SNAP23
synaptosome associated protein 23, the group of SNAREs
Basic information
Region (hg38): 15:42491233-42545356
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 SNAP23 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 | 16 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 16 | 0 | 0 |
Variants in SNAP23
This is a list of pathogenic ClinVar variants found in the SNAP23 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 15-42511850-G-A | not specified | Uncertain significance (Jan 16, 2025) | ||
| 15-42513423-A-G | not specified | Uncertain significance (Jun 17, 2024) | ||
| 15-42513442-A-T | Uncertain significance (Apr 04, 2024) | |||
| 15-42513445-A-G | not specified | Uncertain significance (Jun 16, 2024) | ||
| 15-42515248-C-T | not specified | Uncertain significance (Jul 25, 2023) | ||
| 15-42515299-A-G | not specified | Uncertain significance (Nov 02, 2023) | ||
| 15-42515309-C-T | not specified | Uncertain significance (May 24, 2024) | ||
| 15-42515314-C-A | not specified | Uncertain significance (Nov 10, 2022) | ||
| 15-42528287-G-A | not specified | Uncertain significance (Jun 27, 2023) | ||
| 15-42528287-G-T | not specified | Uncertain significance (Jul 13, 2022) | ||
| 15-42528398-G-A | not specified | Uncertain significance (Aug 20, 2024) | ||
| 15-42529704-T-C | not specified | Uncertain significance (May 31, 2023) | ||
| 15-42529711-G-C | not specified | Uncertain significance (Apr 12, 2022) | ||
| 15-42529751-G-T | not specified | Uncertain significance (Jan 24, 2025) | ||
| 15-42529785-C-T | not specified | Uncertain significance (Jul 16, 2024) | ||
| 15-42531417-A-G | not specified | Uncertain significance (Aug 22, 2023) | ||
| 15-42531432-G-A | not specified | Uncertain significance (Feb 26, 2024) | ||
| 15-42531434-A-G | not specified | Uncertain significance (Aug 28, 2024) | ||
| 15-42544095-C-G | not specified | Uncertain significance (Dec 27, 2023) | ||
| 15-42545097-C-G | not specified | Uncertain significance (Nov 22, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SNAP23 | protein_coding | protein_coding | ENST00000249647 | 7 | 54117 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.924 | 0.0758 | 125689 | 0 | 5 | 125694 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.835 | 88 | 113 | 0.779 | 0.00000555 | 1390 |
| Missense in Polyphen | 13 | 23.111 | 0.5625 | 292 | ||
| Synonymous | 0.955 | 30 | 37.4 | 0.801 | 0.00000176 | 382 |
| Loss of Function | 3.03 | 1 | 12.6 | 0.0791 | 6.34e-7 | 148 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000120 | 0.000120 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Essential component of the high affinity receptor for the general membrane fusion machinery and an important regulator of transport vesicle docking and fusion.;
- Pathway
- Platelet activation - Homo sapiens (human);SNARE interactions in vesicular transport - Homo sapiens (human);miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Insulin Signaling;Clathrin derived vesicle budding;Neutrophil degranulation;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking;Innate Immune System;Immune System;Adaptive Immune System;Antigen processing-Cross presentation;Class I MHC mediated antigen processing & presentation;ER-Phagosome pathway
(Consensus)
Recessive Scores
- pRec
- 0.148
Intolerance Scores
- loftool
- 0.288
- rvis_EVS
- -0.19
- rvis_percentile_EVS
- 39.68
Haploinsufficiency Scores
- pHI
- 0.0954
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.659
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.736
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Snap23
- 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); embryo phenotype;
Gene ontology
- Biological process
- antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent;histamine secretion by mast cell;exocytosis;post-Golgi vesicle-mediated transport;vesicle targeting;vesicle fusion;protein transport;synaptic vesicle priming;synaptic vesicle fusion to presynaptic active zone membrane;neutrophil degranulation;membrane fusion
- Cellular component
- nucleoplasm;cytoplasm;plasma membrane;cell-cell adherens junction;focal adhesion;phagocytic vesicle membrane;SNARE complex;specific granule membrane;specific granule;azurophil granule;mast cell granule;neuron projection;extracellular exosome;tertiary granule membrane;presynapse
- Molecular function
- SNAP receptor activity;protein binding;syntaxin binding