APBA3
protein-codingamyloid beta precursor protein binding family A member 3, the group of PDZ domain containing
Gene summary
The protein encoded by this gene is a member of the X11 protein family. It is an adapter protein that interacts with the Alzheimer's disease amyloid precursor protein. This gene product is believed to be involved in signal transduction processes. This gene is a candidate gene for Alzheimer's disease. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~10.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to APBA3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004886.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | |||
| missense | 149 | 8 | 157 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 151 | 8 | 1 | 160 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004877.1 | 10 | MANE Select | |
| Ensembl | ENSP00000315136.2 | 10 | MANE Select | |
| Ensembl | ENSP00000531629.1 | 9 | Standard | |
| Ensembl | ENSP00000531630.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neuronal System
- Neurexins and neuroligins
- Protein-protein interactions at synapses
Biological Process
- in utero embryonic development
- chemical synaptic transmission
- regulation of gene expression
- protein transport
- negative regulation of catalytic activity
Molecular Function
- amyloid-beta binding
- enzyme inhibitor activity
- protein binding
- enzyme binding
Cellular Component
- cytoplasm
- plasma membrane
- dendritic spine
- synapse
- perinuclear region of cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000316757
- Coding exons
- 10
- Length
- 10881
- Individuals with no LoFs
- 125376
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 307
- Defined
- 125684
- p
- 0.00123
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.236 | 376 | 363 | 1.03 | 0.0000240 | 3613 |
| Missense (PolyPhen) | 130 | 135.64 | 0.95839 | 1356 | ||
| Synonymous | -0.136 | 165 | 163 | 1.01 | 0.0000118 | 1215 |
| Loss of Function | 0.661 | 20 | 23.5 | 0.853 | 0.00000142 | 229 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00036 | 0.00031 | rare |
| Latino/Admixed American | 0.00047 | 0.00046 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0061 | 0.0057 | notable |
| Finnish | 0.000073 | 0.000046 | rare |
| European (Non-Finnish) | 0.00049 | 0.00046 | rare |
| South Asian | 0.0042 | 0.0040 | notable |
| Other | 0.0011 | 0.00098 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May modulate processing of the amyloid-beta precursor protein (APP) and hence formation of APP-beta. May enhance the activity of HIF1A in macrophages by inhibiting the activity of HIF1AN. {ECO:0000269|PubMed:19726677}.;
Recessive Scores
- pRec
- 0.129
Intolerance Scores
- LoFtool
- 0.892
- RVIS EVS
- 0.89
- RVIS percentile EVS
- 89.27
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.884
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |