Table 3 Allele frequencies and in silico predictions of the AIPL1 variants investigated.

Nucleotide change	Protein change	SIFT	Polyphen	Allele frequency		Number of Homozygotes
Nucleotide change	Protein change	SIFT	Polyphen	ExAC	gnomAD	ExAC	gnomAD
c.116C>A	p.T39N	D 0.05	P.D 1	nd	nd	nd	nd
c.157C>T	p.R53W	D 0	P.D 0.96	0.000008358	0.00004246	0	0
c.214T>C	p.W72R	D 0	P.D 1	nd	nd	nd	nd
c.266G>A	p.C89Y	D 0	P.D 1	nd	0.000003996	nd	0
c.364G>A	p.G122R	D 0	P.D 1	0.00000834	0.000003988	0	0
c.390C>A	p.H130Q	D 0	P.D 0.998	nd	0.000003992	nd	0
c.582C>G	p.Y194X	N/A	N/A	0.000008238	0.000003976	0	0
c.593C>T	p.S198F	D 0.01	p.D 0.627	nd	nd	nd	nd
c.617T>A	p.I206N	D 0.03	P.D 0.953	nd	nd	nd	nd
c.666G>A	p.W222X	N/A	N/A	nd	nd	nd	nd
c.733G>T	p.E245X	N/A	N/A	nd	nd	nd	nd
c.809G>A	p.R270H	D 0	P.D 1	nd	nd	nd	nd
c.878T>C	p.L293P	D 0	P.D 1	nd	nd	nd	nd
c.894G>C	p.Q298H	T 0.11	p.D 0.721	nd	nd	nd	nd
c.1091C>G	p.A364G	T 0.1	Benign 0.001	nd	nd	nd	nd
c.1097C>G	p.P366R	D 0.02	p.D 0.637	nd	nd	nd	nd
c.1126C>T	p.P376S	D 0	Benign 0.001	0.00588	0.006198	27	51

The cDNA is numbered according to the longest AIPL1 transcript ENST00000381129, protein ID ENSP00000370521. ExAC allele count: Allele frequency of the AIPL1 variations in a reference data set derived from 61,486 unrelated individuals sequenced as part of various disease-specific and population genetic studies; excludes cases of severe pediatric disease. The dataset provided in gnomAD includes 125,748 exome sequences and 15,708 whole-genome sequences from unrelated individuals sequenced as part of various disease-specific and population genetic studies. SIFT results: tolerance index ≥ 0.05 = tolerated (T), tolerance index < 0.05 = damaging (D). PolyPhen-2: benign, possibly damaging (p.D), probably damaging (P.D). N/A, not applicable; nd, not described.

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