SNAPIN
SNAP associated protein, the group of BLOC-1 related complex subunits|Biogenesis of lysosomal organelles complex 1 subunits
Basic information
Region (hg38): 1:153658703-153661852
Previous symbols: [ "SNAPAP" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
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 SNAPIN 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 1 | 4 | 0 | 0 |
Variants in SNAPIN
This is a list of pathogenic ClinVar variants found in the SNAPIN region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-153658756-G-A | not specified | Uncertain significance (Nov 02, 2023) | ||
| 1-153658769-T-A | not specified | Uncertain significance (Dec 01, 2023) | ||
| 1-153658796-G-A | not specified | Uncertain significance (Nov 25, 2024) | ||
| 1-153658805-G-A | not specified | Uncertain significance (Aug 27, 2024) | ||
| 1-153659157-C-T | Abnormal brain morphology | Likely pathogenic (-) | ||
| 1-153659495-C-G | not specified | Uncertain significance (Jun 07, 2023) | ||
| 1-153659529-G-A | not specified | Uncertain significance (Oct 06, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SNAPIN | protein_coding | protein_coding | ENST00000368685 | 4 | 3177 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00153 | 0.700 | 125724 | 0 | 24 | 125748 | 0.0000954 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.878 | 59 | 81.3 | 0.726 | 0.00000443 | 850 |
| Missense in Polyphen | 10 | 23.207 | 0.43091 | 249 | ||
| Synonymous | -0.691 | 39 | 33.9 | 1.15 | 0.00000167 | 304 |
| Loss of Function | 0.767 | 5 | 7.22 | 0.692 | 4.64e-7 | 64 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000141 | 0.000123 |
| Ashkenazi Jewish | 0.000695 | 0.000695 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.0000528 | 0.0000527 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.000163 | 0.000163 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the BLOC-1 complex, a complex that is required for normal biogenesis of lysosome-related organelles (LRO), such as platelet dense granules and melanosomes. In concert with the AP-3 complex, the BLOC-1 complex is required to target membrane protein cargos into vesicles assembled at cell bodies for delivery into neurites and nerve terminals. The BLOC-1 complex, in association with SNARE proteins, is also proposed to be involved in neurite extension. Plays a role in intracellular vesicle trafficking and synaptic vesicle recycling. May modulate a step between vesicle priming, fusion and calcium-dependent neurotransmitter release through its ability to potentiate the interaction of synaptotagmin with the SNAREs and the plasma- membrane-associated protein SNAP25. Its phosphorylation state influences exocytotic protein interactions and may regulate synaptic vesicle exocytosis. May also have a role in the mechanisms of SNARE-mediated membrane fusion in non-neuronal cells (PubMed:17182842, PubMed:18167355). As part of the BORC complex may play a role in lysosomes movement and localization at the cell periphery. Associated with the cytosolic face of lysosomes, the BORC complex may recruit ARL8B and couple lysosomes to microtubule plus-end-directed kinesin motor (PubMed:25898167). {ECO:0000269|PubMed:17182842, ECO:0000269|PubMed:18167355, ECO:0000269|PubMed:25898167}.;
- Pathway
- Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking
(Consensus)
Recessive Scores
- pRec
- 0.155
Intolerance Scores
- loftool
- 0.672
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.63
Haploinsufficiency Scores
- pHI
- 0.263
- hipred
- Y
- hipred_score
- 0.564
- ghis
- 0.606
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.860
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Snapin
- Phenotype
- cellular phenotype; endocrine/exocrine gland 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); 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); 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;lysosomal lumen acidification;neurotransmitter secretion;anterograde axonal transport;retrograde axonal transport;endosome to lysosome transport;negative regulation of neuron projection development;viral process;synaptic vesicle exocytosis;synaptic vesicle maturation;neuron projection development;synaptic vesicle fusion to presynaptic active zone membrane;lysosome localization;melanosome organization;cellular protein-containing complex localization;regulation of protein binding;synaptic vesicle transport;anterograde synaptic vesicle transport;protein maturation;terminal button organization;autophagosome maturation;late endosome to lysosome transport;positive regulation of late endosome to lysosome transport;regulation of synaptic vesicle exocytosis
- Cellular component
- Golgi membrane;lysosomal membrane;synaptic vesicle;cell junction;secretory granule;synaptic vesicle membrane;BLOC-1 complex;synapse;perinuclear region of cytoplasm;BORC complex;axon cytoplasm
- Molecular function
- SNARE binding;protein binding