SESN3

sestrin 3

Basic information

Region (hg38): 11:95165513-95232541

Links

ENSG00000149212 ∙ NCBI:143686 ∙ OMIM:607768 ∙ HGNC:23060 ∙ Uniprot:P58005 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SESN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SESN3 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					1	1
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	19	0	2

Variants in SESN3

This is a list of pathogenic ClinVar variants found in the SESN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-95173280-C-T		not specified	Uncertain significance (Sep 22, 2022)
11-95177769-G-A			Benign (Mar 09, 2018)
11-95177797-A-C		not specified	Uncertain significance (Mar 01, 2025)
11-95178795-A-G		not specified	Uncertain significance (Jul 14, 2021)
11-95178802-A-T		not specified	Uncertain significance (Jan 29, 2025)
11-95178804-G-A		not specified	Uncertain significance (Nov 30, 2022)
11-95178808-T-C		not specified	Uncertain significance (Sep 10, 2024)
11-95178814-T-C		not specified	Uncertain significance (Jan 07, 2025)
11-95184492-G-A		not specified	Uncertain significance (Apr 17, 2023)
11-95184542-A-G		not specified	Uncertain significance (Dec 18, 2023)
11-95184593-A-G		not specified	Uncertain significance (Jan 28, 2025)
11-95185286-C-G		not specified	Uncertain significance (Apr 25, 2022)
11-95185318-C-T		not specified	Uncertain significance (Mar 30, 2024)
11-95185357-A-C		not specified	Uncertain significance (Jan 19, 2024)
11-95189810-C-T		not specified	Uncertain significance (Aug 11, 2022)
11-95189867-T-C		not specified	Uncertain significance (Jul 26, 2022)
11-95189920-A-T		not specified	Uncertain significance (Aug 22, 2023)
11-95191451-T-C		not specified	Uncertain significance (May 30, 2024)
11-95191454-G-A		not specified	Uncertain significance (Feb 04, 2025)
11-95191580-C-T		not specified	Uncertain significance (Jun 07, 2023)
11-95191585-G-C			Uncertain significance (Oct 25, 2017)
11-95191611-A-C			Benign (Apr 04, 2018)
11-95193491-G-T		not specified	Uncertain significance (Jul 09, 2021)
11-95193498-G-A		not specified	Uncertain significance (Aug 14, 2024)
11-95193521-T-C		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SESN3	protein_coding	protein_coding	ENST00000536441	10	67002

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.685	0.315	125715	0	11	125726	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.61	149	270	0.552	0.0000139	3246
Missense in Polyphen		49	114.39	0.42835		1375
Synonymous	1.20	76	90.5	0.840	0.00000422	917
Loss of Function	3.78	5	25.7	0.195	0.00000150	304

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000148
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000443	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as an intracellular leucine sensor that negatively regulates the TORC1 signaling pathway (PubMed:25263562). May also regulate the insulin-receptor signaling pathway through activation of TORC2 (By similarity). This metabolic regulator may also play a role in protection against oxidative and genotoxic stresses (By similarity). {ECO:0000250|UniProtKB:P58004, ECO:0000250|UniProtKB:Q9CYP7, ECO:0000269|PubMed:25263562}.
• Pathway: p53 signaling pathway - Homo sapiens (human);Longevity regulating pathway - Homo sapiens (human);TP53 Regulates Metabolic Genes;Angiopoietin Like Protein 8 Regulatory Pathway;miRNA regulation of p53 pathway in prostate cancer;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;TP53 Regulates Metabolic Genes;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.109
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.342
• hipred: Y
• hipred_score: 0.662
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.302

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sesn3
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: positive regulation of macroautophagy;response to insulin;cellular response to amino acid starvation;TORC2 signaling;cellular response to glucose starvation;glucose homeostasis;regulation of insulin receptor signaling pathway;regulation of protein kinase B signaling;oxidation-reduction process;cellular response to amino acid stimulus;cellular response to leucine;regulation of response to reactive oxygen species;negative regulation of TORC1 signaling;cellular response to leucine starvation
• Cellular component: nucleus;cytoplasm;TORC2 complex;GATOR2 complex
• Molecular function: protein binding;oxidoreductase activity, acting on peroxide as acceptor;leucine binding