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Table 3 Variants selected for validation, results and corresponding samples

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

variant callSample IDgenderChromosomal regionAberr. typeN. probessize (bp)validation methodvalidatedparental originRET mutationsRET HSCR risk haplotypeHSCR lenghtsyndromiclocusaffected genes (or flanking genes if no gene maps into the region)
(chr:start-end)
1HSCR000F9:110381888–110,401,999gain920,111qPCRYcMinterstitial deletionunknownTCAno9q31(KLF4; ACTL7B)
5HSCR005M7:84217007–84,225,649loss48642qPCRYdMnohomoz.SnoSEMA3A/3D(SEMA3A; SEMA3D)
610:43679892–43,680,816loss5924PCRN
8HSCR006M10:43679612–43,680,816loss61204PCRNnohomoz.Lno
20bHSCR018M9:109336464–109,348,467gain612,003qPCRYMp.P399LwtLno9q31(TMEM38B; ZNF462)
21HSCR019F1:146638075–147,824,207loss42,585,968qPCRYcMnohomoz.SVSD + mandibular hypoplasia1q21PRKAB2, PDIA3P, FMO5, CHD1L, BCL9, ACP6, GJA5, GJA8, GPR89B, GPR89C, PDZK1P1, LOC200030, NBPF11
27bHSCR043M9:109273643–109,275,694loss22051qPCRYMp.K821Qhomoz.Sno9q31(TMEM38B; ZNF462)
28bHSCR045M7:84594683–84,607,065eloss612,382qPCRNn.a.nounknownLno
29b8:32597644–32,598,929loss31285qPCRYNRG1NRG1
3010:43679612–43,680,816loss61204PCRN
35HSCR146M15:58257674–59,009,890gain2752,216aCGH 8x60KYMnohomoz.Sno15q21ALDH1A2, AQP9, LIPC, ADAM10, HSP90AB4P
3619:30888070–30,891,329gain23259qPCRN
42HSCR195M9:112078131–112,089,193loss511,062qPCRnot conclusive cn.a.p.E610Khomoz.Sno9q31EPB41L4B
43HSCR217M16:82200334–82,202,467gain22133qPCRYde novop.R813Lhomoz.Sno16q23MPHOSPH6
60HSCR349F10:43573685–43,574,005egain2320qPCRNnohomoz.?no
61HSCR374F10:43473690–43,474,033egain4343qPCRNnohomoz.Lno
69cHSCR403F4:41746863–41,751,291loss114428qPCRYMnohomoz.SnoPHOX2BPHOX2B
82HSCR481F19:31954093–31,966,036loss511,943qPCRYn.a.nounknown?Down s.19q12(TSHZ3; THEG5)
72aHSCR403F22:21494163–21,704,972egain5210,809 - cnohomoz.Sno22q11GGT2, POM121L7
  1. CNVs reported in bold are those confirmed to be true
  2. a the CNVs reported in the last line was not actually selected for validation and not analyzed for parental origin because considered unlikely at the visual inspection, but lately found confirmed on two replicates and thus included in the present table
  3. b aberration not detected by the software call, but identified by visual inspection
  4. c confirmed on an aCGH replicate
  5. d reported on DGV (freq< 1%)
  6. e unlikely at the visual inspection
  7. f compatible with 1q21.1 recurrent microdeletion
  8. n.a. parents not available
  9. VSD VentricularSeptalDefect