BECN1
Chr 17beclin 1
Also known as: ATG6, VPS30, beclin1
This gene encodes a protein that regulates autophagy, a catabolic process of degradation induced by starvation. The encoded protein is a component of the phosphatidylinositol-3-kinase (PI3K) complex which mediates vesicle-trafficking processes. This protein is thought to play a role in multiple cellular processes, including tumorigenesis, neurodegeneration and apoptosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]
Clinical Summary— BECN1
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Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.94). One damaged copy is likely sufficient to cause disease.
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ClinVar Variants
6 Pathogenic / Likely Pathogenic· 38 VUS of 48 total submissions
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
LoF intolerant — likely haploinsufficient
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.35LOEUF
pLI 0.937
Z-score 4.04
OE 0.15 (0.07–0.35)
Highly LoF-intolerant (top ~10% of genes)
Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.88Z-score
OE missense 0.67 (0.59–0.76)
167 obs / 250.6 exp
Mild missense constraint
Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.15 (0.07–0.35)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.67 (0.59–0.76)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.73
0≤1.21.6
LoF obs/exp: 4 / 26.4Missense obs/exp: 167 / 250.6Syn Z: 2.12
ClinVar Variant Classifications
48 submitted variants in ClinVar
Classification Summary
Pathogenic6
VUS38
Likely Benign3
Benign1
6
Pathogenic
38
VUS
3
Likely Benign
1
Benign
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 6 | 0 | 6 |
Likely Pathogenic | 0 | 0 | 0 | 0 | 0 |
VUS | 0 | 38 | 0 | 0 | 38 |
Likely Benign | 0 | 2 | 0 | 1 | 3 |
Benign | 0 | 0 | 1 | 0 | 1 |
| Total | 0 | 40 | 7 | 1 | 48 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
BECN1 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
OMIM — Genotype-Phenotype Relationships
1 OMIM entry
BECLIN 1; BECN1
MIM #604378 · *
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
Tumor-derived lactate promotes resistance to bevacizumab treatment by facilitating autophagy enhancer protein RUBCNL expression through histone H3 lysine 18 lactylation (H3K18la) in colorectal cancer.
Li W et al.·Autophagy
2024
New insights into the interplay between autophagy, gut microbiota and inflammatory responses in IBD.
Larabi A et al.·Autophagy
2020Review
VCP/p97 UFMylation stabilizes BECN1 and facilitates the initiation of autophagy.
Wang Z et al.·Autophagy
2024
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Baicalein limits subchondral bone lesions via AMPKα/BECN1 activation in osteoarthritis osteoblast.
Zhai Y et al.·Int Immunopharmacol
2026
Tumor-intrinsic PD-L1 drives lung cancer progression in response to TLR stimulation by promoting autophagy through the TRAF6-BECN1 signaling axis.
Sung Y et al.·Exp Hematol Oncol
2026Open Access
YTHDF2-orchestrated m6A methylation of BECN1 induces Scoparone-mediated hepatic stellate cell ferroptosis to attenuate liver fibrosis.
Sun Y et al.·Phytomedicine
2026
Top 5 resultsSearch Europe PMC ↗
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
Beclin-1, an autophagy-related protein, is associated with the disease severity of COVID-19
Okuyan HM et al.·Life Sci
2021
MiR-371a-5p Positively Associates with Hepatocellular Carcinoma Malignancy but Sensitizes Cancer Cells to Oxaliplatin by Suppressing BECN1-Dependent Autophagy
Lv Z et al.·Life (Basel)
2022
Invariant BECN1 CXXC motifs bind Zn2+ and regulate structure and function of the BECN1 intrinsically disordered region.
Mukhopadhyay S et al.·Autophagy
2023
ALS-linked C9orf72 dipeptide repeats inhibit starvation-induced autophagy through modulating BCL2-BECN1 interaction
Xu S et al.·Acta Pharm Sin B
2024
Ginsenoside Rb1 induces hepatic stellate cell ferroptosis to alleviate liver fibrosis via the BECN1/SLC7A11 axis
Lin L et al.·J Pharm Anal
2024
The Regulation of ROS- and BECN1-Mediated Autophagy by Human Telomerase Reverse Transcriptase in Glioblastoma
Ding X et al.·Oxid Med Cell Longev
2021
Autophagy-related gene BECN1 single nucleotide polymorphisms in diseases.
Kaur S et al.·Mol Cell Biochem
2024
Beth Levine's Legacy: From the Discovery of BECN1 to Therapies. A Mentees' Perspective
An Z et al.·Front Cell Dev Biol
2022
Deregulation of the Expression of Beclin1 and Light Chain 3(LC3), Autophagy-Related Genes, in COVID-19 Patients
Boroumand-Noughabi S et al.·Med J Islam Repub Iran
2022Cohort
Top 10 full-text resultsSearch PubTator3 ↗
External Resources
Links to major genomics databases and tools