Targeted next generation sequencing for molecular diagnosis of Usher syndrome

Aparisi, María J; Aller, Elena; Fuster-García, Carla; García-García, Gema; Rodrigo, Regina; Vázquez-Manrique, Rafael P; Blanco-Kelly, Fiona; Ayuso, Carmen; Roux, Anne-Françoise; Jaijo, Teresa; Millán, José M

doi:10.1186/s13023-014-0168-7

Orphanet Journal of Rare Diseases

Table 3 Causative mutations and putative pathogenic variants identified in this study

From: Targeted next generation sequencing for molecular diagnosis of Usher syndrome

Patient	Clinical type	Gene	Exon	Nucleotide variant	Protein variant	Reference	Segregation analysis
Patients with two pathogenic mutations in the same gene
RP-807	USH2	MYO7A	40	c.5516 T > C	p.Leu1839Pro	Novel. UV3	Yes
RP-807	USH2	MYO7A	27	c.3503G > A	p.Arg1168Gln	Novel. UV3
RP-808^¶	USH1	CDH23	47	c.6059-9G > A	---	von Brederlow et al., (2002) [40]	No
RP-808^¶	USH1	CDH23	10	c.871G > A	p.Gly291Arg	Novel. UV3
RP-890	USH3	USH2A	26	c.5278delG	p.Asp1760Metfs*10	Garcia-Garcia et al., (2011) [41]	No
RP-890	USH3	USH2A	26	c.5278delG	p.Asp1760Metfs*10	Garcia-Garcia et al., (2011) [41]
RP-1182	USH1	PCDH15	22_23	Duplication exons 22_23	---	Novel. UV4	No
RP-1182	USH1	PCDH15	22_23	Duplication exons 22_23	---	Novel. UV4
RP-1183	USH1	CDH23	26	c.3016G > A	p.Glu1006Lys	Schultz et al., (2011) [42]	No
RP-1183	USH1	CDH23	26	c.3016G > A	p.Glu1006Lys	Schultz et al., (2011) [42]
RP-1234	USH1	MYO7A	43	c.5884delTTCT	*p.Phe1962Leufs7**	Novel. UV4	Yes
RP-1234	USH1	MYO7A	43	c.5884delTTCT	*p.Phe1962Leufs7**	Novel. UV4
RP-1237	USH1	CDH23	46	c.6049G > A	p.Gly2017Ser	Roux et al., (2006) [43]	No
RP-1237	USH1	CDH23	46	c.6049G > A	p.Gly2017Ser	Roux et al., (2006) [43]
RP-1374^¶	USH1	PCDH15	2	c.7C > T	p.Arg3*	Ahmed et al., (2001) [44]	Yes
RP-1374^¶	USH1	PCDH15	27	c.3717 + 2dupT	---	Jaijo et al., (2012) [45]
RP-1422	USH1	MYO7A	43	c.5944G > A	p.Gly1982Arg	Riazuddin et al., (2008) [46]	Yes
RP-1422	USH1	MYO7A	43	c.5944G > A	p.Gly1982Arg	Riazuddin et al., (2008) [46]
RP-1522^¶	USH2	USH2A	13	c.2299delG	p.Glu767Serfs*21	Liu et al., (1999) [47]	No
RP-1522^¶	USH2	USH2A	20	Deletion exon 20	---	Novel. UV4
RP-1551	USH1	PCDH15	27	c.3511delA	*p.Asp1172Ilefs13**	Novel. UV4	Yes
RP-1551	USH1	PCDH15	27	c.3511delA	*p.Asp1172Ilefs13**	Novel. UV4
RP-1614^¶	USH1	MYO7A	44	c.6025delG	p.Ala2009Profs*32	Bharadwaj et al., (2000) [48]	No
RP-1614^¶	USH1	MYO7A	40	c.5537C > A	p.Pro1846His	Novel. UV3
RP-1760^¶	USH2	USH2A	55	c.10888delA	*p.Gly3631Valfs43**	Novel. UV4	No
RP-1760^¶	USH2	USH2A	13	c.2296 T > C	p.Cys766Arg	Glöcke et al., (2013) [35]
RP-1781	USH2	CDH23	29	Duplication exon 29	---	Novel. UV4	No
RP-1781	USH2	CDH23	68	c.9569C > T	p.Ala3190Val	Novel. UV3
RP-1791	USH1	MYO7A	20	c.2283-1G > T	---	Roux et al., (2006) [43]	Yes
RP-1791	USH1	MYO7A	28	c.3594C > A	p.Cys1198*	Roux et al., (2011) [43]
RP-1802	USH2	USH2A	63	c.13811 + 2 T > G	---	Besnard et al., (2014) [37]	No
RP-1802	USH2	USH2A	50	c.9799 T > C	p.Cys3267Arg	Aller et al., (2006) [49]
RP-1835	USH2	USH2A	57	c.11065C > T	p.Arg3689*	Le Quesne Stabej et al., 2012 [50]	Yes
RP-1835	USH2	USH2A	22	c.4758 + 3A > G	---	Novel. UV3
RP-1864	USH2	MYO7A	6	c.494C > T	p.Thr165Met	Ouyang et al., (2005) [51]	No
RP-1864	USH2	MYO7A	6	c.494C > T	p.Thr165Met	Ouyang et al., (2005) [51]
RP-1895	USH2	GPR98	79_83	Duplication exons 79_83	---	Besnard et al., (2012) [52]	No
RP-1895	USH2	GPR98	79_83	Duplication exons 79_83	---	Besnard et al., (2012) [52]
RP-1904	USH2	GPR98	11	c.2145_2149delGTTTT	*p.Leu715Phefs6**	Novel. UV4	Yes
RP-1904	USH2	GPR98	14	c.2612delG	*p.Gly871Glufs8**	Novel. UV4
RP-1910	USH1	CDH23	60	c.8722 + 1delG	---	Oshima et al., (2008) [53]	Yes
RP-1910	USH1	CDH23	60	c.8722 + 1delG	---	Oshima et al., (2008) [53]
RP-1924	USH1	MYO7A	39	c.5392C > T	p.Gln1798*	Janecke et al., (1999) [54]	Yes
RP-1924	USH1	MYO7A	27	c.3503G > A	p.Arg1168Gln	Novel. UV3
RP-1927	USH2	USH2A	21	c.4474G > T	p.Glu1492*	Bernal et al., (2005) [55]	Yes
RP-1927	USH2	USH2A	2	c.269A > G	p.Tyr90Cys	Novel. UV3
RP-1948	USH1	MYO7A	7	C.707 T > A	p.Leu236Gln	Novel. UV3	No
RP-1948	USH1	MYO7A	42	c.5749G > T	p.Glu1917*	Jacobson et al., (2009) [56]
RP-1960	USH2	USH2A	25	c.5167G > C	p.Gly1723Arg	Novel. UV3	No
RP-1960	USH2	USH2A	7	c.1214delA	p.Asn405Ilefs*3	Bernal et al., (2005) [55]
Patients with three pathogenic mutations in two different genes
RP-1847	USH2	USH2A	62	c.12067-2A > C	---	Kaiserman et al., (2007) [57]	Yes
		USH2A	14	Deletion exon 14	---	Glöckle et al., (2013) [35]
		USH1G	2	c.805C > T	p.Arg269*	Novel. UV4
RP-1923	USH2	USH2A	62	c.12093delC	p.Tyr4031*	Garcia-Garcia et al., (2011) [41]	No
		USH2A	44	Deletion exon 44	---	Glöckle et al., (2013) [35]
		DFNB31	9	c.2234G > A	p.Arg745His	Novel. UV3
Patients with only one pathogenic mutation
RP-1455	USH1	USH2A	28	c.5666A > G	p.Asp1889Gly	Novel. UV3	No
RP-1496	USH3	GPR98	19	c.3443G > A	p.Gly1148Asp	Novel. UV3	No
RP-1741	USH2	USH2A	PE40	c.7592-2144A > G	---	Vaché et al., (2012) [58]	No
RP-1929	USH2	GPR98	58	c.11974G > A	p.Asp3992Asn	Novel. UV3	No
RP-1953	USH2	USH1C	18	c.1859G > T	p.Arg620Leu	Ouyang et al., (2002) [59]	No
Patients with pathologic mutations in different genes
RP-1426^¶	USH1	MYO7A	49	c.6610G > C	p.Ala2204Pro	Jaijo et al., (2007) [60]	Yes
RP-1426^¶	USH1	CDH23	39	c.5068-2A > T	---	Novel. UV4
RP-1950	USH2	USH2A	70	c.2299delG	p.Glu767Serfs*21	Liu et al., (1999) [47]	No
RP-1950	USH2	GPR98	70	c.14278C > T	p.Pro4760Ser	Novel. UV3

Patients previously included in the test group are marked with ¶.
Novel variants are marked in bold.
PE: Pseudoexon 40.

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ISSN: 1750-1172

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