BioMed Research International

Research Article

Unravelling the Complexity of Inherited Retinal Dystrophies Molecular Testing: Added Value of Targeted Next-Generation Sequencing

Table 3


Patient ID	Family	Clinical diagnosis	Clinical reassessment	Genotype	Inheritance	Gene	Mutation type	Region	cds change

IRD027		STGD		Comp Het	ar	ABCA4	Splice_region	INTRON_40	c.5714+5G>A
IRD027		STGD		Comp Het	ar	ABCA4	Frameshift	EXON_11	c.1375delA
IRD036	Familiar case	STGD		Comp Het	ar	ABCA4	Stop_gained	EXON_14	c.2099G>A
IRD036		STGD		Comp Het	ar	ABCA4	Splice_region syn	EXON_6	c.768G>T
IRD037		STGD		Comp Het	ar	ABCA4	Stop_gained	EXON_14	c.2099G>A
IRD037		STGD		Comp Het	ar	ABCA4	Splice_region syn	EXON_6	c.768G>T
IRD042	Familiar case	STGD		Comp Het	ar	ABCA4	Missense	EXON_42	c.5882G>A
IRD042		STGD		Comp Het	ar	ABCA4	Missense	EXON_6	c.634C>T
IRD043		STGD		Comp Het	ar	ABCA4	Missense	EXON_42	c.5882G>A
IRD043		STGD		Comp Het	ar	ABCA4	Missense	EXON_12	c.1622T>C
IRD050		STGD		Comp Het	ar	ABCA4	Missense	EXON_16	c.2461T>A
IRD050		STGD		Comp Het	ar	ABCA4	Missense	EXON_15	c.2300T>A
IRD054		STGD		Comp Het	ar	ABCA4	Stop_gained	EXON_47	c.6445C>T
IRD054		STGD		Comp Het	ar	ABCA4	Missense	EXON_42	c.5882G>A
IRD055		STGD		Comp Het	ar	ABCA4	Missense	EXON_19	c.2842C>T
IRD055		STGD		Comp Het	ar	ABCA4	Missense	EXON_15	c.2300T>A
IRD061		STGD		Comp Het	ar	ABCA4	Missense	EXON_42	c.5882G>A
IRD061		STGD		Comp Het	ar	ABCA4	Missense	EXON_28	c.4139C>T
IRD062		STGD		Comp Het	ar	ABCA4	Missense	EXON_42	c.5882G>A
IRD062		STGD		Comp Het	ar	ABCA4	Missense	EXON_16	c.2549A>G
IRD073		nd IRD	STGD	Hom	ar	ABCA4	Missense	EXON_19	c.2894A>G
IRD077		STGD		Comp Het	ar	ABCA4	Missense	EXON_37	c.5285C>A
IRD077		STGD		Comp Het	ar	ABCA4	Missense	EXON_15	c.2300T>A
IRD047		BMD		Het	ad	BEST1	Missense	EXON_2	c.73C>T
IRD057	Familiar case	BMD		Het	ad	BEST1	Missense	EXON_2	c.80G>C
IRD058	Familiar case	BMD		Het	ad	BEST1	Missense	EXON_2	c.80G>C
IRD064		BMD		Het	ad	BEST1	Missense	EXON_2	c.80G>C
IRD010		LCA		Comp Het	ar	CEP290	Missense	EXON_33	c.4237G>C
IRD010		LCA		Comp Het	ar	CEP290	Frameshift	EXON_23	c.2390delA
IRD066		RP		Comp Het	ar	CEP290	Stop_gained	EXON_48	c.6640A>T
IRD066		RP		Comp Het	ar	CEP290	Frameshift	EXON_14	c.1219_1220delAT
IRD072		nd IRD	LCA	Comp Het	ar	CEP290	Missense	EXON_14	c.1298A>G
IRD072		nd IRD	LCA	Comp Het	ar	CEP290	Frameshift	EXON_3	c.164_167delCTCA
IRD039		RP		Hom	ar	CNGB1	Frameshift	EXON_13	c.875-5_891dup
IRD052		RP		Comp Het	ar	CNGB1	Missense	EXON_29	c.2957A>T
IRD052		RP		Comp Het	ar	CNGB1	Frameshift	EXON_13	c.875-5_891dup
IRD068		RP		Comp Het	ar	CNGB1	Splicing, syn	EXON_26	c.2526C>T
IRD068		RP		Comp Het	ar	CNGB1	Missense	EXON_21	c.2153G>C
IRD085		RP		Hom	ar	CNGB1	Missense	EXON_23	c.2284C>T
IRD032		nd IRD	ACHM	Comp Het	ar	CNGB3	Splice_donor	INTRON_13	c.1578+1G>A
IRD032		nd IRD	ACHM	Comp Het	ar	CNGB3	Frameshift	EXON_10	c.1148delC
IRD029	Familiar case	RP		Hom	ar	CRB1	Missense	EXON_5	c.2200G>A
IRD030		RP		Hom	ar	CRB1	Missense	EXON_5	c.2200G>A
IRD031		RP		Hom	ar	CRB1	Missense	EXON_5	c.2200G>A
IRD035		LCA		Het	ad	CRX	Frameshift	EXON_4	c.514delC
IRD008		RP		Hom	ar	PDE6B	Splice_region	EXON_18	c.2193+1delG
IRD013		RP		Comp Het	ar	PDE6B	Missense	EXON_4	c.794G>A
IRD013		RP		Comp Het	ar	PDE6B	Intron	INTRON_8	c.1108-10G>A
IRD026		RP		Het	ad	RHO	Missense	EXON_3	c.568G>T
IRD016		RP		Comp Het	ar	ROM1	Missense	EXON_1	c.178C>A
IRD016		RP		Comp Het	ar	ROM1	Missense	EXON_1	c.323C>T
IRD033		RP		Hem	xl	RP2	Frameshift	EXON_2	c.382_383delTT
IRD076		RP		Hom	ar	RPE65	Missense	EXON_2	c.65T>C
IRD001		RP		Comp Het	ar	RPE65	Missense	EXON_2	c.65T>C
IRD001		RP		Comp Het	ar	RPE65	Frameshift	EXON_9	c.893delA
IRD074		LCA		Hom	ar	RPE65	Missense	EXON_5	c.430T>G
IRD002		LCA		Comp Het	ar	RPGRIP1	Frameshift	EXON_15	c.2225_2226delGA
IRD002		LCA		Comp Het	ar	RPGRIP1	Frameshift	EXON_17	c.2795_2796insT
IRD012		RP		Hem	xl	RPGR	Missense	EXON_8	c.785C>G
IRD067		RP		Hem	xl	RPGR	Missense	EXON_8	c.814G>T
IRD075		RP		Hem	xl	RPGR	Missense, Splice_region	EXON_2	c.154G>A
IRD017		RP		Hem	De novo	RPGR	Frameshift	EXON_2	c.89delT
IRD059	Familiar case	RP		Comp Het	ar	TULP1	Missense	EXON_15	c.1590C>G
IRD059		RP		Comp Het	ar	TULP1	Missense	EXON_13	c.1255C>T
IRD060		RP		Comp Het	ar	TULP1	Missense	EXON_15	c.1590C>G
IRD060		RP		Comp Het	ar	TULP1	Missense	EXON_13	c.1255C>T
IRD041		RP		Comp Het	ar	TULP1	Splice_region	INTRON_14	c.1496-6C>A
IRD041		RP		Comp Het	ar	TULP1	Missense	EXON_14	c.1445G>A
IRD007		USH		Comp Het	ar	USH2A	Missense	EXON_63	c.12420T>G
IRD007		USH		Comp Het	ar	USH2A	splice_region, syn	EXON_28	c.5775A>T
IRD009		USH		Comp Het	ar	USH2A	Missense	EXON_63	c.13546G>T
IRD009		USH		Comp Het	ar	USH2A	splice_region, Missense	EXON_10	c.1645T>C
IRD021		RP		Comp Het	ar	USH2A	Missense	EXON_69	c.14995A>G
IRD021		RP		Comp Het	ar	USH2A	Missense	EXON_8	c.1481A>G
IRD023	Familiar case	RP	USH	Comp Het	ar	USH2A	Missense	EXON_13	c.2296T>C
IRD023		RP	USH	Comp Het	ar	USH2A	Frameshift	EXON_3	c.545_548delAAGA
IRD024		RP	USH	Comp Het	ar	USH2A	Missense	EXON_13	c.2296T>C
IRD024		RP	USH	Comp Het	ar	USH2A	Frameshift	EXON_3	c.545_548delAAGA
IRD038		RP		Comp Het	ar	USH2A	Missense	EXON_13	c.2296T>C
IRD038		RP		Comp Het	ar	USH2A	Missense	EXON_13	c.2276G>T
IRD084		USH		Hom	ar	USH2A	Frameshift	EXON_69	c.14977_14978delTT
IRD034		RP		Hom	ar	USH2A	Missense	EXON_63	c.12574C>T

Patient ID	Protein change	Frequency (%)	Coverage (# reads)	Segregation and unaffected siblings	Functional predictions (dbNSFP)	Splicing predictions			Reference
Patient ID	Protein change	Frequency (%)	Coverage (# reads)	Segregation and unaffected siblings	Functional predictions (dbNSFP)	Human Splicing Finder	dbscSNV	SPIDEX	Reference

IRD027		44.9	514			Broken WT Donor Site	0.999\|0.988	−3.21	PMID: 15494742
IRD027	p.Thr459GlnfsX2	47.7	1179						PMID: 21911583
IRD036	p.Trp700X	48.2	303		.\|..\|N\|A\|.\|.\|.\|.\|.\|D				PMID: 11702214
IRD036	p.Val256Val	47.2	53			Broken WT Donor Site	1.000\|0.952	−2.43	PMID: 12037008
IRD037	p.Trp700X	44.5	110		.\|..\|N\|A\|.\|.\|.\|.\|.\|D	New Acceptor Site		−5.41	PMID: 11702214
IRD037	p.Val256Val	48.3	29			Broken WT Donor Site	1.000\|0.952	−2.43	PMID: 12037008
IRD042	p.Gly1961Glu	47.1	1325		D\|DD\|D\|D\|N\|D\|D\|D\|D\|D				PMID: 9295268
IRD042	p.Arg212Cys	49.1	432		D\|DD\|D\|A\|M\|D\|D\|D\|D\|D				PMID: 11726554
IRD043	p.Gly1961Glu	46.9	796		D\|DD\|D\|D\|N\|D\|D\|D\|D\|D				PMID: 9295268
IRD043	p.Leu541Pro	51.9	727		D\|DD\|D\|A\|M\|D\|D\|D\|D\|D				PMID: 11527935
IRD050	p.Trp821Arg	43.8	309		D\|DD\|D\|D\|H\|T\|D\|D\|D\|D				PMID: 11527935
IRD050	p.Val767Asp	46.3	452		D\|BB\|D\|D\|M\|D\|T\|D\|D\|D				PMID: 15494742
IRD054	p.Arg2149X	49.1	422		.\|..\|D\|A\|.\|.\|.\|.\|.\|D	New ESS site		−58.3	PMID: 12202497
IRD054	p.Gly1961Glu	49.4	1448		D\|DD\|D\|D\|N\|D\|D\|D\|D\|D				PMID: 9295268
IRD055	p.Arg948Cys	52.0	175		T\|BB\|N\|D\|L\|D\|T\|T\|N\|N				This study
IRD055	p.Val767Asp	51.5	437		D\|BB\|D\|D\|M\|D\|T\|D\|D\|D				PMID: 15494742
IRD061	p.Gly1961Glu	50.0	729		D\|DD\|D\|D\|N\|D\|D\|D\|D\|D				PMID: 9295268
IRD061	p.Pro1380Leu	55.8	437		D\|DP\|N\|A\|M\|D\|D\|D\|D\|D	New ESS site		−5.44	PMID: 11726554
IRD062	p.Gly1961Glu	100	787		D\|DD\|D\|D\|N\|D\|D\|D\|D\|D				PMID: 9295268
IRD062	p.Tyr850Cys	49.4	176		D\|DD\|D\|D\|M\|T\|D\|D\|D\|D				PMID: 23096905
IRD073	p.Asn965Ser	100	225		D\|DD\|D\|D\|L\|D\|D\|D\|D\|D				PMID: 9054934
IRD077	p.Ala1762Asp	50.8	259		D\|DD\|D\|A\|M\|D\|D\|D\|D\|D				PMID: 15192030
IRD077	p.Val767Asp	51.4	752		D\|BB\|D\|D\|M\|D\|T\|D\|D\|D				PMID: 15494742
IRD047	p.Arg25Trp	56.0	348		D\|DD\|U\|D\|M\|D\|D\|D\|D\|D	New Donor Site, New ESS site			PMID: 10798642
IRD057	p.Ser27Thr	46.8	344		D\|DD\|U\|D\|H\|D\|D\|D\|D\|D				This study
IRD058	p.Ser27Thr	45.5	317		D\|DD\|U\|D\|H\|D\|D\|D\|D\|D				This study
IRD064	p.Ser27Thr	47.1	453		D\|DD\|U\|D\|H\|D\|D\|D\|D\|D				This study
IRD010	p.Asp1413His	49.2	413		D\|BB\|D\|D\|N\|T\|T\|T\|N\|D				ClinVar: RCV000082249.5
IRD010	p.Lys797SerfsX2	30.1	163						This study
IRD066	p.Lys2214X	47.5	705		.\|..\|D\|A\|.\|.\|.\|.\|.\|D	ESE Site Broken		−86.6	This study
IRD066	p.Met407GlufsX14	51.1	225						PMID: 17724218
IRD072	p.Asp433Gly	53.4	116		T\|DP\|D\|D\|L\|T\|T\|T\|D\|D	New ESS site, New donor site			This study
IRD072	p.Thr55SerfsX3	43.2	243						PMID: 20690115
IRD039	p.Gly298CysfsX13								This study
IRD052	p.Asn986Ile	51.7	471		D\|DD\|D\|D\|M\|D\|D\|D\|D\|D				PMID: 21147909
IRD052	p.Gly298CysfsX13		258						This study
IRD068	Thr842Thr	52.1	431			ESE Site Broken			This study
IRD068	p.Gly718Ala	47.1	153		D\|PP\|D\|D\|M\|T\|T\|T\|D\|D				This study
IRD085	p.Arg762Cys	100	57		D\|DD\|D\|D\|H\|D\|D\|D\|D\|D				This study
IRD032		47.8	907			Broken WT Donor Site		−8.56	PMID: 15657609
IRD032	p.Thr383IlefsX13	46.5	588						PMID: 15657609
IRD029	p.Gly734Arg	100	397		D\|DD\|.\|D\|M\|T\|D\|D\|D\|D				This study
IRD030	p.Gly734Arg	100	397		D\|DD\|.\|D\|M\|T\|D\|D\|D\|D				This study
IRD031	p.Gly734Arg	100	397		D\|DD\|.\|D\|M\|T\|D\|D\|D\|D				This study
IRD035	p.Pro172LeufsX15	50.5	521						This study
IRD008		100	395	Brother: Het		Broken WT Donor Site			This study
IRD013	p.Arg265Gln	51.7	319	n.a.	T\|DD\|D\|D\|L\|T\|T\|T\|N\|D				ClinVar: RCV000178068.1
IRD013		54.7	75	Mother: Het			0.001\|0.096		PMID: 8698075
IRD026	p.Asp190Tyr	44.6	168		D\|DD\|D\|D\|M\|T\|T\|T\|D\|D				PMID: 8401533
IRD016	p.Pro60Thr	56.1	278		T\|BB\|N\|N\|L\|T\|T\|T\|N\|N				PMID: 8595413
IRD016	p.Thr108Met	52.8	108		T\|PB\|N\|D\|L\|T\|T\|T\|N\|D				PMID: 8595413
IRD033	p.Leu129ValfsX9	100	392						This study
IRD076	p.Leu22Pro	100	495		T\|BB\|D\|D\|M\|D\|D\|D\|N\|D				PMID: 9801879
IRD001	p.Leu22Pro	46.3	257	Brother: wt	T\|BB\|D\|D\|M\|D\|D\|D\|N\|D				PMID: 9801879
IRD001	p.Lys298SerfsX27	98	150	Brother: wt					PMID: 11462243
IRD074	p.Tyr144Asp	100	430	Father: Het	D\|DD\|D\|D\|M\|D\|D\|D\|D\|D				PMID: 11462243
IRD002	p.Glu743ArgfsX24	48.8	570	Father: Het					This study
IRD002	p.Glu933X	48.8	400	Mother: Het					This study
IRD012	p.Ala262Gly	100	280		T\|BB\|N\|N\|L\|D\|T\|T\|N\|N				This study
IRD067	p.Gly272Cys	100	155		D\|DD\|D\|D\|H\|D\|D\|D\|D\|D				This study
IRD075	p.Gly52Arg	100	348		D\|DP\|U\|D\|M\|T\|T\|T\|D\|D	Broken WT Donor Site			PMID: 15364249
IRD017	p.Phe30SerfsX38	100	113	Brother: wt Female twin: wt					This study
IRD059	p.Ile530Met	50.6	682		D\|DD\|D\|D\|H\|D\|D\|D\|D\|N				This study
IRD059	p.Arg419Trp	49.5	645		D\|DD\|D\|D\|H\|D\|D\|D\|D\|D				PMID: 25342620
IRD060	p.Ile530Met	51.0	655		D\|DD\|D\|D\|H\|D\|D\|D\|D\|N				This study
IRD060	p.Arg419Trp	45.3	575		D\|DD\|D\|D\|H\|D\|D\|D\|D\|D				PMID: 25342620
IRD041		54.1	727	Father: Het			0.005\|0.419		PMID: 9660588
IRD041	p.Arg482Gln	48.5	485	Mother: Het	D\|DD\|D\|D\|H\|D\|D\|D\|D\|D	New Acceptor Site		−1.28	PMID: 22665969
IRD007	p.Cys4140Trp	50.5	214		D\|DD\|D\|D\|M\|T\|T\|T\|D\|D				This study
IRD007		49.5	398			Broken WT Donor Site	0.998\|0.986	−4.24	This study
IRD009	p.Gly4516Trp	53.8	239		D\|DD\|U\|D\|H\|T\|D\|D\|D\|D				This study
IRD009	p.Cys549Arg	49.2	566		D\|DD\|U\|D\|H\|D\|D\|D\|D\|D		0.417\|0.520		This study
IRD021	p.Thr4999Ala	51.0	400		D\|DD\|U\|D\|M\|T\|T\|T\|D\|D				This study
IRD021	p.Tyr494Cys	49.0	400		D\|DD\|N\|D\|L\|T\|T\|T\|D\|D				This study
IRD023	p.Cys766Arg	39.0	82		D\|DD\|D\|D\|H\|D\|D\|D\|D\|D				PMID: 23591405
IRD023	p.Lys182ArgfsX9	61.4	202						This study
IRD024	p.Cys766Arg	43.5	124		D\|DD\|D\|D\|H\|D\|D\|D\|D\|D				PMID: 23591405
IRD024	p.Lys182ArgfsX9	48.0	225						This study
IRD038	p.Cys766Arg	47.2	89		D\|DD\|D\|D\|H\|D\|D\|D\|D\|D				PMID: 23591405
IRD038	p.Cys759Phe	51.1	90		D\|DD\|D\|A\|H\|D\|D\|D\|D\|D				PMID: 10775529
IRD084	p.Phe4993ProfsX7	100	483						PMID: 24944099
IRD034	p.Arg4192Cys	100	515		D\|DP\|N\|D\|M\|D\|D\|D\|D\|D				PMID: 24498627

ACHM: Achromatopsia; ad: autosomal dominant; ar: autosomal recessive; BMD: best macular disease; Comp Het: compound heterozygous; ESE: exonic splicing enhancer; ESS: exonic splicing silencer; Hem: Hemizygous; Het: heterozygous; Hom: homozygous; LCA: Leber Congenital Amaurosis; nd IRD: inherited retinal degeneration not otherwise specified without precisely defined diagnosis; RP: Retinitis Pigmentosa; STGD: Stargardt Disease; USH: Usher Syndrome; wt: wild-type; xl: X-linked. For nonsynonymous variants, predictions from dbNSFP are reported, comprising scores from the following alghoritms: SIFT | Polyphen2HDIV Polypehn2HVAR | LRT | MutationTaster | MutationAssessor | FATHMM | MetaSVM | MetaLR | PROVEAN | fathmm-MKL. For splicing variants, predictions from Human Splicing Finder, dbscSNV (ada_score|rf_score) and SPIDEX are reported. For SPIDEX, max dPSI is shown if lower than −1 (maximum mutation − induced change in the percentage of transcripts with the exon spliced in). Familiar case: the patients were from the same family. ^*Sanger sequencing was performed to confirm mutation frequency.