Molecular Vision: Zhang, Mol Vis 2024; 30:175-187. Table 1

Table 1. Pathogenic variants identified in this study and analysis of the variants by predictive programs.

Gene	Exon	Nucleotide Changes	Amino Acid Changes	Variant type	Allele	MT	PP2	SIFT	NG2	NNSP	HSF	In-house	MAF	ACMG	ClinVar ID
PPT1	1	c.24G>A	p.(W8X)	NS	1	DC	-	-	-	-	-	-	-	LP	novel
PPT1	3	c.280A>C	p.(T94P)	MS	1	PO	B	T	N	N	N	-	-	U	novel
PPT1	3	c.338G>T	p.(G113V)	MS	1	DC	PD	D	N	N	N	-	-	LP	novel
PPT1	3	c.348G>C	p.(Q116H)	MS	1	DC	PD	D	N	N	N	-	-	LP	novel
PPT1	5	c.490C>T	p.(R164X)	NS	1	DC	-	-	-	-	-	-	0.0001	P	56,197
PPT1	6	c.595A>G	p.(S199G)	MS	1	DC	PD	D	-	-	-	-	-	LP	novel
CLN3	4	c.206C>A	p.(S69X)	NS	1	DC	-	-	-	-	-	-	-	LP	novel
CLN3	9	c.553T>C	p.(S185P)	MS	1	DC	PD	D	N	N	N	0.00022	0.00022	LP	novel
CLN3	12	c.838G>T	p.(G280C)	MS	1	DC	PD	D	SC	N	N	-	-	LP	novel
CLN3	12	c.906+5G>A	p.(?)	SP	2	-	-	-	SC	SC	SC	-	-	LP	56,291
CLN3	13	c.962+1G>A	p.(?)	SP	1	DC	-	-	SC	SC	SC	0.00022	0.00022	P	370,144
CLN3	14	c.963–13A>G	p.(W321delinsCPNLR)	SP	1	-	-	-	SC	SC	SC	-	-	LP	novel
CLN3	14	c.976dupT	p.(Y326Lfs*56)	FS	1	DC	-	-	-	-	-	-	-	LP	novel
CLN3	14	c.1001G>A	p.(R334H)	MS	2	DC	PD	D	N	N	N	-	0.00002407	P	56,244
CLN3	15	e15–16del	p.(?)	CNV	1	-	-	-	-	-	-	-	-	P	novel
CLN3	16	c.1213C>T	p.(R405W)	MS	1	DC	PD	D	N	N	N	-	0.00003298	LP	418,137
MFSD8	11	c.1006G>A	p.(E336K)	MS	3	DC	PD	D	N	N	N	-	0	LP	284,230
MFSD8	12	c.1268C>G	p.(A423G)	SP	1	PO	B	T	SC	SC	SC	-	-	LP	novel
MFSD8	12	c.1345_1346del	p.(P449Sfs*72)	FS	1	DC	-	-	-	-	-	-	-	LP	novel
MFSD8	13	c.1351–1G>A	p.(?)	SP	2	-	-	-	SC	SC	SC	0.00022	0.0001	LP	1,180,775
MFSD8	13	c.1391C>T	p.(A464V)	MS	1	DC	PD	D	N	N	N	-	0	LP	1,004,070

Ref_Transcript: PPT1:NM_000310; CLN3:NM_001042432; MFSD8:NM_152778. Abbreviations: ACMG, classification of variants according to American College of Medical Genetics; B, benign; CNV, copy number variant; D, Damaging; DC, Disease causing; e, exon; FS, frameshift; HSF, Human Splicing Finder; IF, in-frame; LP, likely pathogenic; MAF, minor allele frequency; MS, missense; MT, Mutation Taster; N, no change; NNSP, NNSplice; NG2, NetGene2; NS, nonsense; P, pathogenic; PD, possible deterioration ; PO, polymorphism; PP2, Polyphen2; SC, Splice site changed; SP, Splice; T, tolerant; U, uncertain of significant.