Implications of copy number variation in people with chromosomal abnormalities: potential for greater variation in copy number state may contribute to variability of phenotype

de Smith, Adam J.; Trewick, Anne L.; Blakemore, Alexandra I. F.

doi:10.1007/s11568-010-9144-z

The HUGO Journal

Official Journal of the Human Genome Organisation

Table 3 Selection of potentially interesting CNV loci on chromosome 21 that may affect phenotypic variability in trisomy 21

From: Implications of copy number variation in people with chromosomal abnormalities: potential for greater variation in copy number state may contribute to variability of phenotype

Chromosome 21 location (hg18)	Genes	Associated disease/phenotype	Exonic	Copy number loss/gain	Frequency in CNV studies (samples with CNV/total samples in study)	Reference
26,173,965–26,174,696	APP	Alzheimer’s disease	No	Gain	1/1	McKernan et al. (2009)
26,196,591–26,196,901	APP	Alzheimer’s disease	No	Loss	1/1	Wang et al. (2008)
31,337,700–31,424,326	TIAM1	Associated with several different cancers	Exons 27–29	Gain	1/50	de Smith et al. (2007)
35,304,204–35,704,075	RUNX1	Acute megakaryoblastic leukaemia	Exon 1	Loss	6/2906	Gusev et al. (2009)
36,748,886–36,783,426	CLDN14	Hearing loss	Exons 1–3	Loss/Gain	Loss 1/50	de Smith et al. (2007)
36,748,886–36,783,426			Exons 1–3	Loss/Gain	Gain 1/50	de Smith et al. (2007)
36,785,973–36,801,336			No	Loss/Gain	Loss 6/90	Matsuzaki et al. (2009)
36,785,973–36,801,336			No	Loss/Gain	Gain 6/90	Matsuzaki et al. (2009)
34,648,096–34,829,283	KCNE1	Down syndrome critical region (DCR)	All exons of KCNE1, KCNE2, FAM165B, and exons 2–4 of RCAN1	Gain	5/1190	Zogopoulos et al. (2007)
	KCNE2
	FAM165
	BRCAN1
37,092,300–37,354,491	DSCR6	DCR	All exons of DSCR6 and exons 1–7 of HLCS	Gain	1/776	Pinto et al. (2007)
37,092,300–37,354,491	HLCS	DCR	All exons of DSCR6 and exons 1–7 of HLCS	Gain	1/776	Pinto et al. (2007)
37,489,474–37,490,172	TTC3	DCR	Exon 41	Gain	1/1	Kim et al. (2009)
40,466,951–40,489,050	DSCAM	Congenital heart defects (CHD)	Exons 12–15	Loss	9/90	Matsuzaki et al. (2009)
40,592,263–40,596,079	DSCAM	Congenital heart defects (CHD)	No	Loss	1/40	Conrad et al. (2010)
41,568,947–41,572,987	BACE2	CHD	Exon 9	Loss	1/36	Mills et al. (2006)
42,123,984–42,136,309	PRDM15	CHD	Exons 14–18	Loss	3/90	Matsuzaki et al. (2009)
42,223,189–42,226,495	C2CD2	CHD	No	Loss	45/450	Conrad et al. (2010)
46,234,806–46,234,806	COL6A1	CHD	No	Gain	1/1	Levy et al. (2007)
46,367,207–46,399,800	COL6A2	CHD	Exons 21–28	Gain	2/2026	Shaikh et al. (2009)

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