AMBRA1
autophagy and beclin 1 regulator 1, the group of WD repeat domain containing|DDB1 and CUL4 associated factors|MicroRNA protein coding host genes
Basic information
Region (hg38): 11:46396414-46594125
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (124 variants)
- AMBRA1-related_disorder (7 variants)
- Neural_tube_defect (5 variants)
- not_provided (4 variants)
- Pyloric_stenosis (1 variants)
- Esophageal_atresia (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMBRA1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001387011.1. 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 | 127 | 134 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 128 | 8 | 3 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| AMBRA1 | protein_coding | protein_coding | ENST00000314845 | 18 | 197712 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 2.44e-7 | 125729 | 0 | 19 | 125748 | 0.0000756 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.95 | 502 | 725 | 0.692 | 0.0000449 | 7798 |
| Missense in Polyphen | 209 | 366.55 | 0.57019 | 3788 | ||
| Synonymous | 1.18 | 254 | 279 | 0.910 | 0.0000161 | 2538 |
| Loss of Function | 6.53 | 3 | 55.5 | 0.0541 | 0.00000305 | 575 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000465 | 0.0000462 |
| European (Non-Finnish) | 0.000126 | 0.000123 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.000333 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Regulates autophagy and development of the nervous system. Involved in autophagy in controlling protein turnover during neuronal development, and in regulating normal cell survival and proliferation (By similarity). {ECO:0000250}.;
- Pathway
- Autophagy - animal - Homo sapiens (human);Mitophagy - animal - Homo sapiens (human);Phosphatidylinositol Phosphate Metabolism;Joubert syndrome;Inositol Metabolism;Nanoparticle triggered autophagic cell death;Senescence and Autophagy in Cancer;Macroautophagy;Cellular responses to external stimuli
(Consensus)
Recessive Scores
- pRec
- 0.104
Intolerance Scores
- loftool
- 0.200
- rvis_EVS
- -0.97
- rvis_percentile_EVS
- 8.95
Haploinsufficiency Scores
- pHI
- 0.369
- hipred
- Y
- hipred_score
- 0.819
- ghis
- 0.571
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.889
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ambra1
- Phenotype
- cellular 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); embryo phenotype;
Zebrafish Information Network
- Gene name
- ambra1a
- Affected structure
- fast muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- undulate
Gene ontology
- Biological process
- autophagosome assembly;autophagy of mitochondrion;mitophagy;autophagy;negative regulation of cell population proliferation;cellular response to starvation;positive regulation of autophagy;negative regulation of cardiac muscle cell apoptotic process;macroautophagy;neural tube development;cell differentiation;negative regulation of neuron apoptotic process;positive regulation of phosphatidylinositol 3-kinase activity;response to mitochondrial depolarisation
- Cellular component
- cytoplasm;mitochondrion;mitochondrial outer membrane;autophagosome;cytosol;axoneme;phagocytic vesicle;perinuclear region of cytoplasm
- Molecular function
- protein binding;ubiquitin protein ligase binding;GTPase binding