Table 2 Exonic SNPs identified by both ROH and non-ROH analysis pipeline
| Gene and description | Cellular functiona | Chromosome location | MAF (<= 0.01) in 1 kg_all ; ExAC_all | rsID (dbSNP) | Pathogenicity scaleb (Suhas et.al 2018) | Tissue expressiona | Gene-Disease Association |
|---|---|---|---|---|---|---|---|
| Exome SNPs assessed by allele frequencies in AR inheritance pattern (non-ROH method) | |||||||
| KCNJ10 (inwardly rectifying potassium channel) | K+ homeostasis | c.A868G:p.T290A | Novel | NA | 6/6 | Brain, kidney | SeSAME syndrome; (Scholl et al., 2009) |
| PI4KB (phosphatidylinositol 4-kinase beta) | Phosphatidylinositol signaling | c.A215G:p.K72R | Novel | NA | 2/6 | Brain, liver | NA |
| PVRL4 (Nectin 4) | Cell Adhesion signaling | c:C320T:p.P107L | 0.004; 0.0052 | rs78105657 | 3/6 | Pancreas, skin |
Ectodermal dysplasia- Syndactyly syndrome 1; (Ahmad et al. 2018) |
| RORC (RAR-related orphan receptor C) | Nuclear signaling | c.G686A:p.S229N | 0.002; 0.0035 | rs41263732 | NP | Kidney, colon | Primary immunodeficiency-43 (Okada et al., 2015) |
| FCRL1 (Fc receptor-like 1) | Immune signaling | c:C1035G:p.S345R | 0.003; 0.003 | rs149687405 | NP | Blood, tonsil | NA |
| FLG2 (Filaggrin-2) | Calcium signaling | c.A6260G:p.H2087R | 0.004; 0.0068 | rs141384852 | NP | Skin, liver | NA |
| NIT1(Nitrilase 1) | Apoptosis | c.A4G:p.T2A | 0.0009; 0.0051 | rs138523655 | 2/6 | Brain, liver | NA |
| Exome SNPs assessed by runs of homozygosity (ROH method) | |||||||
| KCNJ10 (inwardly rectifying potassium channel) | K+ homeostasis | c.A868G:p.T290A | Novel | NA | 6/6 | Brain, kidney |
SeSAME syndrome; (Scholl et al. 2009) |
| HSPA6 (heat shock protein Family A, HSP70) | Molecular chaperone in protein homeostasis | c.C592T:p.L198F | 0.124201;0.1165 | rs1079109 | 3/6 | Brain, muscles, kidney |
Sensory disturbances; (Kobayashi et al. 2013) |