Genetic investigation of 211 Chinese families expands the mutational and phenotypical spectra of hereditary retinopathy genes through targeted sequencing technology

Bai, Zhouxian; Xie, Yanchuan; Liu, Lina; Shao, Jingzhi; Liu, Yuying; Kong, Xiangdong

doi:10.1186/s12920-021-00935-w

Table 2 General situation of families with likely pathogenic mutations or related mutations of undetermined significance

From: Genetic investigation of 211 Chinese families expands the mutational and phenotypical spectra of hereditary retinopathy genes through targeted sequencing technology

Fa	Np	Gene	Transcript RefSeq	Ex	NA Changes	AA changes	Hzyo	Pf	Reported	Gm	OMIM Disease	SPM	ACMG grade
8	1	USH2A	NM_206933	41	c.8002G > T	p.E2668X	Het	–	Novel	AR	Usher 2A/RP, 39	/ / +	PVS1 + PM2
8	1	USH2A	NM_206933	13	c.2802 T > G	p.C934W	Het	2.441^e−3/1.915^e−4	Yes[44]	AR	Usher 2A/RP, 39	+ + +	PS1 + PM2 + PP3
10	1	USH2A	NM_206933	63	c.12608A > G	p.Q4203R	Het	9.457^e−3/ 3.677^e−3	Novel	AR	Usher 2A/RP, 39	–	PM2 + BP4
10	1	USH2A	NM_206933	22	c.4758 + 3A > G	Splicing	Het	1.855^e−2/ 1.457^e−3	Yes[64]	AR	Usher 2A/RP, 39	/ / /	PS1 + PM2
23	1	USH2A	NM_206933	66	c.14411G > A	p.G4804E	Het	–	Novel	AR	Usher 2A/RP, 39	/ / +	PM2
23	1	USH2A	NM_206933	19	c.4217C > A	p.S1406X	Het	–	Novel	AR	Usher 2A/RP, 39	+ + +	PVS1 + PM2 + PP3
53	1	USH2A	NM_206933	65	c.14287G > A	p.G4763R	Het	–	Yes[65]	AR	Usher 2A/RP, 39	+ + +	PS1 + PM2 + PP3
53	1	USH2A	NM_206933	4	c.784 + 2 T > G	Splicing	Het	–	Novel	AR	Usher 2A/RP, 39	/ / /	PVS1 + PM2
19	1	USH1C	NM_153676	5	c.407G > A	p.R136Q	Het	1.16^e−4/ 1.223^e−4	Novel	AR	Usher 1C	/ / +	PM2
19	1	USH1C	NM_153676	15	c.1250C > T	p.T417I	Het	–	Novel	AR	Usher 1C	/ / +	PM2
13	1	BBS2	NM_031885	6	c.626 T > C	p.L209P	Het	–	Yes[66]	AR	RP, 74	+ + +	PS1 + PM2 + PP3
13	1	BBS2	NM_031885	1	c.79A > C	p.T27P	Het	–	Novel	AR	RP, 74	–	PM2 + BP4
25	1	LRP5	NM_002335	15	c.3361A > G	p.N1121D	Het	7.528^e−3/ 5.616^e−4	Yes[67]	AR	FEVR4	+ + +	PS1 + PM2 + PP3
25	1	LRP5	NM_002335	18	c.3901G > A	p.A1301T	Het	2.403^e−3/ 2.149^e−4	Novel	AR	FEVR4	−	PM2 + BP4
56	1	LRP5	NM_002335	15	c.3377 T > C	p.L1126P	Het	–	Novel	AR	FEVR4	+ + +	PM2 + PP3
56	1	LRP5	NM_002335	22	c.4519G > T	p.D1507T	Het	–	Novel	AR	FEVR4	+ + +	PM2 + PP3
24	1	ABCA4	NM_000350	5	c.553C > T	p.Q185X	Het	–	Yes[68]	AD	AMD2	+ + +	PVS1 + PS1 + PM2 + PP3
26	1	RS1	NM_000330	4	c.240G > C	p.Q80H	Hemi	–	Novel	XLR	Retinoschisis	/ / +	PM2 + PP4
29	1	GPR143	NM_000273	2	c.263G > A	p.R88Q	Hemi	–	Novel	XL	Nystagmus 6	+ + +	PM2 + PP3
31	1	FBN2	NM_001999	30	c.3923dupG	p.C1308Wfs*5	Het	–	Novel	AD	EMD	/ / /	PVS1 + PM2

Fa denotes Family No.; Np denotes the number of patients; Ex denotes an exon; NA denotes nucleic acid; AA denotes amino acid; Hzyo denotes heterozygosity; Pf denotes the population frequency recorded in the gnomAD database; Gm denotes the genetic model; Disease denotes OMIM disease; SPM denotes SIFT, PolyPhen_2 and Mutation t@sting predicting, ‘ + ’ denotes damaging, ‘-’ denotes benign, and ‘/’ denotes no data. Usher 2A denotes Usher syndrome, type 2A; RP,39 denotes retinitis pigmentosa, type 39; Usher 1C denotes Usher syndrome, type 1C; RP,74 denotes retinitis pigmentosa, type 74; FEVR4 denotes familial exudative vitreoretinopathy, type 4; AMD2 denotes age-related macular degeneration, type 2; Nystagmus 6 denotes nystagmus, type 6, congenital, X-linked; EMD denotes macular degeneration, early onset

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