APBB1
amyloid beta precursor protein binding family B member 1
Basic information
Region (hg38): 11:6395125-6419414
Previous symbols: [ "RIR" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (72 variants)
- not_provided (7 variants)
- APBB1-related_disorder (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the APBB1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001164.5. 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 | 7 | |||||
| missense | 68 | 75 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 68 | 9 | 5 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| APBB1 | protein_coding | protein_coding | ENST00000299402 | 13 | 24290 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.968 | 0.0319 | 125741 | 0 | 7 | 125748 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.56 | 331 | 421 | 0.786 | 0.0000258 | 4561 |
| Missense in Polyphen | 76 | 131.17 | 0.5794 | 1343 | ||
| Synonymous | 0.122 | 171 | 173 | 0.988 | 0.0000107 | 1448 |
| Loss of Function | 4.49 | 5 | 32.7 | 0.153 | 0.00000159 | 362 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000119 | 0.000119 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.000168 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription coregulator that can have both coactivator and corepressor functions. Adapter protein that forms a transcriptionally active complex with the gamma-secretase-derived amyloid precursor protein (APP) intracellular domain. Plays a central role in the response to DNA damage by translocating to the nucleus and inducing apoptosis. May act by specifically recognizing and binding histone H2AX phosphorylated on 'Tyr-142' (H2AXY142ph) at double-strand breaks (DSBs), recruiting other pro- apoptosis factors such as MAPK8/JNK1. Required for histone H4 acetylation at double-strand breaks (DSBs). Its ability to specifically bind modified histones and chromatin modifying enzymes such as KAT5/TIP60, probably explains its transcription activation activity. Function in association with TSHZ3, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. Associates with chromatin in a region surrounding the CASP4 transcriptional start site(s). {ECO:0000269|PubMed:15031292, ECO:0000269|PubMed:18468999, ECO:0000269|PubMed:18922798, ECO:0000269|PubMed:19234442, ECO:0000269|PubMed:19343227, ECO:0000269|PubMed:25342469}.;
- Pathway
- Alzheimer,s disease - Homo sapiens (human);Alzheimers Disease;DNA Repair;DNA Double-Strand Break Repair;Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks;DNA Double Strand Break Response;Validated nuclear estrogen receptor alpha network
(Consensus)
Recessive Scores
- pRec
- 0.360
Intolerance Scores
- loftool
- 0.121
- rvis_EVS
- -0.55
- rvis_percentile_EVS
- 19.93
Haploinsufficiency Scores
- pHI
- 0.210
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.574
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.894
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Apbb1
- Phenotype
- cellular phenotype; growth/size/body region phenotype; normal 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); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;double-strand break repair;regulation of transcription, DNA-templated;apoptotic process;cellular response to DNA damage stimulus;cell cycle arrest;signal transduction;axonogenesis;response to iron ion;positive regulation of neuron projection development;negative regulation of cell growth;positive regulation of apoptotic process;histone H4 acetylation;positive regulation of DNA repair;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of protein secretion;negative regulation of thymidylate synthase biosynthetic process
- Cellular component
- nucleus;nucleoplasm;cytoplasm;plasma membrane;nuclear speck;lamellipodium;growth cone;protein-containing complex;presynaptic membrane;neuronal cell body;dendritic spine;main axon;synapse;postsynaptic membrane;perinuclear region of cytoplasm;growth cone lamellipodium;growth cone filopodium
- Molecular function
- amyloid-beta binding;chromatin binding;protein binding;transcription factor binding;histone binding;protein-containing complex binding;tau protein binding;proline-rich region binding