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GeneBe

BECN1

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

Basic information

Region (hg38): 17:42810133-42833350

Links

ENSG00000126581NCBI:8678OMIM:604378HGNC:1034Uniprot:Q14457AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BECN1 gene.

  • Inborn genetic diseases (12 variants)
  • not provided (1 variants)

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
0
missense
11
clinvar
1
clinvar
12
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
1
Total 0 0 11 1 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 Inborn genetic diseases Uncertain significance (Feb 28, 2023)2491783
17-42814003-C-T Inborn genetic diseases Uncertain significance (Jan 26, 2022)2394711
17-42814515-A-G Benign (Jul 31, 2018)783784
17-42814651-T-C Inborn genetic diseases Uncertain significance (Dec 01, 2022)2398887
17-42815962-G-A Inborn genetic diseases Likely benign (Jul 13, 2021)2341507
17-42816017-G-C Inborn genetic diseases Uncertain significance (Jul 13, 2022)2301444
17-42816018-C-G Inborn genetic diseases Uncertain significance (May 31, 2023)2554374
17-42818303-C-T Inborn genetic diseases Uncertain significance (Nov 08, 2021)2369401
17-42818395-T-A Inborn genetic diseases Uncertain significance (Jan 23, 2023)2477104
17-42818860-C-T Inborn genetic diseases Uncertain significance (Jun 14, 2022)2291461
17-42819570-G-A Inborn genetic diseases Uncertain significance (Nov 10, 2022)2325507
17-42819599-A-G Inborn genetic diseases Uncertain significance (May 24, 2023)2551516
17-42823843-A-G Inborn genetic diseases Uncertain significance (Aug 30, 2021)2247531

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BECN1protein_codingprotein_codingENST00000361523 1123216
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9370.06281257340121257460.0000477
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.881672510.6660.00001342989
Missense in Polyphen5996.850.609191203
Synonymous2.127096.50.7250.00000540810
Loss of Function4.04426.40.1510.00000138296

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002150.000213
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00005280.0000527
Middle Eastern0.000.00
South Asian0.00006680.0000653
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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