Table 3.
VOUS found in the cohort.
| Case | Type | Microarray Nomenclature | Size (Kbp) | N° of Genes | N° of Genes in OMIM | Important Genes | Phenotype | Gender/Notes |
|---|---|---|---|---|---|---|---|---|
| #1 | Dup | arr[hg19] 2p24.1(23,982,758-24,813,485)x3 | 831 | 18 | 7 | ATAD2B, UBXN2A | MID, overweight | F |
| #5 | Dup | arr[hg19] 6q15(89,917,335-90,485,874)x3 | 568 | 7 | 4 | GABRR1, GABRR2 | MID, Mot Dif and hyperactivity | M |
| #6 | Dup | arr[hg19] 2q37.2q37.3(236,733,535-237,355,774)x3 | 622 | 4 | 2 | AGAP1, GBX2 | DD, convulsions and FD | F |
| #7 | Dup | arr[hg19] 1q44(246,324,898-246,688,599)x3 | 363 | 2 | 1 | SMYD3 | Aut, Mot Dif, convulsions and FD | M |
| #13 | Del | arr[hg19] 11q14.1(84,050,388-84,415,990)x1 | 365 | 1 | 1 | DLG2 | Aut, LDO, Mot Dif, FD and SLD | M |
| #19 | Dup | arr[hg19] 8q21.13(82,061,218-84,515,685)x4 | 2.454 | 10 | 6 | IMPA1 | DD, FD, gastroschisis bladder exstrophy, hydronephrosis and Abnormal growth | M/Affected brother (#18) |
| #21 | Del | arr[hg19] 2q13(110,504,318-111,365,996)x1 | 861 | 16 | 3 | NPHP1 | ID | M |
| #32 | Dup |
arr[hg19] 20q13.33 (61,854,236-62,054,955)x3 |
200 | 9 | 5 | KCNQ2, CHRNA1 |
Convulsions, low weight, prematurity, FD, microcephaly and tracheoesophageal fistula |
M |
| #40 | Del | arr[hg19] 14q24.2(73,590,938-73,776,190)x1 | 185 | 4 | 2 | PSEN1, NUMBP1 | Aut and SLD | M |
| #43 | Del | arr[hg19] 16q23.2(80,260,131-80,701,060)x1 | 440 | 2 | 1 | DYNLRB2, CDYL2 | MID, Aut, Mot Dif, SLD, hyperactivity and FD | M |
| #50 | Del | arr[hg19] 13q12.12(60,425,635-60,688,042)x1 | 262 | 25 | 2 | SGCG, SACS | MID | F |
| #58 | Dup | arr[hg19] 11q22.3(102,946,063-103,827,049)x3 | 880 | 4 | 2 | DYNC2H1 | DD, LDO, Mot Dif and FD | M |
| #64 | Dup | arr[hg19] 9q34.3(139,381,821-140,086,032)x3 | 704 | 48 | 28 | NOTCH1 | DD, SLD, ID and FD | M |
| #81 | Dup | arr[hg19] 16p13.3(549,826-1,449,862)x3 | 900 | 45 | 26 | CACNA1H | SLD, convulsions and FD | M/*Pv |
| #82 | Dup | arr[hg19] 4q35.2(188,106,543-189,797,261)x3 | 1.691 | 5 | 1 | ZFP42 | DD and SLD | M |
| #86 | Del | arr[hg19] 13q21.2(60,425,635-60,688,042)x1 | 262 | 2 | 1 | DIAPH3 | DD and LDO | F |
| #89 | Dup | arr[hg19] 9p24.3(319,876-517,446)x3 | 198 | 2 | 2 | DOCK8, KANK1 | Aut, SLD, mot dif and FD | F |
| #109 | Dup | arr[hg19] 4q31.1(139,758,054-139,988,340)x3 | 230 | 2 | 1 | CCRN4L | DD and FD | M |
| #112 | Dup | arr[hg19] 9p13.3(34,211,157-34,395,294)x3 | 184 | 5 | 3 | UBAP1, NUDT2 | SID, Aut, convulsions, SLD, mot dif and FD | M |
| #117 | Dup | arr[hg19] 19q13.33(48,206,212-48,431,081)x3 | 224 | 25 | 7 | CORD2 |
Short stature, abnormal brain structure, CAs, DD, FD, hirsutism and anemia |
F/− |
| #136 | Dup | arr[hg19] 4q28.1q28.2(128,789,028-128,891,808)x3 | 103 | 3 | 2 | PLK4 |
Low weight, short stature, IUGR, FD, thin hair, and skin spots - no ID |
F/− |
| #138 | Dup | arr[hg19] 6p21.2(37,609,169-37,868,513)x3 | 260 | 2 | 2 | MDGA1 |
Prematurity, DD, polydactyly, aggression, FD, difficulties of swallowing food, vomiting with fatty food, cutis marmorata, microcytic and hypochromic anemia |
M/− |
| #144 | Del | arr[hg19] 8q13.1q13.2(67,999,679-68,190,627)x1 | 191 | 2 | 2 | CSPP1 | DD, SLD, ID and FD | F/− |
| #178 | Dup | arr[hg19] 11q23.3(117,000,284-117,312,611)x3 | 312 | 10 | 7 | DSCAML1, CEP164, BACE1 |
Slender build, DD, Aut, FD, macrocephaly |
M/− |
| #180 | Del | arr[hg19] 16p13.3(6,243,228-6,835,898)x1 | 593 | 1 | 1 | RBFOX1 | DD, hypothyroidism | M/− |
| #215 | Del | arr[hg19] 3q26.33(179,508,262-179,621,954)x1 | 114 | 1 | 1 | PEX5L | Motor Delay, DD, ID, Aut and ADHD | M/− |
| #223 | Dup | arr[hg19] 15q24.1(72,838,805-73,581,757)x3 | 743 | 8 | 4 | BBS4 | Short stature, IUGR, DD, MID and FD | M/*3 V |
| #223 | Dup | arr[hg19] 3p26.3(255,645-1,510,822)x3 | 1.255 | 2 | 2 | CTN6, CHL1 | Short stature, IUGR, DD, MID and FD | M/*3 V |
| #223 | Dup | arr[hg19] 6q25.3(156,488,875-158,534,725)x3 | 2.045 | 9 | 4 | ARID1B, SYNJ2 | Short stature, IUGR, DD, MID and FD | M/*3 V |
| #245 | Dup | arr[hg19] 14q12(26,490,666-27,520,832)x3 | 1.030 | 2 | 1 | NOVA1 | Obesity, encephalopathy, CAs, DD and FD | F/− |
| #248 | Del | arr[hg19] 10q23.1(87,392,282-87,791,684)x1 | 399 | 1 | 1 | GRID1 |
Abnormal brain structure, DD, SLD, FD and microcephaly |
M/− |
| #255 | Del | arr[hg19] 10q23.1(87,691,467-87,843,627)x1 | 152 | 1 | 1 | GRID1 | DD | M/*Pv |
| #268 | Del | arr[hg19] 2q13(110,504,318-111,365,996)x1 | 861 | 16 | 3 | NPH1 | ASD | M/− |
| #276 | Dup | arr[hg19] Xq26.2(130,672,818-130,967,726)x3 | 295 | 2 | 3 | KAL1 | DD, FD, cardiomyopathy, thyroid dysfunction and myopia | F/− |
| #278 | Dup | arr[hg19] 19q13.42(54,201,711-54,420,807)x3 | 219 | 39 | 9 | MIR, NLRP12 |
Epilepsy, abnormal brain structure and ID |
F/− |
| #290 | Dup | arr[hg19] 2q13(110,496,601-110,983,418)x3 | 487 | 14 | 3 | NPHP1 | Genetic counseling | M/− |
| #294 | Dup | arr[hg19] 2q13(110,498,141-110,980,295)x3 | 482 | 14 | 3 | NPHP1 |
DD, ID, FD and Congenital cardiopathy |
F/− |
| #299 | Dup | arr[hg19] 17q11.2(28,952,286-29,150,025)x3 | 198 | 4 | 1 | CRLF3 |
DD, Aut and Behavioral disorder |
M/− |
| #309 | Del | arr[hg19] 17p13.1(6,949,507-7,217,381)x1 | 268 | 16 | 15 | - | Short stature, DD, ID, FD and microcephaly | M/− |
| #311 | Dup | arr[hg19] 1p31.3(61,699,736-62,125,970)x3 | 426 | 2 | 1 | NFIA |
Obesity, CAs, DD, SLD and ID |
F/− |
| #319 | Dup | arr[hg19] 16p13.3(1,252,411-1,404,818)x3 | 152 | 9 | 8 | 5 OMIMs | Anal imperforation, onfalocele and cloacal exstrophy | F/− |
| #331 | Dup | arr[hg19] 4p16.3p16.2(4,025,257-4,618,896)x3 | 594 | 7 | 3 | NSG1 | DD, epilepsy and FD | M/*Pv |
| #336 | Dup | arr[hg19] 1q25.3(183,589,206-183,827,325)x3 | 238 | 3 | 3 | ARPC5, APOBEC4, RGL1 | DD and FD | F/− |
| #342 | Del | arr[hg19] 3p24.2(24,376,230-24,492,572)x1 | 117 | 1 | 1 | THRB | DD, Bilateral hearing impairment and FD | F/− |
| #346 | Del | arr[hg19] 7q31.1(111,485,313-111,922,531)x1 | 437 | 2 | 2 | DOCK4 |
Low weight, slender build, motor delay, DD, SLD, SID and Aut. |
M/− |
| #354 | Dup | arr[hg19] 9q33.1(118,409,943-119,207,073)x3 | 797 | 4 | 3 | NOC2L | Consanguineous parents, quadriparesis, DD, FD and ostium secundum | M/− |
| #359 | Dup | arr[hg19] 5q14.1(80,019,759-80,535,750)x3 | 516 | 6 | 3 | MSH3, RASGRF2, CKMT2 |
Convulsions, LDO, MID and behavioral disorder |
F/− |
| #360 | Del | arr[hg19] 1p31.1(72,257,666-72,499,784)x1 | 242 | 2 | 1 | NEGR1 |
Convulsions, LDO, F MID and hearing loss |
F/− |
| #369 | Dup | arr[hg19] 12p11.22p11.21(30,175,955-31,570,927)x3 | 1.394 | 9 | 3 | IPO8, CAPRIN2, DDX11 |
Abnormal brain structure and DD |
M/− |
| #383 | Dup | arr[hg19] 10q11.23(51,250,417-51,755,110)x3 | 505 | 7 | 4 | PARG, MSMBP, NCOA4, TIMM23 | Convulsions, DD, SLD, Aut., Behavioral disorder and gluten intolerance | M/− |
| #384 | Dup | arr[hg19] 10q21.1(59,984,568-60,285,875)x3 | 301 | 5 | 5 | IPMK, CISD1, UBE2D1, TFAM | Motor delay and chronic encephalopathy | M/− |
| #384 | Del | arr[hg19] 16p13.3(7,108,169-7,225,285)x1 | 117 | 1 | 1 | RBFOX1 | Motor delay and chronic encephalopathy | M/− |
| #384 | Dup | arr[hg19] 18q22.3(72,755,482-73,023,597)x3 | 268 | 3 | 1 | TSHZ1 | Motor delay and chronic encephalopathy | M/− |
| #397 | Dup | arr[hg19] 16p12.2(21,817,921-22,431,357)x3 | 613 | 9 | 3 | UQCRC2, EEF2K, CDR2 | DD, Aut and FD | M/− |
| #401 | Dup | arr[hg19] 2q11.1(95,733,867-96,279,208)x3 | 545 | 8 | 3 | ZNF2, MRPS5, KCNIP3 | Autism | F/− |
| #423 | Dup | arr[hg19] 12q21.31(80,559,698-80,918,615)x3 | 358 | 2 | 2 | OTOGL, PTPRQ | CAs, ID and FD | F/− |
| #444 | Del | arr[hg19] 16p13.3(6,644,079-6,675,606)x1 | 31 | 1 | 1 | RBFOX1 | ASD | M/− |
Variants of unknown significance found in the cohort, with the number of genes present in the region, listing the most relevant genes and phenotypes for each individual. Dup = Duplication, Del = Deletion, CA = Congenital Anomalies, DD = Developmental Delay, ID = Unspecified intellectual disability, MID = Mild Intellectual Disability, MID = Moderate Intellectual Disability, SID = Severe Intellectual Disability, Aut = Autism, Mot Dif = Motor Difficulty and FD = Facial Dysmorphisms, SLD = speech and/or language delay or impairment, IUGR = Intrauterine growth restriction, ADHD = Attention-deficit/hyperactivity disorder, LDO = learning difficulty only, ASD = Autism spectrum disorder, F = Female, M = Male. *3 V = Patients with 3 VOUS (CNV). Pv = Patients with pathogenic CNV. *2Pvp = Patients with 2 pathogenic CNVs.