BACE1

beta-secretase 1, the group of Peptidase family A1

Basic information

Region (hg38): 11:117285232-117316259

Previous symbols: [ "BACE" ]

Links

ENSG00000186318 ∙ NCBI:23621 ∙ OMIM:604252 ∙ HGNC:933 ∙ Uniprot:P56817 ∙ 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 BACE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BACE1 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			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	1	0

Variants in BACE1

This is a list of pathogenic ClinVar variants found in the BACE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-117289613-G-A		not specified	Uncertain significance (Sep 27, 2022)
11-117289696-G-T		not specified	Uncertain significance (Oct 05, 2023)
11-117289699-A-G		not specified	Uncertain significance (Nov 21, 2023)
11-117289706-T-C		not specified	Uncertain significance (Aug 02, 2023)
11-117289711-G-T		not specified	Uncertain significance (Aug 08, 2022)
11-117289712-T-C		not specified	Uncertain significance (Nov 14, 2023)
11-117289719-A-T		not specified	Uncertain significance (Dec 13, 2023)
11-117289762-G-A		not specified	Uncertain significance (Jun 29, 2023)
11-117289802-C-T		not specified	Uncertain significance (Jun 10, 2024)
11-117290526-G-A		not specified	Uncertain significance (May 24, 2023)
11-117290938-C-T		not specified	Uncertain significance (Oct 20, 2023)
11-117291030-C-T		not specified	Uncertain significance (Mar 06, 2023)
11-117291048-G-A		not specified	Uncertain significance (Dec 06, 2021)
11-117291719-G-A		not specified	Uncertain significance (May 08, 2024)
11-117291725-T-C		not specified	Uncertain significance (May 24, 2024)
11-117291768-G-A		not specified	Uncertain significance (Jul 05, 2023)
11-117293066-C-A		not specified	Uncertain significance (Feb 27, 2023)
11-117293124-T-G		not specified	Uncertain significance (Jul 26, 2022)
11-117293130-C-T		not specified	Uncertain significance (Nov 09, 2023)
11-117293131-G-A		not specified	Uncertain significance (Jan 22, 2024)
11-117293158-T-C		not specified	Uncertain significance (Oct 06, 2021)
11-117293899-T-G		not specified	Uncertain significance (Dec 12, 2023)
11-117293926-C-T		not specified	Uncertain significance (Dec 15, 2023)
11-117294002-C-T		not specified	Uncertain significance (Jun 19, 2024)
11-117295291-T-C		not specified	Uncertain significance (Dec 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BACE1	protein_coding	protein_coding	ENST00000313005	9	30574

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.879	0.121	125724	0	22	125746	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.24	186	294	0.632	0.0000166	3245
Missense in Polyphen		52	132.2	0.39335		1470
Synonymous	1.46	98	118	0.829	0.00000680	1030
Loss of Function	3.84	4	24.5	0.163	0.00000133	252

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00169	0.00169
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000366	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Responsible for the proteolytic processing of the amyloid precursor protein (APP). Cleaves at the N-terminus of the A-beta peptide sequence, between residues 671 and 672 of APP, leads to the generation and extracellular release of beta-cleaved soluble APP, and a corresponding cell-associated C-terminal fragment which is later released by gamma-secretase. {ECO:0000269|PubMed:10677483, ECO:0000269|PubMed:20354142}.
• Pathway: Alzheimer,s disease - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Alzheimers Disease;Copper homeostasis;generation of amyloid b-peptide by ps1;Metabolism of proteins;Amyloid fiber formation (Consensus)

Recessive Scores

• pRec: 0.321

Intolerance Scores

• loftool: 0.404
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.33

Haploinsufficiency Scores

• pHI: 0.326
• hipred: Y
• hipred_score: 0.825
• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.420

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bace1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; growth/size/body region 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); 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); 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); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: bace1
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: increased amount

Gene ontology

• Biological process: proteolysis;membrane protein ectodomain proteolysis;response to radiation;response to lead ion;protein catabolic process;positive regulation of neuron apoptotic process;cellular protein metabolic process;amyloid-beta metabolic process;detection of mechanical stimulus involved in sensory perception of pain;prepulse inhibition;cellular response to copper ion;cellular response to manganese ion;cellular response to amyloid-beta;regulation of synaptic vesicle exocytosis
• Cellular component: lysosome;endosome;early endosome;late endosome;multivesicular body;endoplasmic reticulum lumen;Golgi apparatus;trans-Golgi network;plasma membrane;integral component of plasma membrane;synaptic vesicle;cell surface;endosome membrane;membrane;integral component of membrane;axon;dendrite;cytoplasmic vesicle membrane;neuronal cell body;membrane raft;recycling endosome;Golgi-associated vesicle lumen;hippocampal mossy fiber to CA3 synapse
• Molecular function: amyloid-beta binding;endopeptidase activity;aspartic-type endopeptidase activity;protein binding;peptidase activity;beta-aspartyl-peptidase activity;enzyme binding