Table 1. GPATCH3 variants identified in congenital glaucoma patients.
| Patient | Chromosome position (GRCh38.p2) | Nucleotide change (rs# or ss#) | Aminoacid change | Frequency in ExAC (%) | SIFTa/PolyPhenb score | HSF 3.0 predicted effects (# of algorithms) |
|---|---|---|---|---|---|---|
| WES group (n = 26) | ||||||
| PCG-99 | 1:26897476 1:26891164 | c.701A > G (rs35243557) c.1424G > A (rs376709877) | p.Asn234Serp.Gly475Glu | 0.46 0.0016 | 0.15/0.7 0.29/0.97 | — |
| PCG cohort (n = 130) | ||||||
| PCG-30 | 1:26900595 | c.−129C > A (ss2031476744) | — | N.I. | — | — |
| 1:26891208 | c.1380A > G (rs35647061) | p.Leu460= | 0.13 | — | ESEB (4) | |
| PCG-116 | 1:26897476 | c.701A > G (rs35243557) | p.Asn234Ser | 0.46 | 0.15/0.7 | — |
| PCG-145 | 1:2690037 | c.67G > A (rs764461662) | p.Val23Met | 0.002 | — | — |
| PCG-180 PCG-205 | 1:26893277 | c.1111 + 112G > A (rs116417426) | — | 0.0044c | — | ESSB (2), ESEC (3) & CSSA (2) |
| PCG-F203 | 1:26900660 | c.−194 C > G (rs554585879) | — | N.I. | — | — |
| V-0638 | 1:26892473 | c.1299C > T (rs767504926) | p.Cys433 = | 0.001 | ESEB (4) | |
| Secondary congenital glaucoma cohort (n=40) | ||||||
| MOC-F5 | 1:26900760 | c.−298_−295delGAGG (ss2031476745) | — | N.I. | — | — |
| 1:26890747 | c.*263C > T (rs147217101) | — | 1.3c | — | — | |
| 1:26890736 | c.*274C > T (rs115936179) | — | 0.3c | — | — | |
| MOC-F7 | 1:26893315 | c.1111 + 74A > T (ss2031476742) | — | N.I. | — | — |
| ANF-0064-1 ANF-0064-2 (twins) | 1:26900034 | c.409C > T (ss2031476743) | p.Arg137Cys | N.I. | 0.04/0.357 | — |
aRanges from 0 to 1, predicted damaging if the score is ≤0.05 and tolerated if the score is >0.05. bRanges from 0 to 1. Score values are interpreted as follows: 0.0–0.15, benign; 0.15–0.85, possibly damaging; 0.85–1.0, damaging. c1000 Genomes Project (http://www.internationalgenome.org/data). N.I.: Not identified. ESEB: Exonic Splicing Enhancer Broken. ESSB: Exonic Splicing Silencer Broken. ESEC: Exonic Splicing Enhancer Created. CSSA: Cryptic Splicing Site Sctivated. ExAC: Exome Aggregation Consortium (http://exac.broadinstitute.org/). HSF: Human Splicing Finder software (http://www.umd.be/HSF3/HSF.html). PolyPhen: Polymorphism Phenotyping (http://genetics.bwh.harvard.edu/pph/data/). SIFT: Sorting Intolerant From Tolerant (http://sift.bii.a-star.edu.sg/).