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

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