanced translocation No HMZ c.11754G>A (p.W3918*) pathogenic variant in USH2A Usher syndrome 2A [MIM:276901] AR
WD2 1q21.1q21.2 del, inherited 0.847 1q21.1 deletion syndrome [MIM:612474] Yes HTZ c.1396_1399dup (p.Y467fs) pathogenic variant in ZFPM2 Tetralogy of Fallot [MIM: 187500]; diaphragmatic hernia 3 [MIM:610187] AD
WC2*, #,3*, # 1q21.1q21.2 del 1.207 1q21.1 deletion syndrome [MIM:612474] No HTZ c.283C>T (p.R95*) pathogenic variant in CTNNB1, dn Mental retardation, autosomal dominant 19 [MIM:615075] AD
WD3 1q24.2q25.3 gain 10.944 Large gain in 1q Yes HTZ c.182A>G (p.H61R) likely pathogenic variant in PTEN, dn Cowden disease [MIM:158350] AD
WD4 2q21.1 del 0.447 2q21.1 deletion including ARHGEF4 and GPR148 [PMID:22543972] No HTZ c.1615delG (p.E539fs) pathogenic variant in PTCH1 Basal cell nevus syndrome [MIM:109400] AD
WD5 2q36.3 del 0.004 Early language delay and cerebral white matter hyperintensities [PMID:23810381] Yes HTZ c.2155+2T>C pathogenic variant in CASK Mental retardation and microcephaly with pontine and cerebellar hypoplasia [MIM:300749] X-linked
WD6 3pter del 5.15 Distal 3p deletion syndrome [MIM:613792] No HMZ c.836C>T (p.A279V) VUS in SUMF1 Multiple sulfatase deficiency [MIM:272200] AR
WD7 3q21.2q21.3 del 2.053 Global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies [MIM:617260] No HTZ c.706C>T (p.R236*) pathogenic variant in ACAN Spondyloepiphyseal dysplasia type Kimberley [MIM:608361] AD
WD20 4p16.1 gain, mosaic, dn 1.112 4p16.1 duplication [PMID: 15378535] Yes HMZ c.882_883del (p.Q295fs) pathogenic variant in WDR45, dn Brain iron accumulation 5 [MIM:300894] X-linked
WD8** 10q24.31q24.32 gain, dn 0.736 Split hand-split foot malformation 3 [MIM:246560] No HMZ c.2209G>C (p.G737R) pathogenic variant in POLG Leigh syndrome [MIM:256000] AD
WD9 15q13.2q13.3 del BP4-5 1.477 15q13.3 microdeletion syndrome [MIM:612001] No HTZ c.503G>A (p.R168H) pathogenic variant in TPM3, dn Nemaline myopathy 1 [MIM:609284]; Cap myopathy 1 [MIM:609284] AD
WD22 15q15.3 HMZ del 0.049 Deafness, autosomal recessive 16 [MIM:603720] No HMZ c.73G>T (p.E25*) pathogenic variant in EPCAM Diarrhea 5, with tufting enteropathy, congenital [MIM:613217] AR
WD13* 16p13.11 del, dn 1.166 16p13.11 microdeletion syndrome. [PMID:24105370] Yes HTZ c.5351T>C (p.V1784A) likely pathogenic variant in SCN1A, dn Epileptic encephalopathy, early infantile, 6 [MIM:607208] AD
WD23 16p13.11 del 1.166 16p13.11 microdeletion syndrome. [PMID:24105370] Yes HTZ c.2350_2351dupTG (p.W784fs) pathogenic variant in NF1 Neurofibromatosis-Noonan syndrome [MIM:601321] AD
WD14 16p13.11 del, inherited 0.770 16p13.11 microdeletion syndrome. [PMID:24105370] Yes HMZ c.872C>T (p.S291F) VUS in NDE1 Lissencephaly type 4 [MIM:614019] AR
WD15 16p13.11 gain 1.314 16p13.11 microduplication [PMID:21150890] Yes HMZ c.1156C>T (p.R386W) pathogenic variant in FDXR Auditory neuropathy and optic atrophy [MIM:617717] AR
WD15 16p13.11 gain 1.314 16p13.11 microduplication [PMID:21150890] Yes HTZ c.8045delT (p.L2682fs) pathogenic variant in KMT2A Wiedemann-Steiner syndrome [MIM:605130] AD
WD30 16p13.11 gain, inherited 1.165 16p13.11 microduplication [PMID:21150890] Yes HTZ c.1215delA (p.P405fs) pathogenic variant and c.1051A>C (p.T351P) VUS in ROBO3 Familial horizontal gaze palsy with progressive scoliosis [MIM:607313] AR
WD21 16p13.11 gain, inherited 1.166 16p13.11 microduplication [PMID:21150890] No HTZ c.356T>C (p.L119P) pathogenic variant in KRT13, dn White sponge nevus 2 [MIM:615785] AD
WD12 16p12.2 del 0.387 16p12.2 microdeletion (EEF2K) [PMID:27848943] Yes HTZ c.6619_6621delGAG (p.E2207del) pathogenic variant in SPTAN1, dn Epileptic encephalopathy, early infantile, 5 [MIM:613477] AD
WD35 16p11.2 loss, inherited 0.377 16p11.2 deletion syndrome, 220kb [MIM:613444] Yes HTZ c.3280delG (p.E1094fs) in KAT6B, dn Ohdo syndrome, SBBYS variant [MIM:603736] AD
WD33 16p11.2 gain 0.521 16p11.2 duplication syndrome [MIM:614671] Yes HTZ c.1618dupC (p.Q540fs) pathogenic variant in TCF20, dn Autism, intellectual disability, and postnatal overgrowth [PMID:27436265] AD
WD10* 16p11.2 del, inherited 0.526 16p11.2 deletion syndrome, 593Kb [MIM:611913] Yes HTZ c.3505C>T (p.R1169*) likely pathogenic variant in KAT6A; inherited from similarly affected father Mental retardation, autosomal dominant 32 [MIM:616268] AD
WD11 16p11.2 del 0.526 16p11.2 deletion syndrome, 593Kb [MIM: 611913] No HTZ c.649dup (p.R217fs) pathogenic variant in PRRT2 Familial paroxysmal kinesigenic dyskinesia [MIM:602066] AD
WD16 17p12 del, dn 1.448 HNPP [MIM:162500] Yes HTZ c.1264C>T (p.R422*) pathogenic variant in DEPDC5, dn Epilepsy, familial focal, with variable foci [MIM:604364] AD
WD24 17p12 del 1.294 HNPP [MIM:162500] Yes HTZ c.607G>A (p.G203R) likely pathogenic variant in GNAO1, dn Epileptic encephalopathy, early infantile, 17 [MIM:615473] AD
WD17* 17q11.2 gain 1.072 17q11.2 microduplication syndrome [MIM:613675] No HTZ c.1286G>A (p.W429*) pathogenic variant in SOX11 Mental retardation, autosomal dominant 27 [MIM:615866] AD
WD25 17q12 del 1.776 Renal cysts and diabetes syndrome [MIM:137920] No Compound HTZ c.2099C>T (p.P700L) and c.2734C>T (p.R912W) VUS in KIF1C Spastic ataxia 2, autosomal recessive [MIM:611302] AR
WD28 17q12 gain, inherited 1.348 17q12 duplication [PMID:22241097] Yes HTZ c.1592G>T (p.W531L) likely pathogenic variant in BRAF, dn Cardiofaciocutaneous syndrome 1 [MIM:115150] AD
WD26 20p12.2p11.23 gain, inherited 7.614 Large gain in 20p Yes HTZ c.310C>G (p.R104G) VUS in MKL2, dn Autism [PMID:22495311,23,375,656] AD
WD18 22q11.21 gain, dn 2.568 22q11.2 microduplication syndrome [MIM:608363] Yes HMZ c.664delC (p.L222fs) pathogenic variant in AP4B1 Autosomal recessive spastic paraplegia 47 [MIM:614066] AR
WD27 22q11.21q11.23 del 1.833 22q11.2 distal deletion [MIM:611867] Yes HTZ c.1574C>T (p.P525L) pathogenic variant in FUS Amyotrophic lateral sclerosis 6, with or without frontotemporal dementia [MIM:608030] AD
WD34 22q13.33 loss, dn 0.012 22q13.3 deletion syndrome [MIM:606232] No HTZ c.1474_1485del (p.Y492_F495del) likely pathogenic variant in FOXP1, dn Mental retardation with language impairment and autistic features [MIM:613670] AD
WD19* Xp22.31 del 1.413 X-linked ichthyosis in male [MIM:308100] Yes HMZ c.1376_1377del (p.C459*) pathogenic variant in KIAA2022, dn Mental retardation, X-linked 98 [MIM:300912] X-linked
WD31 Xp21.1 HMZ del 0.001 Becker muscular dystrophy [MIM:300376] Yes HTZ c.709G>A (p.E237K) pathogenic variant in KIF5C, dn Complex cortical dysplasia with other brain malformations 2 [MIM:615282] AD
WC17 Xq28 del 0.228 Mental retardation, X-linked, FRAXE type [MIM:309548] No HTZ c.3136-2A>G pathogenic variant in ARID1B Coffin-Siris syndrome 1 [MIM:135900] AD
WD29 47,XXY Entire chrX 47,XXY Yes HTZ c.1726C>T (p.R576W) pathogenic variant (dn) and c.1108-5G>A VUS in ATAD3A Harel-Yoon syndrome [MIM:617183] AR, AD
WD32 47,XYY Entire chrY 47,XYY Yes HTZ c.1478dupT (p.S494fs) pathogenic variant in DYRK1A, dn Mental retardation, autosomal dominant 7 [MIM:614104] AD
  1. HNPP neuropathy, recurrent, with pressure palsies, AD autosomal dominant, AR autosomal recessive, VUS variant of unknown significance, dn de novo, del deletion, HTZ heterozygous, HMZ homozygous or hemizygous
  2. *Reported previously [35]
  3. **WD8 also had UPD15
  4. #WC2 and WC3 are siblings
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