Supplementary Table 1



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Supplementary Table 1 Pathogenic and potentially pathogenic CNVs detected by Affymetrix 262K, Illumina 317K and 370K arrays


13





ID

Platform

Gain/ Loss

Chr

Starting

SNP


Ending

SNP


Size in bp

Inheritance

Ensembl

genes





Known microdeletion syndromes Syndrome

CR30

262K

loss

2q22.3

rs1517914

rs2381683

1339008

de novo

1

Mowat-Wilson syndrome

BC373

370K

loss

2q37.3

rs3935423

rs7577243

1530000

n/a

0

2q37.2 monosomy

BC43

317K

loss

17p11.2

rs9905272

rs9909852

3530000

de novo

7

Smith-Magenis syndrome

CR295

262K

loss

18q21.1-q21.31

rs1383531

rs502430

6300000

n/a

3

Pitt-Hopkins syndrome

BC300

317K

loss

22q11.2

rs2543958

rs140392

2530000

de novo

7

DiGeorge syndrome

CR3531

262K

loss

Xp22.31

rs6654821

rs17300660

1550000

maternal

1

X-linked ichthyosis

Recently described CNVs Syndrome (Phenotype present case)

CR103

262K

gain

3q29

rs9883087

rs1431501

1429695

paternal

0

3q29 microduplication syndrome

BC65

317K

loss

16p11.2

rs8054172

rs7202714

522140

n/a

1

16p11.2 microdeletion syndrome (Mild mental retardation, speech delay. Short palpebral fissures, dysplastic ears, retrognathia, unilateral simian crease, broad neck, sloping shoulders)

BC93

317K

loss

16p11.2

rs8054172

rs7202714

522140

de novo

1

16p11.2 microdeletion syndrome (Mild mental retardation. Short palpebral fissures, mild malaar hypoplasia, simple external ears, retrognathia, broad neck, sloping shoulders)

BC235

370K

loss

16p11.2

rs28455095

rs7202714

554000

paternal

1

16p11.2 microdeletion syndrome (Mild mental retardation, speech delay. Mild malar hypoplasia)

BC245

370K

gain

16p13.11

rs7404843

rs402522

820000

paternal

2

16p13.11 recurrent microduplication syndrome

BC260

370K

gain

16p13.11

rs2941256

rs6498606

1330000

paternal

2

16p13.11recurrent microduplication syndrome (Prominent parietal bones, narrow bitemporal, small and short chin, simple helices, narrow external ears, short upper arms and legs, severe lissencephaly, corpus callosum agnesia)

BC259

370K

gain

22q11.2

rs2543958

rs140391

2530000

maternal

7

22q11 duplication syndrome (Bilateral ptosis, brachycephaly, low set ears, hypertelorism, downslant, bulbous nasal tip, broad nasal bridge, overriding toes, syndactyly, hypospadia, cryptorchism.

BC104

317K

loss

22q11.22-q11.23

rs4481090

rs131690

383630

n/a

1

22q11.2 distal deletion syndrome

Potentially pathogenic CNVs Phenotype

CR19

262K

Gain

1p32.3

rs3013747

rs2793669

2666889

de novo

26

Arched and thick eyebrows, long eyelashes, strabismus, auricular pits, prominent ear helix, cleft palate, cleft upper lip, fetal finger pads, segmentation defects of spine

CR550

262K

loss

1p21.1-p13.3

rs6695016

rs2797520

5160000

n/a

50

Mental retardation, psychotic behavior, sleep disorders, seizures. Blepharophimosis, bulbous nasal tip, thick upper and lower lip, narrow palate, low-pitched voice, deafness, loose skin in neck, joint stiffness,

CR304

262K

loss

1q32.3

rs3768547

rs320391

854000

n/a

9

Mental retardation, autism. Congenital cataract.

BC20

317K

gain

1q44

rs4564164

rs7548751

187220

n/a

9

Mental retardation

BC9

317K

gain

2p25.3

rs11211657

rs4853841

434730

paternal

3

Bitemporal narrowing, small palpebral fissures, broad nasal bridge, small ears, narrow inner ear, small hands, short arms.

BC324

317K

loss

2q11.2-q13

rs1110947

rs832665

6610000

de novo

(pat)


25

Mental retardation

BC322

317K

loss

2q24.2

rs1896270

rs7423892

670910

de novo

(pat)


4

Mental retardation, behavioral problems. Almond shaped palpebral fissures, slant down palpebral fissures, hypotelorism, simple ears, bound tongue, long philtrum, full cheeks, abnormal palmar creases, clinodactlyly, short phalanges, tapering fingers, joint laxity, over-riding toes, sandal gap of toes, short toes, tall stature, generalized obesity.

BC249

370K

loss

2q31.1

rs2676145

rs10497422

3060000

de novo

(pat)


16

Mental retardation. Ear pits, ptosis, mild downslant, long eyelashes, small mouth, abnormal inner ear on right side, mild hypospadia.

CR20

262K

gain

2q35

rs1979028

rs1992235

823000

maternal

4

Mental retardation

BC30

317K

loss

3p25.1-p24.3

rs4685442

rs2638134

5050000

de novo

8

Mental retardation. Large nose, long nasal septum, arachnodactyly, clinodactyly, over-riding toes, short toes, pectus excavatum.

BC103

317K

gain

loss


3p26.3-p26.1

3p26.1


rs9681213

rs11712496



rs2570006

rs7621754



5080000

90080


de novo

de novo

11

1


Mild mental retardation, autism. Low weight

BC17

317K

gain

3q13.13

rs12637387

rs9861358

400060

n/a

3

Mental retardation

CR296

262K

loss

5p12

rs2548343

rs12655990

2250000

paternal

12

Large fontanelles, prominent ear helix, small and absent nails, lung hypoplasia.

BC24

317K

gain

5p12-p11

rs11743392

rs10941803

733510

n/a

1

Mental retardation

BC332

317K

loss

loss


loss

loss


loss

loss


5q14.3

5q14.3


5q14.3

5q14.3


5q33.3

5q33.3


rs4920853

rs16902356

rs7715840

rs357509


rs6556381

rs6884239



rs1862233

rs10051603

rs1062035

rs304151


rs9637861

rs3846687



59000

83000


320000

638000


129940

158600


de novo

de novo

de novo

de novo

de novo

de novo

0

1

3



2

1

2



Mental retardation, sleep disorder, grand-mal seizure. Sensorineural deafness, epicanthic folds, severe visual loss, strabismus, VSD, trachea/laryngeal malacie, general hypotonia.

CR507

262K

gain

6q14.1

rs3828761

rs17783795

989760

maternal

1

Mild mental retardation. Temporal narrowing, plagiocephaly, small ears, earpit, high and narrow arched palate, sacral dimple, café au lait spot.

CR78

262K

loss

6q16.3

rs9376514

rs7754315

333350

paternal

1

Mental retardation

BC313

317K

loss

6q25.3

rs2181068

rs9365947

2660000

n/a

6

Mental retardation. Plagiocephaly, deep-set eyes, up-slant palpebral fissures, small ears, deep palmar creases, clubbed nails, wide-spaced nipples, ASD, lung cysts.

CR14

262K

loss

7q21.11-q21.3

rs2373207

rs17166393

8291932

de novo

(pat)


51

Mental retardation, anxiety disorder, autism.

Small palpebral fissures, simply formed low set ears, abnormal palmar creases, scoliosis, long halluxes, proximally implanted thumbs.



BC333

370K

gain

8q24.22

rs4736413

rs6599566

12870000

maternal

108

Mental retardation, behavioral problems.

CR11

262K

gain

9p21.3-p21.3

rs4618784

rs7389761

164000

paternal

1

Mental retardation.

CR66

262K

loss

10p12.31-p12.33

rs11254467

rs11012683

4396349

de novo

(pat)


18

Blepharophimosis, ptosis, epicanthus, telecanthus, VSD.

BC78

317K

loss

10p12.1-p11.23

rs2998285

rs754865

990454

n/a

5

Mental retardation, autism. Flat occiput, spasticity, strabismus, small ears, coarse hair, short metacarpals, patent ductus arteriosus, scoliosis.

BC63&64

317K

loss

11centr

rs11227836

rs688740

157440

paternal

6

Mild mental retardation. Microcephaly, oligodontia, velopharyngeal insufficiency, abnormal corpus callosum.

BC232

370K

loss

13q12.2

rs9512755

rs881084

188000

n/a

2

Mental retardation.

Treacher-collins like.



BC180

317K

loss

13q12.3

rs1023166

rs7332693

1250000

n/a

7

Mental retardation, hyperactivity. Microcephaly, hypotelorism, large ears, columella below alae nasi, thin nasal bridge, coarse hair, syndactyly of 2-3 toes, patchy depigmentation of skin, pectus excavatum.

BC37

317K

loss

13q34

rs4293272

rs3813131

2590027

n/a

26

Mental retardation.

CR566

262K

loss

15q13.1-q13.2

rs4966231

rs8028345

1340000

maternal

4

Mental retardation, febrile convulsion. Flat occiput, hypotonia, heterotopia, hypertelorism, down-slant palpebral fissures, ptosis, large ears and era lobule, micrognathia, loose skin in neck, short neck, deep palmar creases, abnormal plantar creases, cavernous haemangioma, eczema, dry skin, constipation, feeding problems, pectus excavatum, spina bifida occulta, short stature, thin.

CR506

262K

gain

16p13.2

rs1273350

rs30781

203250

n/a

5

Percepto-motor delay without mental retardation, hypotonia. Down-slant palpebral fissures, flat nasal bridge, large ear lobules, prominent forehead, long toes, syndactyly of toes, patchy pigment of skin, feeding problems, pectus excavatum, recurrent infections.

BC302

317K

gain

16p13.2

rs7186634

rs10500367

236720

paternal

1

Mental retardation.

CR569

262K

loss

16q22.2-q22.3

rs9302640

rs3743977

379140

de novo

(pat)


1

Mental retardation.

BC335

370K

gain

16q23.3

rs1056629

rs4558403

1480000

maternal

2

Mild mental retardation. Congenital nystagmus, VSD, frontal bossing, high frontal hairline, sparse hair, simple ears, deep-set eyes upslant, high and narrow palate, clinodactyly V left, fetal finger pads of fingers and toes.

CR93

262K

gain

17q12

rs17836884

rs4795952

989950

paternal

8

Mental retardation. Blepharophimosis, deep-set eyes, hypertelorism, short palpebral fissures, strabismus, hypoplastic ear lobule, posteriorly rotated ears, prominent anti-helix, choanal atresia, overhanging nasal tip, short nasal septum, high and narrow palate, microstomia, short neck, micrognathia, cavernous haemangioma, flexion deformity of hip, post-axial polydactyly of fingers, short stature.

BC101

317K

gain

17q25.3

rs7219745

rs6502043

2203063

de novo

67

Severe mental retardation. Prominent forehead, small eyes, broad nasal tip, clinodactyly V, abnormal palmar crease right.

CR39

262K

loss

18p11.31-p11.23

rs625106

rs12454998

1226479

maternal

3

Mental retardation. Assymetric ears, plagiocephaly.

CR295

262K

loss

18q21.2-q21.31

rs1383531

rs502430

6300000

n/a

18

Mental retardation, tonic seizures, speech delay. Hypertelorism, myopia, up-slant palpebral fissures, deafness, flat nasal bridge, flat nose, macrostomia, wide-spaced teeth, prominent mandible, round face, clinodactyly, small hands, over-riding toes including clinodactyly, small feet, constipation, scoliosis, short stature, primary amenorrhea, quadriplegia.

BC336

370K

loss

loss


18q21.31

18q21.32-q21.33



rs4940582

rs1877055



rs4940754

rs588677


877000

2600000


n/a


3

9


Mental retardation. Obesity, valvular pulmonary stenosis.

BC320

317K

loss

18q22.1

rs4334403

rs9964774

1320000

maternal

1

Mental retardation.

BC362

370K

gain

19q13.41-q13.42

rs3810115

rs8111919

728000

maternal

26

Mental retardation, seizures, hypotonia. Deep-set eyes, flat nasal bridge, gum hypertrophy, cleft and high palate, high frontal hairline, dolichocephaly, abnormal palmar creases, cryptorchid testes, hypospadias, diastasis recti, joint laxity.

CR273

262K

gain

20p11.21

rs2387578

rs446649

370870

maternal

5

Mental retardation.

BC247

370K

loss

21q22.3

rs2839110

rs2839193

159000

paternal

7

Mental retardation.

CR63

262K

gain

22q11.2

rs361689

rs5762401

718540

paternal

20

Mental retardation, seizures. Oligodontia, posteriorly rotated ears.

CR69

262K

loss

22q13.1

rs3021274

rs11089991

355205

de novo

(pat)


3

Mental retardation, autism. Long philtrum, thick lower lip, wide-spaced teeth, diffuse depigmentation of skin, dolichocephaly, tall stature.

CR100

262K

gain

Xp22.12

rs5955562

rs16981283

349540

maternal

2

Mental retardation.

BC258

370K

loss

Xp22.1

rs5925675

rs5970987

223000

maternal

1

Mental retardation.

CR533

262K

gain

Xp22.31

rs6654821

rs17300660

1550000

maternal

4

Mental retardation. Up-slant palpebral fissures, non-specific vision impairment, large tongue, open mouth appearance, wide-spaced teeth, nasal speech, coarse facial features.

CR306

262K

gain

Xq21.2

rs2887392

rs2369242

325410

de novo

(mat)


1

Mental retardation.

CR177

262K

gain

Xq28

rs732572

rs5983907

606191

maternal

9

Telecanthus, epicanthic folds, hypotelorism, infra-orbital creases, up-slant and short palpebral fissures, small nose, wide nasal bridge, flat face, metopic ridge, narrow and sloping forehead, abnormal palmar creases, fetal finger pads, proximal placement of thumbs, single palmar crease, early closure of fontanelles, trigonocephaly, wide-spaced nipples.

BC319

317K

loss
gain

1p31.1-p22.2
5q11.2

rs1926256
rs169382

rs2991701
rs4865815

18580000
167000

de novo

(mat)


maternal


67
1

Severe mental retardation. Assymetric face, microtia, macrostomia, downslant, high palate, croede teeth, pectus excavatum, scoliosis, fetal finger pads, extreme hyperlaxity of joints, deformaties of feet.

CR416

262K

gain

gain


13q12.11

20p13-p12.1



rs4400902

rs17685809



rs9506958

rs6043648



4410000

15890000


de novo

de novo

25

111


Mild mental retardation, psychiatric disorder.

BC153

317K

gain

loss


15q26.3

21q22.3


rs8030950

rs2839102



rs7183226

rs2839378



348590

583730


paternal

maternal


5

13


Mental retardation. Hypertelorism, strabismus, cleft upper lip, cleft palate, prominent forehead.

CR174

262K

loss

gain


Xp22.32-p22.31

Xq27.3-q28



rs5916033

rs728395


rs16984818

rs6641352



2696475

6306898


maternal

maternal


6


Mental retardation.

1, male; n/a, DNA of parents not available; pat, CNV in paternal chromosome; mat, CNV in maternal chromosome


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