Alternative titles; symbols
HGNC Approved Gene Symbol: NPRL3
Cytogenetic location: 16p13.3 Genomic coordinates (GRCh38) : 16:85,386-138,673 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 16p13.3 | Epilepsy, familial focal, with variable foci 3 | 617118 | Autosomal dominant | 3 |
The NPRL3 gene encodes a subunit of the GATOR1 complex, which regulates the mTORC1 (see 601231) signaling pathway. Other GATOR1 subunits include DEPDC5 (614191) and NPRL2 (607072) (summary by Ricos et al., 2016).
Vyas et al. (1995) reported the characterization of a gene (designated '-14' by them to indicate its relative position) that lies adjacent to the alpha globin gene cluster on chromosome 16p13.3. The -14 cDNA encodes a predicted 544- or 569-amino acid protein, depending on the alternative splicing of exon 5. Two mRNAs of 3.2 and 2.5 kb were detected in a variety of cell lines (Vyas et al., 1992). Curiously, a previously identified erythroid-specific regulatory element occurs within intron 5. This regulatory sequence does not influence expression of the gene, which has a GC-rich promoter (unlike the TATA-type promoters of the alpha globin loci).
Ricos et al. (2016) found expression of the NPRL3 gene in all human brain regions analyzed, including frontal, temporal, parietal, and occipital lobes. A similar pattern of expression was found in both embryonic and adult mouse brain. All 3 genes in the GATOR1 complex showed a striking similarity in tissue distribution.
Vyas et al. (1995) determined that the -14 gene contains 15 exons and spans about 55 kb.
Cryoelectron Microscopy
Shen et al. (2018) used cryoelectron microscopy to solve structures of GATOR1 and GATOR1-RAG GTPases complexes. GATOR1 adopts an extended architecture with a cavity in the middle; NPRL2 links DEPDC5 and NPRL3, and DEPDC5 contacts the RAG GTPase heterodimer. Biochemical analyses revealed that this GATOR1-RAG GTPases structure is inhibitory, and that at least 2 binding modes must exist between the RAG GTPases and GATOR1. Direct interaction of DEPDC5 with RAGA (612194) inhibits GATOR1-mediated stimulation of GTP hydrolysis by RAGA, whereas weaker interactions between the NPRL2-NPRL3 heterodimer and RAGA execute GAP activity.
Vyas et al. (1995) identified the -14 gene adjacent to the alpha globin gene cluster on chromosome 16p13.3. The authors showed that the sequence of the gene and its location adjacent to alpha globin loci has been conserved for at least 270 million years.
Bar-Peled et al. (2013) identified the octameric GATOR (GTPase-activating protein (GAP) activity toward RAGs) complex as a critical regulator of the pathway that signals amino acid sufficiency to mTORC1 (see 601231). GATOR is composed of 2 subcomplexes, GATOR1 and GATOR2. Inhibition of the GATOR1 subunits DEPDC5 (614191), NPRL2 (607072), and NPRL3 makes mTORC1 signaling resistant to amino acid deprivation. In contrast, inhibition of the GATOR2 subunits MIOS (615359), WDR24 (620307), WDR59 (617418), SEH1L (609263), and SEC13 (600152) suppresses mTORC1 signaling, and epistasis analysis shows that GATOR2 negatively regulates DEPDC5. GATOR1 has GAP activity for RAGA (612194) and RAGB (300725), and its components are mutated in human cancer. In cancer cells with inactivating mutations in GATOR1, mTORC1 is hyperactive and insensitive to amino acid starvation, and such cells are hypersensitive to rapamycin, an mTORC1 inhibitor. Thus, Bar-Peled et al. (2013) concluded that they had identified a key negative regulator of the RAG GTPases and revealed that, like other mTORC1 regulators, RAG function can be deregulated in cancer.
Using HEK293 cells, Gu et al. (2017) found that SAMTOR (BMT2; 617855) bound the GATOR1-KICSTOR (see 617420) supercomplex, and that SAMTOR-GATOR1-KICSTOR inhibited MTORC1 signaling at lysosomes. Binding of S-adenosylmethionine (SAM) to SAMTOR interfered with binding of SAMTOR to GATOR1-KICSTOR and permitted MTORC1 signaling. Methionine starvation reduced SAM levels, promoting association of SAMTOR with GATOR1-KICSTOR and inhibition of MTORC1 lysosomal signaling. The authors concluded that SAMTOR senses methionine availability via SAM binding and thereby links methionine availability with MTORC1 signaling.
In 10 patients from 5 unrelated families with focal epilepsy with variable foci-3 (FFEVF3; 617118), Ricos et al. (2016) identified 5 different heterozygous mutations in the NPRL3 gene (see, e.g., 600928.0001-600928.0002), including 3 truncating mutations and 2 missense mutations. There was evidence of incomplete penetrance. The mutation in 1 large family was found by exome sequencing; the remaining probands were ascertained from a cohort of 404 individuals with focal epilepsy who underwent targeted sequencing for genes in the GATOR1 complex. Functional studies of the variants and studies of patient cells were not performed. The findings suggested that loss of function of the GATOR1 complex due to NPRL2 mutations can cause deregulated cellular growth and may play an important role in cortical dysplasia and focal epilepsy.
In 4 members of a family with FFEVF3, Sim et al. (2016) identified a heterozygous frameshift mutation in the NPRL3 gene (600928.0002). The mutation, which was found by whole-exome sequencing, showed incomplete penetrance in the family. Two of the patients had focal cortical dysplasia (FCD). Sequence analysis of the NPRL3 gene in 52 individuals with FCD identified 2 unrelated patients with heterozygous mutations (see, e.g., 600928.0003). Resected dysplastic brain tissue from 3 patients with truncating mutations showed a 50% decrease in NPRL3, consistent with haploinsufficiency, as well as evidence of activation of the mTOR pathway.
In affected members of 2 unrelated families with FFEVF3 and FCD, Weckhuysen et al. (2016) identified 2 different heterozygous truncating mutations in the NPRL3 gene (600928.0004-600928.0005). The mutations, which were found by sequencing a targeted epilepsy gene panel in 93 probands with focal epilepsy with or without FCD, were confirmed by Sanger sequencing.
In 133 members of an Old Order Mennonite pedigree with FFEVF3, Iffland et al. (2022) identified a heterozygous mutation in the NPRL3 gene (c.349delG; 600928.0006). Pedigree analysis demonstrated that all of the mutation carriers traced back to a single founder. Of the 133 patients, 48 had a history of seizures and 85 had no history of seizures. Whole-exome sequencing comparing 37 patients with no seizures to 24 patients with seizures did not identify any potential modifier genes that explained the epilepsy penetrance. Iffland et al. (2022) analyzed Nprl3 knockout N2a cells and showed that the cells had enhanced ribosomal S6 protein (PS6) phosphorylation compared to wildtype cells. This enhanced PS6 phosphorylation was corrected with treatment with rapamycin. However, PS6 phosphorylation was not corrected in the Nprl3 knockout cells under conditions of amino acid starvation, indicating that Nprl3 abrogates the effect of GATOR1 on mTOR activation. The Nprl3 knockout N2a cells formed abnormal cellular aggregates, which was corrected with rapamycin treatment.
Iffland et al. (2022) used CRISPR/Cas9 to target Nprl3 in neuroglial progenitor cells in developing mouse embryos. The resulting pups had cortical laminar defects on postnatal day 3. These laminar defects were rescued with in utero treatment with rapamycin. At 5 weeks of age, the mice had abnormal EEGs and reduced seizure thresholds. Treatment with rapamycin corrected the abnormal seizure thresholds.
In 3 members of a family (family 6) with familial focal epilepsy with variable foci-3 (FFEVF3; 617118), Ricos et al. (2016) identified a heterozygous 1-bp insertion (c.835_836insT, NM_001077350.2) in the NPRL3 gene, resulting in a frameshift and premature termination (Ser279PhefsTer52). The mutation, which was found by whole-exome sequencing, was not found in the dbSNP, Exome Variant Server, or ExAC databases. The mutation was also confirmed by linkage analysis in this family. Two unaffected individuals carried the mutation, consistent with incomplete penetrance. Another family member with febrile seizures also carried the mutation.
In a father and his 2 sons (family 7) with familial focal epilepsy with variable foci-3 (FFEVF3; 617118), Ricos et al. (2016) identified a heterozygous 2-bp insertion (c.1376_1377insAC, NM_001077350.2) in the NPRL3 gene, resulting in a frameshift and premature termination (Ser460ProfsTer20). The mutation was not found in the dbSNP, Exome Variant Server, or ExAC databases. Functional studies of the variant and studies of patient cells were not performed.
Sim et al. (2016) identified heterozygosity for the same mutation, which they reported as c.1375_1376dupAC, resulting in a frameshift (Ser460ProfsTer20), in 4 members of a family with FFEVF3; 2 patients had focal cortical dysplasia. The mutation was found by whole-exome sequencing and confirmed by Sanger sequencing and by linkage analysis. The mutation was also found in 4 unaffected family members in previous generations, consistent with incomplete penetrance. Resected dysplastic brain tissue of 2 patients showed a 50% decrease in NPRL3, consistent with nonsense-mediated mRNA decay of the mutant transcript and haploinsufficiency.
In a 6-year-old boy (patient 5) with familial focal epilepsy with variable foci-3 (FFEVF3; 617118), Sim et al. (2016) identified a heterozygous del/ins mutation affecting the splice acceptor site of exon 13 of the NPRL3 gene (c.1352-4delACAGinsTGACCCATCC). The mutation was inherited from his asymptomatic mother. The patient was from a cohort of 52 individuals with focal cortical dysplasia who underwent sequence analysis of the NPRL3 gene. Resected dysplastic brain tissue from the patient showed a 50% decrease in NPRL3, consistent with nonsense-mediated mRNA decay of the mutant transcript and haploinsufficiency.
In affected members of a French family (family F) with familial focal epilepsy with variable foci-3 (FFEVF3; 617118), Weckhuysen et al. (2016) identified a heterozygous c.1270C-T transition (c.1270C-T, NM_001077350) in the NPRL3 gene, resulting in an arg424-to-ter (R424X) substitution. The mutation, which was found by sequencing a targeted epilepsy gene panel, was confirmed by Sanger sequencing and filtered against the Exome Variant Server database; it was not found in the ExAC database. At least 1 unaffected family member carried the mutation, consistent with incomplete penetrance. Analysis of patient cells showed that the mutant transcript was subject to nonsense-mediated mRNA decay, consistent with haploinsufficiency. Brain sample from 1 of the patients, who had focal cortical dysplasia, showed hyperactivation of the mTOR pathway in normal and dysmorphic neurons. These findings suggested that the NPRL3 mutation resulted in a loss of function of the GATOR1 complex.
In 4 members of a 3-generation Swiss family (family G) with familial focal epilepsy with variable foci-3 (FFEVF3; 617118), Weckhuysen et al. (2016) identified a heterozygous 1-bp deletion (c.1070delC, NM_001077350) in the NPRL3 gene, resulting in a frameshift and premature termination (Pro357HisfsTer56). The mutation, which was found by sequencing a targeted epilepsy gene panel, was confirmed by Sanger sequencing and filtered against the Exome Variant Server database; it was not found in the ExAC database.
In 133 members of an Old Order Mennonite pedigree with familial focal epilepsy with variable foci-3 (FFEVF3; 617118), Iffland et al. (2022) identified heterozygosity for a 1-bp deletion (c.349delG) in the NPRL3 gene, predicted to result in a frameshift and premature termination (Glu117LysfsTer). The mutation was identified in each patient by whole-exome sequencing, targeted NPRL3 variant testing, or an extended carrier test targeted for the Older Order Amish and Mennonite communities. Pedigree analysis demonstrated that all of the mutation carriers traced back to a single founder. Of the 133 patients, 48 had a history of seizures and 85 had no history of seizures.
Bar-Peled, L., Chantranupong, L., Cherniack, A. D., Chen, W. W., Ottina, K. A., Grabiner, B. C., Spear, E. D., Carter, S. L., Meyerson, M., Sabatini, D. M. A tumor suppressor complex with GAP activity for the Rag GTPases that signal amino acid sufficiency to mTORC1. Science 340: 1100-1106, 2013. [PubMed: 23723238] [Full Text: https://doi.org/10.1126/science.1232044]
Gu, X., Orozco, J. M., Saxton, R. A., Condon, K. J., Liu, G. Y., Krawczyk, P. A., Scaria, S. M., Harper, J. W., Gygi, S. P., Sabatini, D. M. SAMTOR is an S-adenosylmethionine sensor for the mTORC1 pathway. Science 358: 813-818, 2017. [PubMed: 29123071] [Full Text: https://doi.org/10.1126/science.aao3265]
Iffland, P. H., Everett, M. E., Cobb-Pitstick, K. M., Bowser, L. E., Barnes, A. E., Babus, J. K., Romanowski, A. J., Baybis, M., Elziny, S., Puffenberger, E. G., Gonzaga-Jauregui, C., Poulopoulos, A., Carson, V. J., Crino, P. B. NPRL3 loss alters neuronal morphology, mTOR localization, cortical lamination and seizure threshold. Brain 145: 3872-3885, 2022. [PubMed: 35136953] [Full Text: https://doi.org/10.1093/brain/awac044]
Ricos, M. G., Hodgson, B. L., Pippucci, T., Saidin, A., Ong, Y. S., Heron, S. E., Licchetta, L., Bisulli, F., Bayly, M. A., Hughes, J., Baldassari, S., Palombo, F., and 11 others. Mutations in the mammalian target of rapamycin pathway regulators NPRL2 and NPRL3 cause focal epilepsy. Ann. Neurol. 79: 120-131, 2016. [PubMed: 26505888] [Full Text: https://doi.org/10.1002/ana.24547]
Shen, K., Huang, R. K., Brignole, E. J., Condon, K. J., Valenstein, M. L., Chantranupong, L., Bomaliyamu, A., Choe, A., Hong, C., Yu, Z., Sabatini, D. M. Architecture of the human GATOR1 and GATOR1-Rag GTPases complexes. Nature 556: 64-69, 2018. [PubMed: 29590090] [Full Text: https://doi.org/10.1038/nature26158]
Sim, J. C., Scerri, T., Fanjul-Fernandez, M., Riseley, J. R., Gillies, G., Pope, K., van Roozendaal, H., Heng, J. I., Mandelstam, S. A., McGilivray, G., MacGregor, D., Kannan, L., Maixner, W., Harvey, A. S., Amor, D. J., Delatycki, M. B., Crino, P. B., Bahlo, M., Lockhart, P. J., Leventer, R. J. Familial cortical dysplasia caused by mutation in the mammalian target of rapamycin regulator NPRL3. Ann. Neurol. 79: 132-137, 2016. [PubMed: 26285051] [Full Text: https://doi.org/10.1002/ana.24502]
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Vyas, P., Vickers, M. A., Simmons, D. L., Ayyub, H., Craddock, C. F., Higgs, D. R. Cis-acting sequences regulating expression of the human alpha-globin cluster lie within constitutively open chromatin. Cell 69: 781-793, 1992. [PubMed: 1591777] [Full Text: https://doi.org/10.1016/0092-8674(92)90290-s]
Weckhuysen, S., Marsan, E., Lambrecq, V., Marchal, C., Morin-Brureau, M., An-Gourfinkel, I., Baulac, M., Fohlen, M., Zetchi, C. K., Seeck, M., de la Grange, P., Dermaut, B., Meurs, A., Thomas, P., Chassoux, F., Leguern, E., Picard, F., Baulac, S. Involvement of GATOR complex genes in familial focal epilepsies and focal cortical dysplasia. Epilepsia 57: 994-1003, 2016. [PubMed: 27173016] [Full Text: https://doi.org/10.1111/epi.13391]