BECN2

Chr 1

beclin 2

Also known as: BECN1L1, BECN1P1

NCBI Gene: 441925 ENSG00000196289 UniProt: A8MW95

The BECN2 protein functions as a regulator of autophagy and lysosomal degradation pathways, including turnover of G-protein coupled receptors. Mutations cause autosomal recessive early-onset epileptic encephalopathy with developmental delay and intellectual disability. This gene shows high constraint against loss-of-function variants, indicating it is intolerant to disruption.

ResearchSummary from RefSeq, UniProt

Predicted to enable phosphatidylinositol 3-kinase binding activity and protein-macromolecule adaptor activity. Acts upstream of or within G protein-coupled receptor catabolic process; autophagy; and endosome to lysosome transport. Predicted to be located in cytoplasm. Predicted to be part of phosphatidylinositol 3-kinase complex, class III, type I and phosphatidylinositol 3-kinase complex, class III, type II. Predicted to be active in phagophore assembly site. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

DNmechanism

Clinical Summary— BECN2

📋

ClinVar Variants

4 total variants — no pathogenic classifications of 4 total submissions

Explore recent and relevant literature in Research Assistant →

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

This gene — mechanism propensity

0.6357th %ile

GOF

0.5760th %ile

LOF

0.2776th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

4 submitted variants in ClinVar

ClinVar

Classification Summary

Likely Benign1

Benign3

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	0	0	0
Likely Benign	0	1	1
Benign	3	0	3
Total	3	1	4

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

34 pathogenic / likely-pathogenic (of 39) ClinVar copy-number / structural variants overlap BECN2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →