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