Supp. Table S2.
In-silico predictions of the novel missense variants and known unclassified variants identified in this study using the Alamut software
| PolyPhen | SIFT | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene | Nucleotide change | Amino acid change | Domain/Region | Prediction | PSIC score difference | Prediction | Score | Median sequence conservation | Grantham score | Nucleotide conservation | Amino acid conservation | Remarks |
| CEP290 | c.5081T>C | p.Leu1694Pro UV | Coiled coil | Possibly damaging | 1.995 | Affect protein function | 0.00* | 3.44 | 98 | Weakly conserved (score: 0.0) | Moderately conserved (considering 12 species) | |
| CEP290 | c.4696G>C | p.Ala1566Pro UV | Coiled coil | Possibly damaging | 1.638 | Tolerated | 0.10 | 3.44 | 27 | Highly conserved (score: 1.0) | Highly conserved, up to Frog (considering 12 species) | |
| CRB1 | c.929G>A | p.Cys310Tyr | EGF-like 8, extracellular domain | Probably damaging | 3.761 | Affect protein function | 0.00* | 3.96 | 194 | Highly conserved (score: 1.0) | Highly conserved, up to Cow (considering 8 species) | Disruption of annotated bond formation site (PolyPhen) |
| CRB1 | c.1472A>T | p.Asp491Val UV | Laminin G-like1, extracellular domain | Benign | 1.410 | Affect protein function | 0.01* | 3.96 | 152 | Highly conserved (score: 1.0) | Weakly conserved (considering 8 species) | |
| RPE65 | c.253C>T | p.Arg85Cys | Probably damaging | 2.476 | Tolerated | 0.05 | 2.90 | 180 | Highly conserved (score: 1.0) | Moderately conserved (considering 18 species) | ||
| RPE65 | c.542C>T | p.Pro181Leu | Probably damaging | 2.956 | Affect protein function | 0.04 | 2.90 | 98 | Highly conserved (score: 1.0) | Highly conserved, up to Fruitfly (considering 18 species) | Located next to metal ion binding site (UniProtKB) | |
| GUCY2D | c.587A>T | p.Glu196Val UV | Extracellular domain | Possibly damaging | 1.650 | Affect protein function | 0.00* | 4.32 | 121 | Weakly conserved (score: 0.3) | Highly conserved, up to Opossum (considering 10 species) | |
| GUCY2D | c.1724C>T | p.Pro575Leu UV | Cytoplasmic domain | Benign | 1.433 | Affect protein function | 0.00* | 4.32 | 98 | Weakly conserved (score: 0.0) | Highly conserved, up to Opossum (considering 10 species) | rs28743021 |
| GUCY2D | c.2132C>T | p.Pro711Leu UV | Protein kinase, Cytoplasmic domain | Probably damaging | 3.140 | Affect protein function | 0.00* | 4.32 | 98 | Highly conserved (score: 1.0) | Highly conserved, up to Opossum (considering 10 species) | |
| GUCY2D | c.2598G>C | p.Lys866Asn | Cytoplasmic domain | Probably damaging | 2.236 | Affect protein function | 0.00* | 4.32 | 94 | Highly conserved (score: 1.0) | Highly conserved, up to Opossum (considering 10 species) | |
| AIPL1 | c.341C>T | p.Thr114Ile UV | PPIase FKBP-type | Benign | 0.179 | Tolerated | 0.13 | 3.34 | 89 | Weakly conserved (score: 0.0) | Moderately conserved (considering 12 species) | rs8069375 |
| AIPL1 | c.1126C>T | p.Pro376Ser UV | Benign | ? | Tolerated | 0.48 | 4.32 | 74 | Weakly conserved (score: 0.0) | Weakly conserved (considering 12 species) | ||
| CRX | c.425A>G | p.Tyr142Cys UV | Benign | 1.458 | Affect protein function | 0.00* | 4.32 | 194 | Highly conserved (score: 1.0) | Highly conserved, up to Little brown bat (considering 8 species) | rs61748442 | |
| CRX | c.724G>A | p.Val242Met UV | Benign | 1.033 | Tolerated | 0.20 | 4.32 | 21 | Weakly conserved (score: 0.2) | Highly conserved, up to Dog (considering 8 species) | RS61748459 VAR_007949 | |
| RDH12 | c.524C>T | p.Ser175Leu | Probably damaging | Prediction basis: sequence annotation | Affect protein function | 0.00* | 3.61 | 145 | Weakly conserved (score: 0.2) | Highly conserved, up to Fruitfly (considering 15 species) | Disruption of annotated binding site (PolyPhen) | |
| RDH12 | c.698T>A | p.Val233Asp | Probably damaging | 2.616 | Affect protein function | 0.00* | 3.60 | 152 | Weakly conserved (score: 0.0) | Highly conserved, up to Fruitfly (considering 15 species) | ||
| AHI1 | c.2273A>C | p.His758Pro | WD4 | Probably damaging | 2.679 | Affect protein function | 0.03* | 3.39 | 77 | Highly conserved (score: 1.0) | Moderately conserved (considering 12 species) | |
| AHI1 | c.2433T>G | p.Asn811Lys | WD5 | Possibly damaging | 1.719 | Affect protein function | 0.00* | 3.39 | 94 | Highly conserved (score: 1.0) | Highly conserved, up to Tetraodon (considering 12 species) | |
| AHI1 | c.3368C>T | p.Ser1123Phe | Probably damaging | Prediction basis: sequence annotation | Tolerated | 0.07 | 3.67 | 155 | Highly conserved (score: 0.9) | Weakly conserved (considering 12 species) | Disruption of annotated functional site (modified residue) (PolyPhen) | |
Alamut provides for each variant the HGVS nomenclature and a nucleotide conservation score which was computed at UCSC from 17 vertebrates and has a range between 0 and 1 (http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=multiz17way). For missense variants, Alamut calculates the Grantham distance and automatically fills in queries for PolyPhen and SIFT prediction servers, based on the UniProt protein identifiers and FASTA sequences of several orthologs, respectively. In addition, information on topological as well as functional domains and variations (VAR) was extracted from the UniProtKB database using the following identifiers: O15078 (CEP290), P82279 (CRB1), Q16518 (RPE65), Q02846 (GUCY2D), Q9NZN9 (AIPL1), O43186 (CRX), Q96NR8 (RDH12) and Q8N157 (AHI1) (http://www.uniprot.org/uniprot/). Variants were designated as “unclassified variant (UV)” if no consensus was seen in all prediction programs used.
These substitutions may have been predicted to affect function just because the sequences used were not diverse enough.