NPRL3

NPR3 like, GATOR1 complex subunit, the group of GATOR1 subcomplex

Basic information

Region (hg38): 16:84270-138677

Previous symbols: [ "C16orf35" ]

Links

ENSG00000103148 ∙ NCBI:8131 ∙ OMIM:600928 ∙ HGNC:14124 ∙ Uniprot:Q12980 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• familial focal epilepsy with variable foci (Supportive), mode of inheritance: AD
• focal epilepsy (Definitive), mode of inheritance: AD
• epilepsy, familial focal, with variable foci 3 (Moderate), mode of inheritance: AD
• epilepsy, familial focal, with variable foci 3 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Epilepsy, familial focal, with variable foci 3	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	26285051; 26505888; 27173016

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NPRL3 gene.

• Epilepsy, familial focal, with variable foci 3 (640 variants)
• not provided (222 variants)
• Inborn genetic diseases (29 variants)
• NPRL3-related condition (3 variants)
• Seizure (3 variants)
• not specified (2 variants)
• Focal epilepsy (1 variants)
• Intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPRL3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			16	122	4	142
missense	1		259	5	3	268
nonsense	25	5	1			31
start loss						0
frameshift	36	8	5	1	1	51
inframe indel			13			13
splice donor/acceptor (+/-2bp)	4	19	2	1		26
splice region		2	36	18	3	59
non coding			28	94	56	178
Total	66	32	324	223	64

Highest pathogenic variant AF is 0.00000657

Variants in NPRL3

This is a list of pathogenic ClinVar variants found in the NPRL3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-85401-G-C		not specified	Uncertain significance (Apr 05, 2023)
16-85481-C-G		not specified	Uncertain significance (Feb 21, 2024)
16-85493-G-A		not specified	Uncertain significance (Sep 17, 2021)
16-85508-A-G		not specified	Uncertain significance (Mar 20, 2023)
16-85517-G-A		not specified	Uncertain significance (Feb 09, 2023)
16-85536-C-G		not specified	Uncertain significance (May 31, 2023)
16-85583-G-A		not specified	Uncertain significance (Dec 31, 2023)
16-85592-C-A		not specified	Uncertain significance (Dec 20, 2023)
16-85609-G-T		not specified	Uncertain significance (Nov 27, 2023)
16-85616-C-T		not specified	Uncertain significance (Sep 22, 2022)
16-85659-C-T		not specified	Uncertain significance (Oct 25, 2022)
16-85661-C-T		not specified	Uncertain significance (Jul 06, 2021)
16-85673-G-A		not specified	Uncertain significance (Feb 01, 2023)
16-85694-C-T		not specified	Uncertain significance (Jun 18, 2021)
16-85701-C-T		not specified	Uncertain significance (May 01, 2022)
16-85707-G-A		not specified	Uncertain significance (Sep 17, 2021)
16-85733-G-A		not specified	Uncertain significance (Nov 08, 2022)
16-85742-G-A		not specified	Uncertain significance (Dec 20, 2023)
16-86520-C-T			Likely benign (Jul 21, 2018)
16-86630-C-T			Likely benign (Aug 03, 2018)
16-86637-A-C			Benign (Jul 26, 2018)
16-86662-G-A			Likely benign (Aug 30, 2018)
16-86667-C-G			Benign (Nov 02, 2020)
16-86697-G-A		NPRL3-related disorder	Likely benign (Jul 21, 2020)
16-86706-CAG-C		Epilepsy, familial focal, with variable foci 3	Uncertain significance (Jan 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPRL3	protein_coding	protein_coding	ENST00000399953	14	54587

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.190	0.810	729	123969	7	124705	0.924

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.84	245	340	0.720	0.0000216	3661
Missense in Polyphen		65	93.976	0.69166		1084
Synonymous	-0.152	149	147	1.02	0.00000998	1131
Loss of Function	3.42	6	24.1	0.249	0.00000118	281

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	2.00	1.89
Ashkenazi Jewish	1.00	0.928
East Asian	1.00	0.955
Finnish	1.00	0.934
European (Non-Finnish)	1.00	0.913
Middle Eastern	1.00	0.955
South Asian	1.00	0.956
Other	1.00	0.917

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As a component of the GATOR1 complex functions as an inhibitor of the amino acid-sensing branch of the TORC1 pathway. The GATOR1 complex strongly increases GTP hydrolysis by RRAGA and RRAGB within RRAGC-containing heterodimers, thereby deactivating RRAGs, releasing mTORC1 from lysosomal surface and inhibiting mTORC1 signaling. The GATOR1 complex is negatively regulated by GATOR2 the other GATOR subcomplex in this amino acid-sensing branch of the TORC1 pathway. {ECO:0000269|PubMed:23723238}.
• Disease: DISEASE: Epilepsy, familial focal, with variable foci 3 (FFEVF3) [MIM:617118]: An autosomal dominant form of epilepsy characterized by focal seizures arising from different cortical regions, including the temporal, frontal, parietal, and occipital lobes. Seizure types commonly include temporal lobe epilepsy, frontal lobe epilepsy, and nocturnal frontal lobe epilepsy. Some patients may have intellectual disability or autism spectrum disorders. Seizure onset usually occurs in the first or second decades, although later onset has been reported, and there is phenotypic variability within families. A subset of patients have structural brain abnormalities. Penetrance of the disorder is incomplete. {ECO:0000269|PubMed:26285051, ECO:0000269|PubMed:26505888, ECO:0000269|PubMed:27173016}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: mTOR signaling pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.147

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.481
• ghis: 0.422

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nprl3
• Phenotype: immune system phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; liver/biliary system phenotype; homeostasis/metabolism phenotype; muscle phenotype; craniofacial phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: ventricular septum development;negative regulation of TOR signaling;cellular response to amino acid starvation;aorta morphogenesis;TORC1 signaling;positive regulation of GTPase activity;cardiac muscle tissue development;roof of mouth development;regulation of autophagosome assembly
• Cellular component: lysosomal membrane;GATOR1 complex
• Molecular function: GTPase activator activity;protein binding