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. 2008 Feb 1;82(2):477–488. doi: 10.1016/j.ajhg.2007.12.009

Table 3.

Recurrent and Overlapping Loci in ASD

Chromosome FamID Sex Typea Size (bp)b CNV Origin Genesc Phenotype Comments
1 2q14.1 SK0147-003 F SPX 478,370 loss paternal DPP10 exonic IQ/LOFd unknown, RL/ELe sev delay, RB2+,f dysmorph 3+,g neurofibromatosis type 1, abnormal EEG
SK0288-003 F SPX-MZ 105,120 gain paternal DPP10 intronic IQ/LOF 73, RL/EL average/mild delay, RB 2+, dysmorph N/A
2 2q32.1 SK0306-004 F SPX 97,130 loss de novo none IQ/LOF 68, RL/EL mild delay, speech 2+,h RB2+, dysmorph 3+, severe hypotonia
NA0030-000 M SPX 112,323 loss maternal none IQ/LOF 69, RL/EL mod delay, RB2+, dysmorph 1+, seizures, medicated for OCD, motor incoordination
3 6q22.31 MM0220-003 M MPX 318,000 gain paternal PLN whole IQ/LOF 82, language average, dysmorph 2+, high myopia, fine motor difficulties
NA0025-000 M SPX 293,989 gain paternal PLN whole IQ/LOF unknown, language: regression/mild delay, RB2+, dysmorph 0
4 7q36.2 SK0190-003 M SPX 1,780,000 gain maternal DPP6 whole IQ/LOF 55, RL/EL sev delay, speech 2+, RB1+, dysmorph N/A, parents 1st cousins
SK0115-003 M SPX 274,000 gain unknown DPP6 exonic IQ/LOF 86, RL/EL average, RB2+, ysmorph N/A,
SK0058-003 M MPX 16,788 gain maternal DPP6 intronic IQ/LOF 111, RL/EL average, RB1+, ysmorph N/A
NA0002-000 M SPX 66,462 loss de novo DPP6 exonic IQ/LOF unknown, RL/EL severe delay, RB3+, dysmorph 0
5 8q11.23 SK0143-003 M SPX 285,200 gain unknown UNQ9433 whole, RB1CC1 exonic IQ/LOF 65, RL/EL sev delay, speech 2+, RB2+, dysmorph 2+, seizures, hypoplastic left heart syndrome, left hemidiaphragm paralysis
MM0236-004 M MPX 271,679 gain unknown RB1CC1 exonic IQ/LOF 84, language average, RB1+, dysmorph 0, central auditory processing difficulty
6 9p24.1 SK0270-003 M SPX 38,900 loss unknown none IQ/LOF 67, RL/EL mild/mod delay, speech 1+, RB3+, dysmorph N/A
MM0103-003 M MPX 34,950 loss paternal none IQ/LOF 100, language mild delay, speech 0, RB2+, dysmorph 0, twin preg (other twin lost in 1st trimester), premature (34 wks with respiratory distress syndrome), club feet
7 11p12 MM0272-003 M MPX 262,938 loss maternal none IQ/LOF 74, language mild delay, speech 3+, RB2+, dysmorph N/A, seizures, unilateral congenital ptosis
SK0167-003 F MPX 192,846 loss unknown none IQ/LOF 62, RL/EL average/mild delay, speech apraxia 2+, dysmorph N/A
8 13q21.32 SK0023-003 M SPX 189,438 gain unknown PCDH9 intronic IQ/LOF 82, RL/EL mod/sev delay, speech 2+, RB2+, dysmorph N/A; seizures
MM0299-003 F MPX 172,401 gain paternal PCDH9 intronic IQ/LOF 43, language nonverbal, RB2+, dysmorph 0, hypotonia, gags/chokes, fine motor delay
9 15q11.2-q13.3 SK0073-003 F CHR 11,922,600 gain de novo >50 genes IQ/LOF 49, RL/EL mod delay, RB3+, dysmorph N/A, premature (34 wks)
SK0245-005 M CHR 11,871,747 gain de novo >50 genes IQ/LOF 47, RL/EL sev delay, RB3+, dysmorph N/A
10 16p12.2 MM0109-003 F SPX 1,246,288 gain maternal 8 genes IQ/LOF 27, language nonverbal, RB3+, dysmorph 1+
MM0289-003 F MPX 802,555 loss maternal 5 genes IQ/LOF 45, language delay, RB2+, dysmorph 0
11 16p11.2 NA0133-000 F SPX 525,319 gain maternal 29 genes IQ/LOF & language moderate delay, speech 2+, RB1+, dysmorph 0, early motor delay
SK0102-004 M SPX 432,600 gaini de novo 24 genes IQ/LOF 39, RL/EL sev delay, speech 2+, RB3+, dysmorph 2+, epilepsy, congenital diaphragmatic hernia
MM0088-003 F MPX 675,829 loss de novo 32 genes IQ/LOF 82, RL/EL mod delay, RB3+, dysmorph 1+
SK0019-004 M SPX 675,829 loss de novo 32 genes IQ/LOF 93, RL/EL average, speech 2+, RB3+, dysmorph 1+, hyperphagia and severe obesity
12 22q11.2 SK0119-003j M MPX 2,771,300 loss de novo >50 genes IQ/LOF 77, RL/EL mod/sev delay, dysmorph 3+, velocardiofacial syndrome
SK0091-004 F MPX 4,281,262 gain paternal >50 genes IQ/LOF 92, RL/EL average/mod delay, RB3+, dysmorph 0, placental insufficiency
SK0297-003 M SPX-MZ 4,281,262 gain de novo >50 genes IQ/LOF 74, language average; RB3+, dysmorph 2+, seizures, MZ twin (discordant for ASD)
SK0323-003 M MPX 743,100 gain unknown 7 genes IQ/LOQ 43, language sev delay, RB4+, dysmorph N/A
13 22q13.31 SK0123-004 M MPX 601,528 gain maternal none IQ 93, language mod delay, RB4+, dysmorph 0, nonidentical triplet, Hirschsprung disease
MM0102-003 M MPX 80,380 loss maternal none IQ/LOF 60, language mild delay, dysmorph 0, weakness & hypotonia of arms
a

Probands are ordered by chromosome location. Families are grouped based on simplex (SPX), multiplex (MPX), and chromosomal abnormalities (CHR). Simplex families with affected monozygotic twins are denoted as SPX-MZ. The de novo cases also appear in Table 2 and some of the family pedigrees are shown in Figure 2 and Figure S2.

b

All recurrent and overlapping CNVs were detected by the array validated with qPCR. The breakpoints have not been accurately defined, and CNVs may be smaller or larger than noted.

c

If the CNV intersects only a single gene (suggesting that it may disrupt the gene), the term “exonic” is used, and if the CNV encompasses the entire gene, the term “whole” is used. The term “intronic” is used for CNV that overlaps noncoding parts of a single gene.

d

IQ/LOF (level of functioning) denotes average of Vineland Social, Communication and daily living scores and nonverbal IQ, when available.

e

Language (RL, receptive language; EL, expressive language) was rated as average, nonverbal, or mild, mod (moderately), or sev (severely) delayed.

f

RB (repetitive behavior) score was derived from ADI and ADOS ratings (1+, mild; 2+, moderate; 3+, severe repetitive behaviors; or 0, no repetitive behaviors).

g

Dysmorphology scores were based on anthropometric measurement abnormalities and qualitative features documented either by a clinical geneticist or a developmental pediatrician. Anomalies were reviewed by a single clinical geneticist and assigned score 0, not dysmorphic; 1+, mild; 2+, moderate; 3+, severe degree of dysmorphism. Children with known genetic syndromes received a score of 3+. N/A, not assessed for dysmorphic features.

h

Speech refers to the severity of impaired speech intelligibility, most likely resulting from oral motor apraxia (1+, mild; 2+, moderate; 3+, severe unintelligibility).

i

CNV is called by only one algorithm.

j

SK0119-003 originally entered the study with an ASD diagnosis but upon re-examination after CNV detection was assessed to be below cutoffs for ASD.