Research Article
ABCC6 Gene Analysis in 20 Japanese Patients with Angioid Streaks Revealing Four Frequent and Two Novel Variants and Pseudodominant Inheritance
Table 2
Variants in the ABCC6 gene identified in the 20 patients with angioid streaks.
| | Exon | Nucleotide | Amino acid | Homozygous | Heterozygous | Total (alleles) | dbSNP ID | HGVD (allele frequency) | ExAC East Asian (allele frequency) | ExAC total (allele frequency) | Polyphen-2 results (HumVar) | SIFT results | PROVEAN results | Pathogenicity | References |
| | 9 | c.1132C>T | p.Q378X | 1 | 5 | 7/40 | rs72650699 | 0.002% (2/427) | 0.000% (0/8646) | 0.000% (1/121188) | | | | Pathogenic | Le Saux et al. [2001], Pulkkinen et al. [2001] |
| | 10 | c.1256G>A | p.R419Q | 0 | 4 | 4/40 | rs772434460 | 0.001% (2/1077) | 0.001% (10/8204) | 0.000% (10/111520) | 0.742 (possibly damaging) | 0.00 (damaging) | −3.27 (deleterious) | Pathogenic | Iwanaga et al. [2017] | | c.1283A>G | p.N428S | 0 | 1 | 1/40 | rs201880691 | 0.009% (20/1123) | 0.001% (12/8524) | 0.000% (13/117386) | 0.999 (probably damaging) | 0.00 (damaging) | −4.69 (deleterious) | Pathogenic | Sato et al. [2009] (reported in the controls) |
| | 15 | c.1939C>T | p.H647Y | 0 | 1 | 1/40 | Not reported | Not reported | Not reported | Not reported | 0.127 (benign) | 0.01 (damaging) | −3.32 (deleterious) | Pathogenic | N/A (novel variant) |
| | 19 | c.2542delG | p.V848CfsX83 | 2 | 10 | 14/40 | rs67867306 | Inconclusive | 0.003% (27/8654) | 0.000% (27/121324) | | | | Pathogenic | Sato et al. [2009] |
| | 24 | c.3340C>T | p.R1114C | 0 | 1 | 1/40 | rs63749794 | Not reported | 0.000% (0/8608) | 0.000% (12/120184) | 0.998 (probably damaging) | 0.00 (damaging) | −7.13 (deleterious) | Pathogenic | Gheduzzi et al. [2004] | | c.3374C>T | p.S1125F | 0 | 1 | 1/40 | Not reported | Not reported | Not reported | Not reported | 0.992 (probably damaging) | 0.00 (damaging) | −4.85 (deleterious) | Pathogenic | N/A (novel variant) |
| | 29 | c.4069C>T | p.R1357W | 0 | 6 | 6/40 | rs63750428 | 0.006% (14/1099) | 0.001% (5/7944) | 0.000% (6/107190) | 1.000 (probably damaging) | 0.00 (damaging) | −6.56 (deleterious) | Pathogenic | Miksch et al. [2005] |
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N/A = not applicable; HGVD = Human Genetic Variation database (http://www.hgvd.genome.med.kyoto-u.ac.jp/index.html); ExAC = Exome Aggregation Consortium database (http://exac.broadinstitute.org); Polyphen-2 (http://genetics.bwh.harvard.edu/pph2/); SIFT (http://sift.jcvi.org); PROVEAN (http://provean.jcvi.org).
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