Table 1.
Details of the 41 Rare Candidate NMTC Predisposing Variants with Co-Segregation in NMTC Families
| Family ID | Position (Hg19) | dbSNP ID | Gene | Variant type | Effect | Z-scorea |
|---|---|---|---|---|---|---|
| B | chr6:46655960 | rs1177620240 | TDRD6 | frameshift_variant | p.Leu32fs | 1.387 |
| A | chr10:94267395 | rs749353444 | IDE | frameshift_variant | p.Met394fs | 1.378 |
| I | chr14:24710238 | N/A | TINF2 | frameshift_variant | p.Gly197fs | 4.583 |
| O | chr17:78318734 | N/A | RNF213 | frameshift_variant | p.His2200fs | 0.456 |
| H | chr7:141321533 | rs1228071168 | AGK | frameshift_variant & splice_region_variant | p.His174fs | 1.382 |
| M | chr1:160340766 | N/A | NHLH1 | missense_variant | p.Thr82Lys | 0.628 |
| O | chr3:129390026 | N/A | TMCC1 | missense_variant | p.Ser41Ala | 0.447 |
| H | chr4:74270076 | N/A | ALB | missense_variant | p.Phe11Tyr | 1.242 |
| B | chr5:79368179 | N/A | THBS4 | missense_variant | p.Asp600Gly | 1.342 |
| B | chr5:133295603 | rs769385290 | C5orf15 | missense_variant | p.Gln83Arg | 2.218 |
| O | chr5:136997689 | rs1234320567 | KLHL3 | missense_variant | p.Tyr223Cys | 0.447 |
| B | chr5:176520192 | N/A | FGFR4 | missense_variant | p.Ile371Val | 1.37 |
| A | chr7:150938678 | rs139896646 | SMARCD3 | missense_variant | p.Arg280His | 1.639 |
| O | chr9:132845876 | N/A | GPR107 | missense_variant | p.Ser187Pro | 0.244 |
| B | chr9:140352197 | N/A | NSMF | missense_variant | p.Pro97 his | 2.198 |
| B | chr10:29782280 | N/A | SVIL | missense_variant | p.Lys86Asn | 1.389 |
| N | chr10:120832522 | rs1241413917 | EIF3A | missense_variant | p.Thr141Ala | 3.331 |
| L | chr11:74459941 | rs749118015 | RNF169 | missense_variant | p.Pro6Ser | 2.813 |
| A | chr11:129744416 | rs200192480 | NFRKB | missense_variant | p.Pro680Ser | 1.682 |
| O | chr12:7171685 | N/A | C1S | missense_variant | p.Lys169Thr | 0.446 |
| Q | chr16:65005565 | rs776739314 | CDH11 | missense_variant | p.Asp520Gly | 1.755 |
| A | chr16:67916998 | N/A | EDC4 | missense_variant | p.Ser1256Cys | 1.367 |
| M | chr19:46376146 | rs372848865 | FOXA3 | missense_variant | p.Asp295His | 1.264 |
| L | chr20:5155891 | N/A | CDS2 | missense_variant | p.Ile86Ser | 2.78 |
| O | chr20:23358093 | N/A | NAPB | missense_variant | p.Asp273Asn | 1.342 |
| O | chr20:50407707 | N/A | SALL4 | missense_variant | p.Pro439Thr | 1.342 |
| H | chr14:55836494 | N/A | ATG14 | missense_variant | p.Pro441Leu | 1.381 |
| P | chr14:94088825 | N/A | UNC79 | missense_variant | p.Leu1572His | 1.94 |
| A | chr22:21351254 | N/A | LZTR1 | missense_variant and splice_region_variant | p.Lys802Arg | 1.228 |
| A | chr1:17316456 | rs866035312 | ATP13A2 | stop_gained | p.Arg819Ter | 1.382 |
| B | chr2:219267800 | N/A | CTDSP1 | stop_gained | p.Arg141Ter | 1.388 |
| H | chr3:50684626 | rs768275251 | MAPKAPK3 | stop_gained | p.Glu330Ter | 1.382 |
| Q | chr16:70304179 | rs756337758 | AARS | stop_gained | p.Arg246Ter | 1.755 |
| B | chr18:61006104 | rs377122315 | KDSR | stop_gained | p.Arg172Ter | 2.172 |
| F | chr19:35175846 | rs775988983 | ZNF302 | stop_gained | p.Gln302Ter | 0.632 |
| H | chr19:57932175 | rs375034689 | ZNF17 | stop_gained | p.Glu441Ter | 1.737 |
| Q | chr16:31434433 | rs769152136 | ITGAD | splice_acceptor_variant | c.2781-2A>C | 1.382 |
| Q | chr16:31434434 | rs759944116 | ITGAD | splice_acceptor_variant | c.2781-1G>A | 1.382 |
| F | chr12:95486473 | N/A | FGD6 | splice_donor_variant | c.3747 + 2A>G | 0.632 |
| Q | chr16:70161297 | N/A | PDPR | splice_donor_variant | c.361 + 1G>C | 1.755 |
| O | chr20:31466614 | N/A | EFCAB8 | splice_donor_variant | c.431 + 1G>C | 1.341 |
a
Value represents the average Z-score of the two adjacent single nucleotide polymorphism (SNP) markers in linkage analysis within each family.