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Table 1 Disease-causing CNVs identified in the presented patient group listed by chromosome

From: Clinical evaluation of rare copy number variations identified by chromosomal microarray in a Hungarian neurodevelopmental disorder patient cohort

Copy Number Variation

GRCh

Patient

Size (Kb)

Class.

Dosage Sensitivity#

Candidate genes (number of protein coding genes within CNV)

Syndrome/disorder

1p36.33p36.22(820001_9348000)x1

37

SEG2_52

8528.0

P

HI: 3; TS: 2

KLH17, HES4, AGRN, VWA1, MMP23B, CDC2L2, GABRD, SKI, PLCH2, CAMTA1 (HI: 3, TS: 0) (111)

1p36 microdeletion [OMIM#607,872, (44)]

2q23.1(149060704_149313819)x3

37

SEG2_44

253.1

LP

-

MBD5 (HI: 3, TS: 1) (1)

2q23.1 microduplication (49)

4q32.2q35.2(161869551_190790881)x1

37

SEG2_70

28921.3

P

-

CLCN3, HAND2, TEN3 (84)

4q32.2q35.2 deletion (51)

8p23.1(7117851_11969155)x1

37

SEG2_50

4851.3

P

HI: 3, TS: 2

GATA4 (48)

8p23.1 microdeletion (ORPHA:251,071)

14q11.2(21414942_21966929)x1

37

SEG2_49

552.0

LP

HI: 2, TS: 0

CHD8, SUPT16H (19)

14q11.2 microdeletion (20)

14q11.2(21438704_22101647)x1

37

SEG2_68

662.9

LP

HI: 2, TS: 0

CHD8, SUPT16H (21)

14q11.2 microdeletion (20)

14q11.2(21511829_22131455)x1

37

SEG2_89

619.6

LP

HI: 2, TS: 0

CHD8, SUPT16H (18)

14q11.2 microdeletion (20)

15q11.2q13.1(22765628_29060493)x1

37

SEG2_33

6294.9

P

HI: 3; TS: 3

UBE3A, SNRPN (22)

Angelman syndrome (OMIM#105,830)

16p13.3(3263725_4309863)x1

38

SEG2_5

1046.1

P

HI: 3; TS: 1

CREBBP (20)

16p13.3 microdeletion (OMIM#610,543)

16p12.2(21953152_22480514)x3

37

SEG2_32

527.4

LP

HI: 2, TS: 0

UQCRC2, EEF2K, CDR2 (7)

16p12.2 microduplication (39)

16p11.2(28824802_29040571)x1

37

SEG2_53

215.8

P

HI: 3; TS: 1

SH2B1 (9)

Distal 16p11.2 microdeletion (OMIM#613,444)

16p11.2(29620689_30190568)x3

37

SEG2_17

569.9

P

HI: 3; TS: 3

KIF22, MAZ, PRRT2, KCTD13, TBX6, MAPK3 (26)

16p11.2 microduplication (OMIM#614,671)

16p11.2(29624765_30199351)x3

37

SEG2_26

574.6

P

HI: 3; TS: 3

KIF22, MAZ, PRRT2, KCTD13, TBX6, MAPK3 (27)

16p11.2 microduplication (OMIM#614,671)

16p11.2(29624765_30199351)x3

37

SEG2_27

574.6

P

HI: 3; TS: 3

KIF22, MAZ, PRRT2, KCTD13, TBX6, MAPK3 (27)

16p11.2 microduplication (OMIM#614,671)

16p11.2(29656684_30190568)x1

37

SEG2_39

533.9

P

HI: 3; TS: 3

KIF22, MAZ, PRRT2, KCTD13, TBX6, MAPK3 (26)

Proximal 16p11.2 microdeletion (OMIM#611,913)

16q12.2q21(56340118_60294492)x1

37

SEG2_85

3954.4

LP

-

GNAO1 (HS:1, TS: 0) (55)

16q12.2q21 microdeletion (40)

16q22.2q23.3(72155844_82148404)x1

37

SEG2_37

9992.6

LP

-

WWOX, MAF, CMIP, CNTNAP4 (49)

16q22.2q23.3 microdeletion [OMIM#614,541, (41)]

17p13.3(7_2084490)x1

37

SEG2_30

2084.5

LP

-

CRK, YWHAE (34)

17p13.3 microdeletion syndrome (42,43)

17p11.2(16727490_20433502)x1

37

SEG2_59

3706.0

P

HI: 3; TS: 3

RAI1, FLCN (49)

Smith-Magenis syndrome (OMIM#182,290)

17q12(34835983_36243365)x3

37

SEG2_87

1407.4

P

HI: 3; TS: 3

HNF1B (15)

17q12 microduplication (OMIM#614,526)

18q22.1q23(69071896_80256240)x1

38

SEG2_21

11184.3

P

-

RTTN, SOCS6, CYB5A, ZNF407, TSHZ1 (33)

18q22.1q23 microdeletion (OMIM#601,808)

19p13.3(753219_1477508)x3

37

SEG2_15

724.3

LP

-

STK11, APC2

19p13.3 microduplication (ORPHA:447,980)

19q13.43(57243585_58445449)x3

38

SEG2_82*

1201.9

P

-

RPS5 (50)

19q13.43 microduplication (45,46)

22q11.21q11.22(21460640_22962962)x1

37

SEG2_80

1502.3

P

HI: 3; TS: 3

MAPK1 (19)

22q11.21q11.22 microdeletion (47)

22q11.21q11.22(21934268_22336871)x3

37

SEG2_7

402.6

P

HI: 3; TS: 3

MAPK1 (9)

22q11.2 microduplication [OMIM#608,363, (48)]

22q13.33(49368551_50759338)x1

38

SEG2_82*

1390.8

P

-

SHANK3 (HI: 3, TS: 0) (34)

Phelan-McDermid syndrome (OMIM#606,232)

22q13.33(50971316_51224252)x3

37

SEG2_12

252.9

LP

-

SHANK3 (HI: 3, TS: 0) (9)

22q13 microduplication (OMIM#615,538)

Xp22.33(566719_807207)x3

37

SEG2_61

240.5

P

-

SHOX (1)

Léri-Weill dyschondrosteosis (OMIM#127,300), idiopathic short stature (OMIM#300,582)

Xp22.31(6537108_8167604)x0

37

SEG2_62

1630.5

86819.2

P

HI: 3; TS: 40

STS (5)

X-linked ichtyosis (OMIM#308,100)

Xq22.1q23(101597527_111626047)x1

38

SEG2_78

10028.5

P

-

PLP1 (HI: 3, TS: 3) (79)

Xq22 microdeletion (50)

  1. *: Patient with more than one disease-causing copy number variation (CNV); Kb: kilobase; Class.: classification; P: pathogenic; LP: likely pathogenic; OMIM: Online Mendelian Inheritance in Man;
  2. #Based on ClinGen Dosage Sensitivity Curations (https://clinicalgenome.org). HI: haploinsufficiency; TS: triplosensitivity;
  3. 3: Sufficient Evidence
  4. 2: Emerging Evidence
  5. 1: Little Evidence
  6. 0: No evidence
  7. 40: Dosage Sensitivity Unlikely
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Molecular Cytogenetics

ISSN: 1755-8166