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Table 1 Clinical findings of 23 patients and CNV status

From: Importance and usage of chromosomal microarray analysis in diagnosing intellectual disability, global developmental delay, and autism; and discovering new loci for these disorders

Case

Age

Region

OMIM Phenotype (number)

Comment

Type/Size

Inheritance

Genes involved

Likely pathogenic genes

Intellectual Disability

Developmental Delay

Dysmorphic features

Other findings

1

1,5 y

chr1:849466–3,152,968

1p36 deletion syndrome (607872)

Path

Del

2.3 Mb

De novo

76

DVL1, ATAD3A, GNB1, GABRD, SKI, PEX10, PRDM16

N/A

+

prominent forehead, pointed chin, deep-set eyes, straight eyebrows

dilated cardiomyopathy, epilepsy

2

4 m

chr1:145927661–148,588,367

1q21.1 deletion syndrome (612474)

Path

Del

2.6 Mb

Mot her

31

NBPF10, HYDIN2, NBPF12, PRKAB2, FMO5, CHD1L, BCL9, ACP6, GJA5, GJA8, GPR89B, NBPF11, PPIAL4A, NBPF14, NBPF9

N/A

N/A

wide nasal bridge, bulbous nose and retrognathia.

pectoral muscle hypoplasis, radius and humerus hypoplasis, short and curved ribs

3

6 y

chr1:145607915–146,497,779

 

UCS/L-Path

Del 0.9 Mb

De novo

14

GPR89A, PDZK1, CD160, POLR3C, NBPF12

+

+

strabismus, hypertelorism

congenital hypothyroidism

4

2,5y

chr2:10266562–16,826,500

 

Path

Dup

6.5 Mb

De novo

20

ODC1, LPIN1, MYCN, NBAS,

N/A

+

prominent forehead, retrognathia, broad eyelashes, cupped ear, uplifted lobe

dysplastic aortic valve, hydrocephalus, cerebral atrophy

5

8 m

chr2:222686398–226,097,873

 

Path

Del

3.4 Mb

De novo

16

PAX3, AP1S3, MRPL44, CUL3

N/A

+

prominent forehead, hypoplastic alae nasi, epicanthal fold

 

6

14,5 y

chr6:6806969–13,794,521

 

Path

Del

6.9 Mb

De novo

46

DSP, TFAP2A, GCNT2, MAK, GCM2, EDN1, TBC1D7

+

+

dolicocephaly, facial asymmetry, open mouth, depressed nasal tip, absent ear lobe,

atrial septal defect, bilateral cleft lip

7

8,5 y

chr6:70373236–79,654,154, chr8:78808754–81,835,864

 

Path

Path

Del 9.2 Mb/Del 3 Mb

De novo

49

LMBRD1, COL9A1, RIMS1, KCNQ5, KHD3CL, MYO6,MTO1, SLC17A5, COL12A1,IMOG1

+

+

long face, wide mouth, high arched palate

potent ductus arteriosus, renal agenesis, pes equinovarus

8

4 m

chr6:151310706–170,919,482

 

Path

Del 19.6 Mb

De novo

115

SYNE1,ESR1, ARİD1B, LPA, PDE10A,T, ERMARD,TBP,

N/A

+

sunset eye sign, low set ears, pointed chin

hydrocephalus, cerebral atrophy

9

1 m

chr6:163378290–16,709,184, chr6:160713926–16,287,570, chr6:141494387–144,877,906

 

Path

UCS/L-Path

Path

Dup 3.7 Mb

Del 2.1 Mb

Del 3.3 Mb

De novo

17

8

19

PACRG, QKI, PDE10A, T, MPC1, RPS6KA2, SLC22A3, LPAL2, LPA, PLG, MAP3K4, AGPAT4, PARK2, NMBR, VTA1, GPR126, HIVEP2, AIG1, PEX3, PLAGL1, HYMAI, STX11, UTRN

N/A

+

upslanting palpebral fissures, round face

neonatal diabetus, hypotonia, deafness

10

9 y

chr14:103255460–107,285,437

 

Path

Del 4 Mb

De novo

56

TRAF3, APOPT1, RCC3, INF2, AKT1, BRF1,IGHM

+

+

long face, pointed chin, anterverted ears, epicanthal fold

11

11,5 y

chr14:99528241–107,285,437

 

Path

Dup 7.7 Mb

De novo

183

YY1, DYNC1H1, TECPR2, APOPT1, XRCC, ADSSL1, AKT1, ZBTB42, BRF1, IGHG2,

+

+

facial asymmetry, downslanting palpebral fissures, prognathism, macrocephaly

strabismus, ptosis,

12

5 y

chr15:22770421–30,295,864

 

Path

Dup 7.5 Mb

De novo

131

MKRN3, MAGEL2, NDN, SNRPN,UBE3A,GABRB3,OCA2, HER2

+

+

hypertelorism, depressed nasal bridge,

unilateral deafness, autism spectrum disorder

13

6 y

chr15:22770421–23,276,605

 

UCS/L-Path

Del 0.5 Mb

De novo

7

NIPA1, NIPA2, CYFIP1, TUBGCP5

+

+

hypertelorism, short palpebral fissures, blepharophimosis

corpus callosum agenesis, hypothyroidism

14

15 y

chr16:89342189–89,552,394

KBG Syndrome (148050)

Path

Del

0.2 Mb

De novo

2

ANKRD11

+

+

long and triangular face structure, large, protruding ears

degenerative myopia

15

13,5 y

chr18:136226–6,992,327

 

Path

Del 6.8 Mb

De novo

41

SMCHD1, LPIN2, TGIF1, LAMA1

+

+

hypertelorism, broad nasal bridge

obesity

16

10 y

chr18:59720983–78,014,123

 

Path

Del 18.2 Mb

De novo

72

PIGN,TNFRSF11A, BCL2, KDSR, SERPINB7, RTTN, CYB5A, TSHZ1, CTDP1, XNL4A

+

+

frontal bossing, deep set eyes, depressed nasal bridge

sensorineural deafness, strabismus

17

3 y

chr18:67847004–70,771,041

 

UCS/L-Path

Del 2.9 Mb

De novo

6

RTTN, SOCS6, CBLN2, NETO1

N/A

hypertelorism, broad nasal bridge

autism spectrum disorder

18

13 y

chr18:65852206–76,107,497

 

Path

Del 10 Mb

De novo

32

RTTN, SOCS6, CBLN2, NETO1, CYB5A, TSHXZ1, GALR1

+

+

frontal bossing, deep set eyes, protruding ears

feeding difficulties

19

9 m

chr19:11284538–13,555,660

 

UCS/L-Path

Del 2.2 Mb

De novo

78

KANK2, DOCK6, EPOR, PRKCSH, ACP5, MAN2B1, RNASEH2A, KLF1, CALR, NFIX, LYL1, NACC1, CACNA1A

N/A

+

deep set eyes, micrognatia

hypotonia

20

5 y

chr22:18917030–21,465,662

DiGeorge syndrome (188400)

Path

Del 2.5 Mb

De novo

66

PRODH, SLC25A, CDC45, GPİBB, TBX1, COMT, TANGO2, RTN4R, CARF2, PI4KA, SERPIND1,

+

+

hypertelorism, blunted nose, high arched palate,

tetralogy of fallot

21

5 y

chr22:19004771–21,443,283

22q11.2 microdup lication syndrome (608363)

Path

Dup 2.4 Mb

Father

63

SLC25A, CDC45, GPİBB, TBX1, COMT, TANGO2, RTN4R, CARF2, PI4KA, SERPIND1,

+

+

frontal bossing, synophrys, pytosis,

strabismus,

22

11,5 y

chr22:19077926–21,804,886

22q11.2 microdup lication syndrome (608363)

Path

Dup 2.7 Mb

De novo

65

SLC25A, CDC45, GPİBB, TBX1, COMT, TANGO2, RTN4R, CARF2, PI4KA, SERPIND1,

no dysmorphic features

loss of cognitive functioning

23

11 y

chr22:18917030–21,421,425

22q11.2 microdup lication syndrome (608363)

Path

Hom dup 2.5 Mb

Mother and father

66

PRODH, SLC25A, CDC45, GPİBB, TBX1, COMT, TANGO2, RTN4R, CARF2, PI4KA, SERPIND1,

+

+

Round face, broad nasal bridge, hypertelorism, downslanting palpebral fissures, long philtrum, overfolded helix

patent ductus arteriosus, hypoplasia of clivus