BECN1

beclin 1, the group of PIK3C3 complex subunits|Autophagy related|MicroRNA protein coding host genes

Basic information

Region (hg38): 17:42810133-42833350

Links

ENSG00000126581 ∙ NCBI:8678 ∙ OMIM:604378 ∙ HGNC:1034 ∙ Uniprot:Q14457 ∙ 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 BECN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BECN1 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			15	1		16
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	15	2	1

Variants in BECN1

This is a list of pathogenic ClinVar variants found in the BECN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-42811778-G-C		not specified	Uncertain significance (Feb 28, 2023)
17-42811789-C-T		not specified	Likely benign (Feb 05, 2024)
17-42813956-T-C		not specified	Uncertain significance (Oct 10, 2023)
17-42814003-C-T		not specified	Uncertain significance (Jan 26, 2022)
17-42814515-A-G			Benign (Jul 31, 2018)
17-42814651-T-C		not specified	Uncertain significance (Dec 01, 2022)
17-42815921-T-C		not specified	Uncertain significance (Nov 07, 2023)
17-42815962-G-A		not specified	Likely benign (Jul 13, 2021)
17-42816017-G-C		not specified	Uncertain significance (Jul 13, 2022)
17-42816018-C-G		not specified	Uncertain significance (May 31, 2023)
17-42818303-C-T		not specified	Uncertain significance (Nov 08, 2021)
17-42818395-T-A		not specified	Uncertain significance (Jan 23, 2023)
17-42818860-C-T		not specified	Uncertain significance (Jun 14, 2022)
17-42819569-C-A		not specified	Uncertain significance (Jan 16, 2024)
17-42819570-G-A		not specified	Uncertain significance (Nov 10, 2022)
17-42819599-A-G		not specified	Uncertain significance (May 24, 2023)
17-42823763-T-G		not specified	Uncertain significance (Jun 13, 2024)
17-42823810-T-A		not specified	Uncertain significance (Sep 01, 2021)
17-42823843-A-G		not specified	Uncertain significance (Aug 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BECN1	protein_coding	protein_coding	ENST00000361523	11	23216

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.937	0.0628	125734	0	12	125746	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.88	167	251	0.666	0.0000134	2989
Missense in Polyphen		59	96.85	0.60919		1203
Synonymous	2.12	70	96.5	0.725	0.00000540	810
Loss of Function	4.04	4	26.4	0.151	0.00000138	296

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000215	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000668	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a central role in autophagy (PubMed:23184933, PubMed:28445460). Acts as core subunit of the PI3K complex that mediates formation of phosphatidylinositol 3-phosphate; different complex forms are believed to play a role in multiple membrane trafficking pathways: PI3KC3-C1 is involved in initiation of autophagosomes and PI3KC3-C2 in maturation of autophagosomes and endocytosis. Involved in regulation of degradative endocytic trafficking and required for the abcission step in cytokinesis, probably in the context of PI3KC3-C2 (PubMed:20643123, PubMed:20208530, PubMed:26783301). Essential for the formation of PI3KC3-C2 but not PI3KC3-C1 PI3K complex forms. Involved in endocytosis (PubMed:25275521). Protects against infection by a neurovirulent strain of Sindbis virus (PubMed:9765397). May play a role in antiviral host defense. {ECO:0000269|PubMed:20208530, ECO:0000269|PubMed:20643123, ECO:0000269|PubMed:23184933, ECO:0000269|PubMed:25275521, ECO:0000269|PubMed:26783301, ECO:0000269|PubMed:28445460, ECO:0000269|PubMed:9765397, ECO:0000305}.
• Pathway: Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Apoptosis - multiple species - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);Autophagy - other - Homo sapiens (human);Mitophagy - animal - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Phosphatidylinositol Phosphate Metabolism;Joubert syndrome;Inositol Metabolism;Nanoparticle triggered autophagic cell death;Senescence and Autophagy in Cancer;Post-translational protein modification;Metabolism of proteins;Macroautophagy;Cellular responses to external stimuli;Ub-specific processing proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.374
• rvis_EVS: -0.18
• rvis_percentile_EVS: 39.95

Haploinsufficiency Scores

• pHI: 0.512
• hipred: Y
• hipred_score: 0.825
• ghis: 0.579

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.886

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Becn1
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland 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; embryo phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); neoplasm; reproductive system phenotype; normal 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: becn1
• Affected structure: cell
• Phenotype tag: abnormal
• Phenotype quality: decreased process quality

Gene ontology

• Biological process: autophagosome assembly;autophagy of mitochondrion;mitophagy;response to hypoxia;autophagy;apoptotic process;cellular defense response;cellular response to nitrogen starvation;lysosome organization;mitotic metaphase plate congression;aging;negative regulation of cell population proliferation;response to iron(II) ion;response to lead ion;positive regulation of cardiac muscle hypertrophy;positive regulation of phosphatidylinositol 3-kinase signaling;viral process;macroautophagy;protein deubiquitination;protein localization by the Cvt pathway;regulation of cytokinesis;receptor catabolic process;response to vitamin E;cellular response to amino acid starvation;cellular response to glucose starvation;negative regulation of apoptotic process;engulfment of apoptotic cell;early endosome to late endosome transport;late endosome to vacuole transport;neuron development;amyloid-beta metabolic process;regulation of catalytic activity;cell division;defense response to virus;negative regulation of cell death;cellular response to hydrogen peroxide;cellular response to aluminum ion;cellular response to copper ion;cellular response to epidermal growth factor stimulus;response to mitochondrial depolarisation;positive regulation of attachment of mitotic spindle microtubules to kinetochore;negative regulation of autophagosome assembly;negative regulation of lysosome organization;negative regulation of reactive oxygen species metabolic process;positive regulation of autophagosome assembly
• Cellular component: phagophore assembly site;nucleus;mitochondrion;endosome;autophagosome;endoplasmic reticulum;endoplasmic reticulum membrane;trans-Golgi network;cytosol;endosome membrane;extrinsic component of membrane;dendrite;mitochondrial membrane;phosphatidylinositol 3-kinase complex, class III, type I;phosphatidylinositol 3-kinase complex, class III, type II;phosphatidylinositol 3-kinase complex, class III;phagocytic vesicle
• Molecular function: protein binding;protein kinase binding;ubiquitin protein ligase binding;protein homodimerization activity;phosphatidylinositol 3-kinase binding;GTPase binding