Table 2.
Selected functional annotations of highest 20 single variants along 1q43-44 linked haplotype for family 4
| CHR | SNP | LOD | HLOD | Gene | FUNC | EXON | FRQ | SIFT | POLYPH |
|---|---|---|---|---|---|---|---|---|---|
| 1 | rs71585189:g.246021494C>A | 2.9 | 2.2 | SMYD3 | Intronic | . | 0.16 | . | . |
| 1 | rs1058305:g.243664642A>G | 2.9 | 2.2 | AKT3 | UTR3 | . | 0.26 | . | . |
| 1 | rs1058304:g.243664857C>T | 2.9 | 2.2 | AKT3 | UTR3 | . | 0.26 | . | . |
| 1 | rs9428966:g.243667900T>G | 2.9 | 2.2 | AKT3 | UTR3 | . | 0.26 | . | . |
| 1 | rs76577803:g.245247095G>A | 2.9 | 2.9 | EFCAB2 | Intronic | . | 0.026 | . | . |
| 1 | rs143882766:g.246704348G>A | 2.9 | 2.9 | TFB2M | Exonic | Syn | 0.004 | . | . |
| 1 | rs190157408:g.243335862C>T | 2.9 | 2.9 | CEP170 | Intronic | . | 0.007 | . | . |
| 1 | rs189525806:g.248042279T>G | 2.9 | 2.9 | TRIM58 | UTR3 | . | . | . | . |
| 1 | rs61749963:g.245006474A>G | 2.9 | 2.9 | COX20 | Exonic | Nonsyn | 0.012 | T | B |
| 1 | rs150412216:g.248569960G>A | 2.9 | 2.6 | OR2T1 | Exonic | Nonsyn | 0.005 | T | P |
| 1 | rs73141283:g.248309356A>G | 2.8 | 2.8 | OR2M5 | Exonic | Nonsyn | 0.065 | T | B |
| 1 | rs1339847:g.248039294G>A | 2.8 | 2.0 | TRIM58 | Exonic | Nonsyn | 0.097 | T | B |
| 1 | rs112566218:g.245517151A>G | 2.8 | 2.0 | KIF26B | Intronic | . | 0.061 | . | . |
| 1 | rs12401701:g.247737928A>T | 2.8 | 3.0 | GCSAML | UTR3 | . | 0.19 | . | . |
| 1 | rs12405268:g.247740764C>A | 2.7 | 3.0 | GCSAML | UTR3 | . | 0.19 | . | . |
| 1 | rs12402077:g.247739213A>G | 2.7 | 3.0 | GCSAML | UTR3 | . | 0.19 | . | . |
| 1 | rs34220133:g.247695427C>G | 2.7 | 2.3 | OR2C3 | Exonic | Nonsyn | 0.14 | D | B |
| 1 | rs1435953:g.242283940G>A | 2.7 | 1.9 | PLD5 | Intronic | . | 0.34 | . | . |
| 1 | rs6672510:g.242284412A>G | 2.7 | 1.9 | PLD5 | Intronic | . | 0.34 | . | . |
Selected functional annotations for the SNVs with the highest 19 LOD scores in Family 4. All variants are on chromosome 1 and mapped with hg19. Headers represent CHR = chromosome, ID = rsID, position, and allele change for SNV, LOD = LOD score for variant in Family 4, HLOD = Cumulative HLOD score across all 7 families, GENE = gene location of variant, FUNC = functional region of gene where variant is located, EXON = nonsynonymous (nonsyn), synonymous (syn) FRQ = 1000Genomes frequency of variant in Europeans, SIFT = protein damaging prediction based on SIFT (where T = tolerated, D = damaging), POLYPH = protein damage prediction based on PolyPhen2 (P = possibly damaging, B = benign)