Molecular Vision: Alayed, Mol Vis 2025; 31:486-500. Table 3

Table 3. Single nucleotide variants identified in FECD cases that did not have an expanded repeat (A), had an expanded repeat (B) and in non-FECD controls (C).

HGNC gene symbol	Sample ID	Genomic nomenclature	Transcript	c.Nomen	p.Nomen	dbSNP ID	ExAC frequency	CADD score	gnomAD frequency	SpliceAI score	Franklin
(A)
COL8A2	1068	chr1:g.36565837C>T	NM_005202.4	c.7G>A	p.(Gly3Arg)	rs115156902	0.007	15.17	0.005322	0.07	B
AGBL1	758	chr15:g.86800154C>T	NM_152336.4	c.806C>T	p.(Pro269Leu)	rs185896474	0.0083	31	0.01173	0.01	B
AGBL1	589	chr15:g.87531321dup	NM_152336.4	c.3323+2dup	NK	rs547400346	0.0015	16.4	0.001999	0.34	VUS
LOXHD1	831	chr18:g.44057151C>T	NM_001145472.3	c.3340G>A	p.(Gly1114Arg)	rs142931455	0.0018	17.26	0.001364	0.05	B
LOXHD1	596	chr18:g.44085948C>T	NM_144612.7	c.5545G>A	p.(Gly1849Arg)	rs780560784	4.36E-05	32	1.03E-05	0.79	LP
LOXHD1	817	chr18:g.44109166G>A	NM_144612.7	c.4504C>T	p.(Arg1502Trp)	rs200819355	0.0002	28.2	0.000405	0.05	VUS
LOXHD1	765	chr18:g.44137400C>T	NM_144612.7	c.3269G>A	p.(Arg1090Gln)	rs118174674	0.0096	20.2	0.01747	0.01	B
LOXHD1	596	chr18:g.44171980G>A	NM_144612.7	c.1570C>T	p.(Arg524Cys)	rs192376005	0.0019	33	0.003051	0	LB
(B)
AGBL1	558	chr15:g.86800154C>T	NM_152336.4	c.806C>T	p.(Pro269Leu)	rs185896474	0.0083	31	0.01173	0.01	B
AGBL1	948	chr15:g.87531321dup	NM_152336.4	c.3323+2dup	NK	rs547400346	0.0015	16.4	0.001999	0.34	VUS
LOXHD1	558	chr18:g.44140109G>A	NM_144612.7	c.2998C>T	p.(Arg1000Trp)	rs199847981	0.0005	21.1	0.000841	0	VUS
LOXHD1	778	chr18:g.44137400C>T	NM_144612.7	c.3269G>A	p.(Arg1090Gln)	rs118174674	0.0096	20.2	0.01747	0.01	B
SLC4A11	958	chr20:g.3209766C>T	NM_032034.4	c.2041G>A	p.(Ala681Thr)	rs770312190	4.58E-05	24	5.96E-05	0.01	VUS
(C)
AGBL1	1149	chr15:g.86807754C>A	NM_152336.4	c.1352C>A	p.(Ser451Tyr)	rs79186009	0.0009	25	0.000577	0	LB
AGBL1	1149	chr15:g.86940679G>T	NM_152336.4	c.2457G>T	p.(Glu819Asp)	rs200431794	0.0002	25.7	0.000147	0	LB
SLC4A11	1159	chr20:g.3211846G>A	NM_032034.4	c.1039C>T	p.(Arg347Trp)	rs138137682	0.001	21.6	0.001843	0	LB

Genomic coordinates reported for the human reference genome are according to build hg19. ACMG classification determined using Franklin. This classification system considers up to 28 specific criteria with varying degrees of strength for pathogenic or benign prediction. Combining the scores for these criteria, assigns each variant to one of five tiers. The variant can either be pathogenic (P), likely pathogenic (LP), variant of unknown significance (VUS), likely benign (LB) or benign (B). Nomen=Nomenclature. ExAc=Exome Aggregation Consortium, version 0.3, included all populations. CADD=Combined Annotation Dependent Depletion, version 1.3. NK=the consequence on the protein is not known.