Table 5.
Predicted functional rare variants in CFHR5
| Position | Location | Nucleotide | Amino Acid | Identified in Population | dbSNP (Build142) | Function Change Prediction | Software |
|---|---|---|---|---|---|---|---|
| Chr1:196946445 | Promoter | c.-350G>T | — | Patients | — | Not transcript elements binding sites | Promoter 2.0 |
| Chr1:196946448 | Promoter | c.-347G>A | — | Controls | rs9427942 | Not transcript elements binding sites | Promoter 2.0 |
| Chr1:196946881 | Intron 1 | c.58+29A>C | — | Controls | — | Not branch-point mutation | HSF 2.4.1 |
| Chr1:196951903 | Intron 1 | c.59–112G>A | — | Patients | — | Not branch-point mutation | HSF 2.4.1 |
| Chr1:196953025 | Intron 2 | c.254–66A>T | — | Patients | rs570596954 | Not branch-point mutation | HSF 2.4.1 |
| Chr1:196953169 | Exon 3 | c.332A>C | p.Gln111Pro | Patients and controls | — | Tolerated/benign | SIFT-Polyphen-2 |
| Chr1:196953379 | Intron 3 | c.430+112T>C | — | Patients | — | Not branch-point mutation | HSF 2.4.1 |
| Chr1:196963287 | Exon 4 | c.508G>A | p.Val170Met | Patients and controls | rs201073457 | Tolerated/probably damaging | SIFT-Polyphen-2 |
| Chr1:196963312 | Exon 4 | c.533A>G | p.Asn178Ser | Patients | rs200427185 | Damaging/benign | SIFT-Polyphen-2 |
| Chr1:196965015 | Exon 5 | c.776T>A | p.Leu259Termination | Patients | — | Stop gain | — |
| Chr1:196965031 | Intron 5 | c.790+2T>C | — | Patients | — | Splicing site | BDGP, ASSP |
| Chr1:196965076 | Intron 5 | c.790+47A>G | — | Patients | — | Not branch-point mutation | HSF 2.4.1 |
| Chr1:196965183 | Exon 6 | c.822A>T | p.Glu274Asp | Patients | — | Tolerated/benign | SIFT-Polyphen-2 |
| Chr1:196967528 | Intron 7 | c.1147+94G>T | — | Patients and controls | rs116891819 | Not branch-point mutation | HSF 2.4.1 |
| Chr1:196971491 | Intron 7 | c.1148–121G>A | — | Patients | — | Not branch-point mutation | HSF 2.4.1 |
| Chr1:196971504 | Intron 7 | c.1148–108A>G | — | Controls | rs147231103 | Not branch-point mutation | HSF 2.4.1 |
| Chr1:196971544 | Intron 7 | c.1148–68C>T | — | Controls | rs181464041 | Not branch-point mutation | HSF 2.4.1 |
| Chr1:196971637 | Exon 8 | c.1173G>A | p.Pro391Pro | Controls | rs200148491 | Synonymous mutation | — |
| Chr1:196971814 | Intron 8 | c.1330+20G>A | — | Controls | — | Not branch-point mutation | HSF 2.4.1 |
| Chr1:196971834 | Intron 8 | c.1330+40G>A | — | Controls | rs116937944 | Not branch-point mutation | HSF 2.4.1 |
| Chr1:196971872 | Intron 8 | c.1330+78A>G | — | Patients and controls | — | Not branch-point mutation | HSF 2.4.1 |
| Chr1:196973817 | Exon 9 | c.1357C>T | p.Pro453Ser | Controls | rs184883943 | Tolerated/probably damaging | SIFT-Polyphen-2 |
| Chr1:196974101 | Intron 9 | c.1513+126A>G | — | Patients | — | Not branch-point mutation | HSF 2.4.1 |
| Chr1:196974110 | Intron 9 | c.1513+137G>A | — | Controls | rs142743076 | Not branch-point mutation | HSF |
| Chr1:196977744 | Exon 10 | c.1641G>A | p.Ala547Ala | Patients | rs74323799 | Synonymous mutation | — |
| Chr1:196977811 | Exon 10 (stop codon) | c.1708T>C | p.Termination570Arg | Patients and controls | — | Stop loss | — |
| Chr1:196977816 | 3′ UTR | c.1710*3C>G | — | Patients | — | Not microRNA binding site | TargetScanHuman 6.2 |
| Chr1:196977981 | 3′ UTR | c.1710*168G>T | — | Patients | — | hsa-mir-2117/hsa-mir-4273 binding site | TargetScanHuman 6.2 |
dbSNP, single nucleotide polymorphism database; —, inapplicable; HSF, Human Splicing Finder; SIFT, Sorting Intolerant from Tolerant; Polyphen-2, Polymorphism Phenotyping v2.