Table 4 Annotation of all exonic variants in MYOC.

No.	Exon	Chrom	POS	Ref	Alt	Variant type	Amino acid	dbSNP144	1000 G EUR	ExAC NFE	Sample count	Study AF	myocDB	CLINSIG	SIFT	gerp++ gt2	PhastCons	CADD Phred	MutPred Splice
1	1	chr1	171,652,385	C	T	nonsynonymous	R76K	rs2234926	0.14120	0.13650	92	0.13700	Neutral	Benign	0.049	3.43	0.945	9.00	0.116
2	1	chr1	171,652,269	C	T	nonsynonymous	E115K	rs757551979	—	0.00003	1	0.00140	—	—	0.589	3.53	0.268	9.37	0.159
3	1	chr1	171,652,246	G	A	synonymous	G122G	rs145354114	—	0.00300	4	0.00559	Neutral	Uncertain	—	—	0.000	0.17	0.494
4	1	chr1	171,652,236	G	A	nonsynonymous	R126W	rs200120115	—	0.00007	1	0.00140	Glaucoma	—	0.019	−1.13	0.008	23.50	0.605
5	2	chr1	171,638,679	C	T	synonymous	K216K	rs141584495	—	0.00050	3	0.00419	Neutral	—	—	—	0.992	15.63	0.165
6	3	chr1	171,636,585	C	A	synonymous	T285T	rs146606638	0.00800	0.00480	2	0.00279	Neutral	Benign	—	—	0.591	14.00	0.126
7	3	chr1	171,636,534	G	A	synonymous	D302D	rs148433908	—	0.00030	1	0.00140	Neutral	—	—	—	0.000	0.07	0.137
8	3	chr1	171,636,399	A	G	synonymous	Y347Y	rs61730974	0.02090	0.03050	17	0.02400	Neutral	—	—	—	0.024	0.00	0.140
9	3	chr1	171,636,338	G	A	stopgain	Q368*	rs74315329	0.00200	0.00150	7	0.00978	Glaucoma	Pathogenic	—	4.52	0.283	37.00	0.374
10	3	chr1	171,636,247	T	C	nonsynonymous	K398R	rs56314834	0.00700	0.00480	10	0.01400	Neutral	—	0.618	−1.17	0.843	3.87	0.268
11	3	chr1	171,636,185	T	C	nonsynonymous	T419A	—	—	—	2	0.00279	—	—	0.000	5.04	0.945	23.50	0.196
12	3	chr1	171,636,126	G	A	synonymous	T438T	rs375235405	—	0.00004	1	0.00140	—	—	—	—	0.898	11.66	0.125

Exon, exon number; Feature, genetic feature within MYOC; Chrom, chromosome; POS, location of 5′ base of variant in hg38; Ref, reference allele; Alt, alternate allele; Variant type, type of variant observed; Amino Acid, amino acid single letter abbreviation of reference amino acid and the amino acid substituted to; dbSNP144, rs ID if the variant is known; 1000 G EUR, allele frequency from 1000 Genomes Project (European ethnic sub-group); ExAC NFE, allele frequency from ExAC Non-Finnish European ethnic sub-group; Sample count, number of patients with the variant in the n = 358 POAG cohort; Study AF, allele frequency of the variant within the n = 358 POAG cohort; myocDB, known MYOC variants database²⁴; CLINSIG, pathogenicity of the variant in ClinVar; SIFT, sorts intolerant from tolerant substitutions; gerp++, Genomic Evolutionary Rate Profiling; PhastCons, conservation scoring and identification of conserved elements; CADD Phred, Combined Annotation Dependent Depletion on a Phred scale; MutPred Splice, machine learning-based predictor of exonic splice variants. Bold indicates variants which are causal candidates.

Search