AP3S1
Basic information
Region (hg38): 5:115841592-115914081
Previous symbols: [ "CLAPS3" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the AP3S1 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 | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 2 | 0 | 1 |
Variants in AP3S1
This is a list of pathogenic ClinVar variants found in the AP3S1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-115842054-T-C | not specified | Uncertain significance (Feb 14, 2023) | ||
| 5-115866743-A-G | not specified | Uncertain significance (May 08, 2024) | ||
| 5-115870030-T-A | not specified | Uncertain significance (Mar 24, 2023) | ||
| 5-115902965-T-G | not specified | Uncertain significance (Jun 07, 2024) | ||
| 5-115913381-C-T | Benign (Dec 31, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| AP3S1 | protein_coding | protein_coding | ENST00000316788 | 6 | 72601 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000102 | 0.357 | 124445 | 0 | 1283 | 125728 | 0.00512 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.36 | 56 | 92.9 | 0.603 | 0.00000436 | 1248 |
| Missense in Polyphen | 5 | 19.257 | 0.25965 | 300 | ||
| Synonymous | 0.811 | 27 | 32.9 | 0.820 | 0.00000165 | 325 |
| Loss of Function | 0.262 | 8 | 8.84 | 0.905 | 3.70e-7 | 129 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0106 | 0.0102 |
| Ashkenazi Jewish | 0.00236 | 0.00228 |
| East Asian | 0.00540 | 0.00507 |
| Finnish | 0.00618 | 0.00565 |
| European (Non-Finnish) | 0.00637 | 0.00585 |
| Middle Eastern | 0.00540 | 0.00507 |
| South Asian | 0.00365 | 0.00347 |
| Other | 0.00524 | 0.00490 |
dbNSFP
Source:
- Function
- FUNCTION: Part of the AP-3 complex, an adaptor-related complex which is not clathrin-associated. The complex is associated with the Golgi region as well as more peripheral structures. It facilitates the budding of vesicles from the Golgi membrane and may be directly involved in trafficking to lysosomes. In concert with the BLOC-1 complex, AP-3 is required to target cargos into vesicles assembled at cell bodies for delivery into neurites and nerve terminals.;
- Pathway
- Lysosome - Homo sapiens (human);Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking
(Consensus)
Recessive Scores
- pRec
- 0.142
Intolerance Scores
- loftool
- 0.613
- rvis_EVS
- 0.39
- rvis_percentile_EVS
- 75.87
Haploinsufficiency Scores
- pHI
- 0.534
- hipred
- Y
- hipred_score
- 0.673
- ghis
- 0.486
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ap3s1
- Phenotype
- homeostasis/metabolism phenotype; hearing/vestibular/ear phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Gene ontology
- Biological process
- intracellular protein transport;anterograde axonal transport;insulin receptor signaling pathway;anterograde synaptic vesicle transport
- Cellular component
- Golgi apparatus;AP-type membrane coat adaptor complex;AP-3 adaptor complex;transport vesicle;cytoplasmic vesicle membrane;intracellular membrane-bounded organelle;axon cytoplasm
- Molecular function
- transporter activity;protein binding