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Table 2 Variants defined as “true”

From: Copy number variations in candidate genomic regions confirm genetic heterogeneity and parental bias in Hirschsprung disease

Chromosomal region (chr:start-end)

candidate region

aberrat. Type

# probes

reported on DGV

reported on decipher (# individuals)

confirmation on available replicate/s

selected for validation

sample(s) and variant # (N) b

genes

1:146638075–147,824,207

genome (1q21)

loss

4

N

Y (1q21.1 recurrent microdel)

confirmed

Y

HSCR019, #21 (1)

PRKAB2, PDIA3P, FMO5, CHD1L, BCL9, ACP6, GJA5, GJA8, GPR89B, GPR89C, PDZK1P1, LOC200030, NBPF11

4:41746863–41,751,291

PHOX2B

loss

11

N

N

confirmed

Y

HSCR403, #69 (1)

PHOX2B

5:69288477–70,309,855

genome (5q13)

gain

3

Y (freq ≥5%)

N

not excluded

N

HSCR016, #18 (1)

SERF1A, SMN2, NAIP, SMA4, GTF2H2B, LOC441081, DQ591060

7:84217007–84,225,649

SEMA3A/ SEMA3D

loss

4

Y (freq < 1%)

N

Y

HSCR005, #5 (1)

(SEMA3A; SEMA3D)(SEMA3A; SEMA3D)

8:32597644–32,598,929

NRG1

loss

3

N

N

Y

HSCR045, #29 (1)

NRG1

9:109273643–109,275,694

9q31

loss

2

N

N

Y

HSCR043, #27 (1)

(TMEM38B; ZNF462)(TMEM38B; ZNF462)

9:109336464–109,348,467

9q31

gain

6

N

N

Y

HSCR018, #20 (1)

(TMEM38B; ZNF462)(TMEM38B; ZNF462)

9:110381888–110,401,999

9q31

gain

9

N

N

confirmed

Y

HSCR000, #1 (1)

(KLF4; ACTL7B)(KLF4; ACTL7B)

9:112078131–112,089,193

9q31

loss

5

N

N

confirmed

Y

HSCR195, #42 (1)

EPB41L4B

9:113025039–113,029,430

9q31

loss

2

Y (freq ≥5%)

Y (1)

N

HSCR415, #77 (1)

(TXN; TXNDC8)(TXN; TXNDC8)

9:43659247–43,659,512

genome (9p11)

loss (3) / gain (1)

2

Y (freq ≥5%)

N

confirmed

N

HSCR162, #38; HSCR403, #70; HSCR421, #78; HSCR426, #80 (4)

(SPATA31A6; CNTNAP3B)(SPATA31A6; CNTNAP3B)

15:20848460–22,432,687

genome (15q11)

loss (4) / gain (6)

5

Y (freq ≥5%)

N

not excluded

N

HSCR010, #13; HSCR033, #22; HSCR064, #33; HSCR160, #181; HSCR181, #39; HSCR231, #45; HSCR335, #54; HSCR382, #67; HSCR409, #74; HSCR414, #76 (10)

NBEAP1, POTEB, CXADRP2, OR4M2, OR4N4, OR4N3P

15:58257674–59,009,890

genome (15q21)

gain

2

N

N

Y

HSCR146, #35 (1)

ALDH1A2, AQP9, LIPC, ADAM10, HSP90AB4P

16:82200334–82,202,467

16q23.3

gain

2

N

N

Y

HSCR217, #43 (1)

MPHOSPH6

19:31954093–31,966,036

19q12

loss

5

N

N

not evaluable

Y

HSCR481, #82 (1)

(TSHZ3; THEG5)(TSHZ3; THEG5)

22:18661724–18,920,001

22q11.2

gain

7

Y (freq ≥5%)

N

not evaluable

N

HSCR58, #32 (1)

AK302545, BC112340, DGCR6, PRODH

22:20345868–20,499,789

22q11.2

gain

4

Y (freq ≥5%)

N

not excluded

N

HSCR335, #56 (1)

TMEM191B, RIMBP3

22:21494163–21,704,972a

22q11.2

gain

5

N

N

confirmed

N

HSCR403, #72 (1)c

GGT2, POM121L7

22:22417683–23,228,483

22q11.2

loss

15

Y (freq ≥5%)

N

N

HSCR014, #17 (1)

VPREB1, ZNF280B, ZNF280A, PRAME, LOC648691, GGTLC2

22:22781091–23,228,483

22q11.2

loss

8

Y (freq ≥5%)

N

N

HSCR036, #23; HSCR183, #41 (2)

ZNF280B, ZNF280A, PRAME, LOC648691, GGTLC2

22:23056562–23,228,483

22q11.2

loss

3

Y (freq ≥5%)

N

confirmed

N

HSCR403, #73 (1)

(GGTLC2; IGLL5)

22:25672585–25,892,401

22q11.2

loss (1) / gain (2)

5

Y (freq ≥5%)

Y (3)

not excluded

N

HSCR016, #19; HSCR228, #44; HSCR421, #79 (3)

LRP5L, CRYBB2P1

  1. Variants have been defined as “true” when either reported on DGV, confirmed on a second array replicate, or validated with a different approach (see follow up in Table 4)
  2. Genes between brackets are those flanking the CNV when no gene is affected by the aberration
  3. not selected for validation because initially considered unlikely at the visual inspection
  4. b the code for the sample in which the CNVs has been detected is reported, together with the variant call # as indicated in the Additional file 1 and, among brackets, the number of times the CNVs has been detected in the 59 samples
  5. c this CNV was detected also in other two samples, for which neither replication nor validation through a different approach were carried out. For this reason, these are not included in the count of the true variants