Table 1.
Information of the variants identified in this study
| Patient No. | Variant No. | Gene (transcript) | Genomic alteration | Protein alteration | Frequencies in 3 databases* | Revel score* | HGMD* level (PMID*) | ACMG* level (evidence) |
|---|---|---|---|---|---|---|---|---|
| 1 | 1 | CC2D2A (NM_001080522) | c.2444delC | p.P815fs*2 | 0; 0; 0 | / | / | Likely pathogenic (PVS1+PM2) |
| 2 | c.4238G>A | p.C1413Y | 0.002; 0.004406; 0.004347 | 0.306 | DM (27491411) | Likely pathogenic (PM3_Strong+PM3+BP4) | ||
| 2 | 3 | NPHP1 | del exon (1-20) | null | / | / | DM (multi studies) | Likely pathogenic (PVS1+PM2) |
| 3 | 4 | AHI1 (NM_017651) | c.910dupA | p.T304Nfs*5 | 0; 0; 0 | / | DM (16453322) | Pathogenic (PVS+PS1+PM2) |
| 5 | del exon (15-17) | uncertain | / | / | / | Pathogenic (PVS1+PM2+PM3) | ||
| 4 | 6 | C5orf42 (NM_023073) | c.4006C>T | p.R1336W | 0; 0; 0 | 0.273 | DM (22425360) | Likely pathogenic (PM2+PM3) |
| 7 | c.3551G>A | p.R1184H | 0; 0; 0 | 0.797 | DM (25407461) | Likely pathogenic (PM2+PM3+PM5+PP3) |
*
1000g2015aug_eas (https://www.internationalgenome.org/); ExAC_EAS (http://exac.broadinstitute.org); gnomAD_exome_EAS (http://gnomad.broadinstitute.org/); Revel: An ensemble method for predicting the pathogenicity of missense variants on the basis of individual tools: MutPred, FATHMM, VEST, PolyPhen, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP, SiPhy, phyloP, and phastCons (http://dx.doi.org/10.1016/j.ajhg.2016.08.016); HGMD®: Human Gene Mutation Database (Professional Version 2019.4); PMID: PubMed ID (https://pubmed.ncbi.nlm.nih.gov/); ACMG: The American College of Medical Genetics and Genomics; P: pathogenic; LP: likely pathogenic; VUS: variants of unknown significance.