BACE2
Basic information
Region (hg38): 21:41167801-41282530
Previous symbols: [ "AEPLC" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (59 variants)
- not_provided (7 variants)
- BACE2-related_disorder (6 variants)
- PLAC4-related_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BACE2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012105.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | |||||
| missense | 54 | 62 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 54 | 10 | 2 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BACE2 | protein_coding | protein_coding | ENST00000330333 | 9 | 114718 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00676 | 0.990 | 125734 | 0 | 14 | 125748 | 0.0000557 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.60 | 201 | 276 | 0.729 | 0.0000165 | 3305 |
| Missense in Polyphen | 73 | 129.88 | 0.56207 | 1535 | ||
| Synonymous | 0.914 | 106 | 119 | 0.893 | 0.00000822 | 1104 |
| Loss of Function | 2.56 | 7 | 19.1 | 0.367 | 8.97e-7 | 233 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000872 | 0.0000872 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000792 | 0.0000791 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Responsible for the proteolytic processing of the amyloid precursor protein (APP). Cleaves APP, between residues 690 and 691, leading 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. It has also been shown that it can cleave APP between residues 671 and 672. {ECO:0000269|PubMed:10591213, ECO:0000269|PubMed:11083922, ECO:0000269|PubMed:11423558, ECO:0000269|PubMed:15857888, ECO:0000269|PubMed:16816112}.;
- Pathway
- Alzheimer,s disease - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.355
Intolerance Scores
- loftool
- 0.302
- rvis_EVS
- -0.36
- rvis_percentile_EVS
- 29.16
Haploinsufficiency Scores
- pHI
- 0.242
- hipred
- Y
- hipred_score
- 0.768
- ghis
- 0.511
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.637
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bace2
- Phenotype
- cellular 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; pigmentation 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); vision/eye 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);
Zebrafish Information Network
- Gene name
- bace2
- Affected structure
- myelinating Schwann cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- proteolysis;membrane protein ectodomain proteolysis;peptide hormone processing;protein catabolic process;glucose homeostasis;negative regulation of amyloid precursor protein biosynthetic process;astrocyte activation;amyloid-beta metabolic process
- Cellular component
- endosome;endoplasmic reticulum;Golgi apparatus;trans-Golgi network;plasma membrane;cell surface;membrane;integral component of membrane;dense core granule
- Molecular function
- amyloid-beta binding;aspartic-type endopeptidase activity