Molecular Vision: Panagiotou, Mol Vis 2022; 28:57-69. Table 2

Table 2. List of homozygous variants identified after filtering the exome sequencing data from patient IV:1 of family MEP68.

Chr	Position	Gene	Coding Effect	Transcript Accession Code: Exon: cDNA change: Protein change	Read Depth	EVS	1000g	gnomAD	PolyPhen2	Mutation Taster	CADD
6	108395543	OSTM1	Missense	NM_014028:exon1:c.A313G:p.(Ser105Gly)	62	0.000077	0	0.000152	0.001 (B)	N	13.08
6	155561703	TIAM2	Missense	NM_012454:exon15:c.G3208A:p.(Asp1070Asn)	16	0	0.0002	0.000138	0.004 (B)	N	14.67
11	64056081	GPR137	Missense	NM_001170880:exon6:c.A919G:p.(Ser307Gly),	22	0	0	0	0.348 (B)	DC	10.77
				NM_001170881:exon6:c.A769G:p.(Ser257Gly),
				NM_020155:exon6:c.A919G:p.(Ser307Gly),
				NM_001170726:exon8:c.A1093G:p.(Ser365Gly)
14	60976663	SIX6	Missense	NM_007374:exon1:c.G547C:p.(Asp183His)	27	0	0	0	0.999 (D)	DC	27.6
20	37263365	ARHGAP40	Missense	NM_001164431:exon6:c.G883A:p.(Ala295Thr)	21	0	0.000799	0	U	N	16.64

The chromosome, position, gene, coding effect, transcript accession number, exon, cDNA and protein changes, variant read depth, minor allele frequency in the Exome Variant Server, 1000 Genomes and gnomAD databases are shown as well as the PolyPhen2, Mutation Taster and CADD scores for the 5 homozygous variants. B=benign, D=possibly damaging, U=unknown, N=probably neutral, DC=probably. A CADD score of 20 or above indicates that the variant is among the top 1% of deleterious changes in the human genome. For the purposes of this study, variants with CADD scores greater than 15 were prioritised. Note 3 variants (GPR137, SIX6 and ARHGAP40) were prioritised for further investigation based on the criteria of having at least one deleterious pathogenicity prediction score (highlighted in red).