TABLE 5.
Examples of 10 nonsyndromic human deafness intervals for which no causative gene has been identified to date, and candidate genes in these intervals identified in the current study
| Genes differentially expressed by ≥1.5-fold | Interval (size in Mb) | Markers | Total no. of genes in interval |
|---|---|---|---|
| ACTR10, C14ORF100 | DFNA23 (8.03) | D14S980–D14S1046 | 79 |
| DACT1, HIF1A, HSPA2 | |||
| MNAT1, MTHFD1, OTX2a | |||
| PPM1A, PRKCH, PSMA3 | |||
| RHOJ, RTN1, SIX1a | |||
| TIMM9, TMEM30B | |||
| AP3S2, BLM, CIB1a | DFNA30 (7.11) | D15S151–D15S130 | 74 |
| FURIN, IQGAP1 | |||
| LOC400451, MRPL46 | |||
| MRPS11, NTRK3 | |||
| PEX11A, POLG, PRC1 | |||
| RLBP1, VPS33B | |||
| CHFR, DDX51, EP400 | DFNA41 (4.05) | D12S1609-tel | 48 |
| GOLGA3, POLE, PXMP2, RANa | |||
| ANKHD1, APBB3, BRD8 | DFNA42 (11.99) | D5S2056–D5S638 | 172 |
| C5ORF5, CDC23, CDC25C | |||
| CTNNA1a, CXCL14, CXXC5 | |||
| EGR1, ETF1, GNPDA1 | |||
| H2AFY, HARS, HARSL | |||
| HSPA9B, IK, KIAA0141 | |||
| KIF20A, LOC340061 | |||
| MATR3, NDFIP1, NDUFA2 | |||
| NME5, ORF1-FL49, PCDHB13 | |||
| PCDHB17, PCDHB9, PFDN1 | |||
| POU4F3, PPP2R2B, PURA | |||
| RNF14, SIL1, SLC35A4 | |||
| SMAD5, SRA1, TAF7 | |||
| TCERG1, TGFBI, UBE2D2 | |||
| C14ORF21, DHRS1 | DFNA53 (6.97) | D14S581–D14S1021 | 60 |
| DHRS4, FOXG1Ba | |||
| GMPR2, IPO4, ISGF3G | |||
| NEDD8, NFATC4, PRKCM | |||
| PSME2, RABGGTA, SCFD1 | |||
| STXBP6, TINF2, WDR23 | |||
| ARPC1B, ARS2, ASNS | DFNB14 (11.93) | D7S527–D7S3074 | 172 |
| ATP5J2, BCAP29, BRI3 | |||
| CBLL1, COPS6a, CPSF4 | |||
| CUTL1, CYP3A5 | |||
| DKFZP434B0335, DKFZP434K1815 | |||
| DLX5, EMID2, EPHB4 | |||
| GNB2, HBP1, HRBL | |||
| LAMB1, LRCH4, MCM7 | |||
| MLL5, ORC5L, PBEF1 | |||
| PCOLCE, PDAP1, PIK3CG | |||
| PILRB, POLR2Ja, POP7 | |||
| PSMC2, PTCD1, SHFM1 | |||
| SLC12A9, SLC25A13a | |||
| SLC26A4a, SRPK2, SVH | |||
| SYPL, TAC1, TAF6, ZNF3 | |||
| ZNF38, ZNF394, ZNHIT1 | |||
| BCAP29, CBLL1, DNAJB9 | DFNB17 (3.99) | D7S2453–D7S525 | 24 |
| HBP1, IPLA2(GAMMA) | |||
| LAMB1, NRCAM, PBEF1 | |||
| PIK3CG, SLC26A4a, SYPL | |||
| ABCD4, ACYP1, ALDH6A1 | DFNB35 (7.85) | D14S588–D14S59 | 110 |
| C14ORF112, C14ORF133 | |||
| C14ORF169, CHX10, EIF2B2 | |||
| ENTPD5, ESRRB, FOS, GSTZ1 | |||
| JDP2, MED6, NEK9, NPC2 | |||
| NUMB, PCNX, PGF, POMT2 | |||
| PSEN1, RBM25, SMOC1a | |||
| SYNJ2BP, TGFB3 | |||
| AUTS2, BAZ1B, CACNA2D1 | DFNB39 (17.93) | D7S3046–D7S644 | 114 |
| CALN1, CLDN3a, CLDN4a | |||
| ELN, FZD9, GNAI1, GTF2I | |||
| GTF2IRD1, GTF2IRD2, HGF | |||
| HIP1a, LIMK1, LOC54103 | |||
| MDH2, PCLO, PHTF2, POM121 | |||
| PTPN12, SEMA3A, SEMA3E | |||
| STX1A, WBSCR1, YWHAG | |||
| ADAMTS7, ARID3B, ARIH1a | DFNB48 (11.66) | D15S216–D15S1041 | 155 |
| CIB2, COX5Aa, CRABP1 | |||
| CSPG4, CTSH, ETFA, FAH | |||
| HEXA, HMG20A, IDH3A | |||
| ISL2, ISLR, MAN2C1 | |||
| MORF4L1, MTHFS, NEO1 | |||
| PKM2, PTPN9, RASGRF1 | |||
| SCAMP2, SCAMP5, SDFR1 | |||
| SIN3A, STARD5, TLE3 |
The human nonsyndromic deafness intervals shown here contain mouse orthologs found in this study to be differentially expressed (listed in the first column). Refer to supplemental Table 8 for a listing of all 54 intervals.
a
Genes upregulated in at least 30% of all IE samples relative to at least one NIE sample.