Targeted Next Generation Sequencing Identifies Novel Mutations in RP1 as a Relatively Common Cause of Autosomal Recessive Rod-Cone Dystrophy

Table 2

List of mutations detected by next generation sequencing after applying relevant filters.

Patient	Gene	Exon	Allele state	Nucleotide exchange	Protein effect	rs ID	Conservation	Polyohen 2	SIFT	Pathogenicity	Note
F303: II.1 (CIC00445)	NPHP4	12	HTZ	A>G	p.Ser481Asn	no	N C	B	T	Neutral
	RP1	4	HTZ	c.1625C>G	p.Ser542^*	—	—	—	—	Disease causing	R M [12]
	RP1	4	HTZ	c.4587_4590delTAAG	p.Ser1529Argfs^*9	—	—	—	—	Disease causing	N M
F335: III.1 (CIC00491)	PROM1	4	HTZ	T>C	p.Ile178Val	—	N C	B	T	Neutral
	GPR98	29	HTZ	G>A	p.Arg2128Gln	rs149390094	N C	B	T	Neutral
	RP1	4	HMZ	c.4089_4092delAAGA	p.Arg1364Valfs^*8	—	—	—	—	Disease causing	N M
F674: III.6 (CIC01106)	USH2A	39	HTZ	T>G	p.Ser2450Arg	No	H C	P D	D	Probably disease causing
	RP1	4	HMZ	c.1205delG	p.Gly402Alafs^*7	—	—	—	—	Disease causing	N M
F752: II.1 (CIC01245)	USH1C	17	HTZ	G>A	p.Arg477Trp	TMP_ESP_11_17532053	H C	P D	D	Probably disease causing
	PDE6B	10	HTZ	T>C	p.Thr432Ile	—	H C	B	T	Uncertain pathogenicity
	RP1	4	HTZ	c.2025dupA	p.Ser676Ilefs^*22	—	—	—	—	Disease causing	N M
	RP1	4	HTZ	c.2377delA	p.Arg793Glufs^*55	—	—	—	—	Disease causing	N M
F782: II.5 (CIC01300)	RP1	4	HMZ	c.1719_1723delCTCAA	p.Ser574Cysfs^*7	—	—	—	—	Disease causing	N M
	TULP1	5	HMZ	c.395_418dup	p.Asp124_Glu131del	rs63749128	—	—	—	Neutral
F1941: III.1 (CIC04130)	PCDH15	33	HTZ	C>T	p.Arg1889His	rs145851144	N C	B	T	Neutral
	C2orf71	1	HTZ	C>A	p.Arg656Ser	rs201980758	N C	B	T	Neutral
	CACNA2D4	Exon37-Intron 37	HTZ	C>T	—	rs80092457	N C	—	—	Neutral
	RP1	4	HMZ	c.1329delG	p.Lys443Asnfs^*12	—	—	—	—	Disease causing	N M
F3110: III.5 (CIC05941)	EYS	6	HTZ	C>T	p.Ser326Asn	rs112822256	N C	B	T	Neutral
	MERTK	8	HTZ	C>G	p.Arg421Trp	rs138908058	N C	B	D	Neutral
	PRPF6	21	HTZ	A>G	p.Val915Met	rs139778757	M C	P D	D	Uncertain pathogenicity
	TULP1	14	HTZ	G>A	p.Ala496Thr	rs141980901	M C	B	D	Neutral
	EYS	26	HTZ	G>A	p.Lys1365Glu	rs16895519	N C	B	D	Neutral
	MERTK	18	HTZ	G>C	p.Glu823Gln	rs55924349	M C	B	D	Neutral
	RP1	4	HMZ	c.2391_2392delAA	p.Asp799^*	—	—	—	—	Disease causing	N M

Probably disease causing mutations are highlighted in bold.
B: benign, HMZ: homozygous, HTZ: heterozygous, M C: marginally conserved, N C: not conserved, N M: novel mutation, R M: recurrent mutation, T: tolerated, P.D: possibly damaging.