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Table 1 Pathogenic copy number variations identified by whole genome low-coverage sequencing

From: The diagnostic yield of intellectual disability: combined whole genome low-coverage sequencing and medical exome sequencing

Patient CNV variation Region size Known genomic disease Patient documented in Decipher Database Patient Phenotype in this study
1 del(2q24.1)(155.48 Mb–158.4 Mb)*1
del(2q31.1-q31.2)(176.16 Mb–178.22 Mb)*1
2.92 Mb
2.06 Mb
2q31.1 microdeletion syndrome 2:154,961,717–158,712,890*1, Pathogenic, 3.75 Mb, Autistic behavior, Clinodactyly of the 5th finger, Cognitive impairment, Intellectual disability, mild, Joint laxity, Kyphoscoliosis, Language impairment, Mandibular prognathia, Muscular hypotonia, Seizures, Synophrys, Thick eyebrow, Tremor
2:156,830,779–159,106,872*1, Unknown, 2.28 Mb, Delayed speech and language development, Intellectual disability, Macrocephaly, Tall stature 2:155,796,265–157,725,469*1, Unknown, 1.93 Mb, Global developmental delay, Intellectual disability, severe
Mental retardation, Abnormal finger, CHD
2 Dup(5q35.2-q35.3)(175.74 Mb–180.08 Mb)*3 4.43 Mb Sotos syndrome 5:175,714,974–180,696,832*3, Pathogenic, 4.98 Mb, Brachycephaly, Hypertelorism, Microcephaly, Short stature, Unilateral ptosis
5:175,207,164–180,694,002*3, Unknown, 5.49 Mb
Mental retardation, Recurrent respiratory infections, Simiancrease, Limbs Hypotonia
3 del(7q31.1-q31.33)(113.9 Mb–125.52 Mb)*1 11.62 Mb 7q31 microdeletion syndrome 7:114,921,919–126,025,662*1, Unknown, 11.10 Mb,
7:114,236,695–127,881,806*1, Unknown, 13.65 Mb, Delayed speech and language development, Intellectual disability, Muscular hypotonia
7:112,510,560–121,723,279*1,Unknown, 9.21 Mb, Delayed speech and language development, Intellectual disability, Seizures
7:112,137,064–119,186,429*1, Pathogenic, 7.05 Mb, Abnormal facial shape, Moderate global developmental delay
Mental retardation, Asophia, Simiancrease, Facial abnormality
4 dup(7p14.3-p22.3)(0.1 Mb–30.82 Mb)*3 30.82 Mb 7p duplicationsyndrome 7:10,239–25,112,979*3, Unknown, 25.10 Mb, Absent speech, Constipation, Global developmental delay, Intellectual disability, severe, Long fingers, Low-set ears, Micrognathia, Muscular hypotonia, Narrow mouth, Pancreatitis, Thoracolumbar scoliosis
7:503,373–11,090,297*3, Pathogenic, 10.59 Mb, Autism, Broad forehead, Diastema, Generalized joint laxity, Global developmental delay, Micrognathia, Self-injurious behavior, Wide nose
7:109,626–16,317,319*3, Unknown, 16.21 Mb, Abnormality of prenatal development or birth, Cleft palate, Depressed nasal bridge, Low-set ears, Micrognathia
Mental retardation, Poor hearing, Wide set eyes, Simiancrease, Hypotonia, Low set ears, Microphallus, Scrotum, High-vaulted arch
5 dup(9p22.2-p23)(10.06 Mb–16.78 Mb)*3 6.72 Mb 9p duplication syndrome 9:9,910,369–19,437,090*3, Likely pathogenic, 9.53 Mb, Aplasia/Hypoplasia of the distal phalanges of the hand, Aplasia/Hypoplasia of the distal phalanges of the toes, Aplasia/Hypoplasia of the middle phalanges of the hand, Aplasia/Hypoplasia of the middle phalanges of the toes, Cupped ear, Diastasis recti, Epicanthus, Glabellar hemangioma, Hemangioma, Hypertelorism, Low-set ears, Nail dystrophy, Relative macrocephaly
9:8,266,233–16,527,801*3, Unknown, 8.26 Mb, Global developmental delay
Mental retardation, Abnormality of the palmar creases, Laryngomalacia, Muscular hypertonia, Facial abnormality
6 del(10q26.13-q26.3)(126.62 Mb–135.52 Mb) *1 8.9 Mb 10q deletion syndrome 10:126198009–135,430,043*1, Pathogenic, 9.23 Mb (Imbalance arising from a balanced parental rearrangement)
10:127,120,633–135,427,143*1, Likely pathogenic, 8.31 Mb, Congenital strabismus, Constipation, Generalized hypotonia, Language impairment, Microcephaly, Moderate expressive language delay, Sleep-wake cycle disturbance, Temperature instability
10:125,632,306–135,434,148*1, Unknown, 9.80 Mb, Functional abnormality of the bladder, Intellectual disability, moderate, Patent urachus, Strabismus (Imbalance arising from a balanced parental rearrangement)
Mental retardation, Small hands and feet, Hypoplastic labia minora, Hypotonia
7 del(11q24-q25)(124.55 Mb–134.94 Mb)*1 10.39 Mb Jacobsen syndrome 11:124,205,261–134,868,378*1, Pathogenic, 10.66 Mb, Abnormal platelet count, Epicanthus, Global developmental delay, Hypertelorism, Low-set ears, Short nose, Short stature, Smooth philtrum, Thin upper lip vermilion, Thrombocytopenia Mental retardation, Facial abnormality, Simiancrease
8 del(15q11.2-q13.2)(23.62 Mb–30.38 Mb)*1 6.76 Mb Prader-Willi and Angelman syndrome 15:23,619,912–28,438,266*1, Pathogenic, 4.82 Mb, EEG abnormality, Intellectual disability, Microcephaly, Seizures, Truncal ataxia
15:23,619,912–28,438,266*1, Pathogenic, 4.82 Mb, Feeding difficulties in infancy, Hypogonadism, Intellectual disability, Muscular hypotonia, Truncal obesity
15:23,699,760–30,322,138*1, Pathogenic, 6.62 Mb, Absent speech, Global developmental delay, Seizures
Mental retardation, Hypotonia, Microphallus, Scrotum
9 chr17: 34918482–36,408,851*1 1.49 Mb Renal cysts and diabetes (RCAD) 17:34,815,072–36,215,917*1, Pathogenic, 1.40 Mb, Abnormality of the liver, Diabetes mellitus, Multiple renal cysts
17:34,911,952–36,510,799*1, Pathogenic, 1.60 Mb, Fetal choroid plexus cysts, Multicystic kidney dysplasia
Mental retardation, asophia, and brain dysplasia
10 dup(17p11.2-p12)(14.76 Mb–19.48 Mb)*3 4.72 Mb 17p11.2 duplication syndrome 17:16,773,072–20,222,149*3, Pathogenic, 3.45 Mb, Autism, Hyperactivity, Short attention span, Short stature
17:14,097,915–15,470,903*3, Pathogenic, 1.37 Mb, Abnormality of the motor neurons, Decreased motor nerve conduction velocity, Hypertrophic nerve changes, Impaired pain sensation, Impaired proprioception, Impaired temperature sensation, Impaired vibratory sensation, Pes cavus
Mental retardation, Shrill crying, Poor skin, Hypotonia, Cryptorchidism
11 del(17p11.2)(16.6 Mb–20.5 Mb)*1 3.9 Mb Smith-Mageni syndrome 17:16,590,776–20,463,301*1, Pathogenic, 3.87 Mb, Brachydactyly, Severe global developmental delay, Specific learning disability Mental retardation, Dwarfism, Abnormal appearance of skull
12 del(2q37.2–37.3)(235.16 Mb– 243.08 Mb) *1
dup(19q13.42-q13.43)(52.76 Mb– 59.12 Mb)*3
7.92 Mb
6.36 Mb
2q37 deletion syndrome 2:235,875,302–243,041,364*1, Pathogenic, 7.17 Mb, Cognitive impairment, Horseshoe kidney, Postnatal microcephaly, Seizures, Underdeveloped nasal alae
19:51,294,464–56,379,713*3, Likely pathogenic, 5.09 Mb, Intellectual disability, Seizures, Short stature, Specific learning disability
19:53,181,823–59,095,418*3, Unknown, 5.91 Mb, Hypodysplasia of the corpus callosum, Mild global developmental delay, Noncommunicating hydrocephalus
19:53,569,329–59,052,715*3, Unknown, 5.48 Mb, Global developmental delay
Mental retardation, facial dysmorphism and global developmental delay, neonatal hypoglycemia
13 del(2q37.3)(240.70 Mb–243 Mb)*1
dup(20p12.1-p13)(0.1 Mb–15.14 Mb)*3
2.30 Mb
15.04 Mb
2q37 deletion syndrome 2:235,875,302–243,041,364*1, Pathogenic, 7.17 Mb, Cognitive impairment, Horseshoe kidney, Postnatal microcephaly, Seizures, Underdeveloped nasal alae
20:121,521–9,691,972*3, Pathogenic, 9.57 Mb, Intellectual disability, mild, Tall stature
20:121,521–3,783,829*3, Pathogenic Partial, 3.66 Mb, Global developmental delay
20:207,270–5,862,333*3, Unknown, 5.66 Mb, Abnormality of the nervous system, Tremor
Mental retardation, facial dysmorphism and global developmental delay, reproductive system abnormality
14 del(9p24.3-p23)(1 Mb–12.66 Mb)*1
dup(7p22.3-p21.2)(1 Mb–15 Mb)*3
11.66 Mb
14 Mb
9p deletion syndrome
7p duplication syndrome
9:271,257–12,907,826*1, Pathogenic, 12.64 Mb, Abnormality of the eye, Absent speech, Bilateral cryptorchidism, Bilateral talipes equinovarus, Cognitive impairment, Downslanted palpebral fissures, Generalized hypotonia, Hypoplasia of the corpus callosum, Micrognathia, Seizures, Synophrys, Ventricular septal defect
7:109,626–16,317,319*3, Unknown, 13.64 Mb, Deep plantar creases, Frontal bossing, Hydrocephalus, Hypertelorism, Intellectual disability, Midface retrusion, Stenosis of the external auditory canal
Mental retardation, Cheilopalatognathus, CHD, Simiancrease, Low set ears, Blepharophimosis, Hyperspasmia
15 47, XXY X chromosome Klinefelter syndrome X:166,314-155,246,643*3, Pathogenic, 155.08Mb, Delayed speech and language development, Microcephaly, Tetralogy of Fallot  Mental retardation
16 47, XXY X chromosome Klinefelter syndrome X:166,314-155,246,643*3, Pathogenic, 155.08Mb, Delayed speech and language development, Microcephaly, Tetralogy of Fallot Mental retardation, Autism