Alternative titles; symbols
HGNC Approved Gene Symbol: NPRL2
Cytogenetic location: 3p21.31 Genomic coordinates (GRCh38): 3:50,347,330-50,350,775 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 3p21.31 | Epilepsy, familial focal, with variable foci 2 | 617116 | Autosomal dominant | 3 |
The NPRL2 gene encodes a subunit of the GATOR1 complex, which regulates the mTORC1 (see 601231) signaling pathway. Other GATOR1 subunits include DEPDC5 (614191) and NPRL3 (600928) (summary by Ricos et al., 2016).
By physical cloning methodologies and bioinformatic computational analyses, Lerman and Minna (2000) identified a number of genes, including NPR2L, which they called NPRL2, in a region of chromosome 3p21.3 that is associated with a putative lung cancer tumor suppressor gene. The deduced 380-amino acid conserved soluble protein, which is 97% identical to the mouse protein and orthologous to the yeast nitrogen permease gene Npr2, contains a bipartite nuclear localization signal and a granulin protein-binding domain. The authors identified multiple NPRL2 splice variants. Northern blot analysis revealed expression of a 1.5-kb transcript that was most abundant in skeletal muscle, followed by brain, liver, and pancreas, with lower amounts in lung, kidney, placenta, and heart. NPRL2 was expressed in most lung cancer cell lines tested. Mutations, including stop mutations, were found in approximately 5% of cell lines tested, but none of the genes identified in the search had a high frequency of mutations. Lerman and Minna (2000) proposed that NPRL2 is a candidate for functional tumor suppressor gene studies.
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.
By genomic sequence analysis, Lerman and Minna (2000) determined that the NPRL2 gene contains 11 exons and spans 3.3 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.
By genomic sequence analysis, Lerman and Minna (2000) determined that the NPRL2 gene resides in a 120-kb critical region for a lung cancer tumor suppressor gene on chromosome 3p21.3.
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, and NPRL3 (600928) 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 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-2 (FFEVF2; 617116), Ricos et al. (2016) identified 5 different heterozygous mutations in the NPRL2 gene (see, e.g., 607072.0001-607072.0003), including 2 truncating mutations and 3 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 2 French sisters with FFEVF2, Weckhuysen et al. (2016) identified a heterozygous frameshift mutation in the NPRL2 gene (607072.0004). The mutation, which was found by sequencing a targeted epilepsy gene panel, was confirmed by Sanger sequencing. The unaffected father and an unaffected sib also carried the mutation, consistent with incomplete penetrance. Brain sample from 1 of the patients, who had focal cortical dysplasia, showed hyperactivation of the mTOR pathway in neurons of normal appearance. These findings suggested that the NPRL2 mutation resulted in a loss of function of the GATOR1 complex.
In a father and daughter (family 1) with familial focal epilepsy with variable foci-2 (FFEVF2; 617116), Ricos et al. (2016) identified a heterozygous c.100C-T transition (c.100C-T, NM_006545.4) in the NPRL2 gene, resulting in an arg34-to-ter (R34X) substitution. 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.
In a woman (family 2) with familial focal epilepsy with variable foci-2 (FFEVF2; 617116), Ricos et al. (2016) identified a heterozygous c.883C-T transition (c.883C-T, NM_006545.4) in the NPRL2 gene, resulting in an arg295-to-ter (R295X) substitution. The patient's unaffected daughter also carried the mutation, consistent with incomplete penetrance. 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.
In 5 members of a 3-generation family (family 5) with familial focal epilepsy with variable foci-2 (FFEVF2; 617116), Ricos et al. (2016) identified a heterozygous c.314T-C transition (c.314T-C, NM_006545.4) in the NPRL2 gene, resulting in an leu105-to-pro (L105P) substitution. One unaffected family member carried the mutation, consistent with incomplete penetrance. The mutation, which was found by exome sequencing, 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.
In 2 French sisters (family E) with familial focal epilepsy with variable foci-2 (FFEVF2; 617116), Weckhuysen et al. (2016) identified a heterozygous 2-bp deletion (c.68_69delCT, NM_006545) in exon 1 of the NPRL2 gene, resulting in a frameshift and premature termination (Ile23AspfsTer6). 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. The unaffected father and an unaffected sib also carried the mutation, consistent with incomplete penetrance. A distant relative on the paternal side of the family with an unspecified epilepsy also carried the mutation. Analysis of patient cells showed that the mutant transcript was not subject to nonsense-mediated mRNA decay, but was predicted to result in a very truncated protein. Brain sample from 1 of the patients, who had focal cortical dysplasia, showed hyperactivation of the mTOR pathway in neurons of normal appearance. These findings suggested that the NPRL2 mutation resulted in a loss of function of the GATOR1 complex.
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]
Lerman, M. I., Minna, J. D. The 630-kb lung cancer homozygous deletion region on human chromosome 3p21.3: identification and evaluation of the resident candidate tumor suppressor genes. Cancer Res. 60: 6116-6133, 2000. [PubMed: 11085536]
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]
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]