SNX18
Basic information
Region (hg38): 5:54517759-54546586
Previous symbols: [ "SNAG1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (91 variants)
- not_provided (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX18 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001102575.2. 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 | 2 | |||||
| missense | 78 | 79 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 78 | 0 | 3 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SNX18 | protein_coding | protein_coding | ENST00000326277 | 1 | 28827 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.956 | 0.0436 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.97 | 257 | 363 | 0.709 | 0.0000222 | 3995 |
| Missense in Polyphen | 61 | 135.38 | 0.45057 | 1509 | ||
| Synonymous | -0.147 | 180 | 178 | 1.01 | 0.0000133 | 1241 |
| Loss of Function | 3.25 | 1 | 14.2 | 0.0703 | 6.15e-7 | 155 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in endocytosis and intracellular vesicle trafficking, both during interphase and at the end of mitosis. Required for efficient progress through mitosis and cytokinesis. Required for normal formation of the cleavage furrow at the end of mitosis. Plays a role in endocytosis via clathrin-coated pits, but also clathrin-independent, actin-dependent fluid-phase endocytosis. Plays a role in macropinocytosis. Binds to membranes enriched in phosphatidylinositol 4,5-bisphosphate and promotes membrane tubulation. Stimulates the GTPase activity of DNM2. Promotes DNM2 location at the plasma membrane. {ECO:0000269|PubMed:18411244, ECO:0000269|PubMed:20427313, ECO:0000269|PubMed:21048941, ECO:0000269|PubMed:22718350}.;
- Pathway
- Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis
(Consensus)
Recessive Scores
- pRec
- 0.0980
Intolerance Scores
- loftool
- 0.583
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 34.71
Haploinsufficiency Scores
- pHI
- 0.258
- hipred
- Y
- hipred_score
- 0.538
- ghis
- 0.570
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.936
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Snx18
- Phenotype
Gene ontology
- Biological process
- mitotic cytokinesis;endocytosis;protein transport;endosomal transport;cleavage furrow formation;positive regulation of GTPase activity
- Cellular component
- endosome membrane;clathrin-coated vesicle;cytoplasmic vesicle membrane;extrinsic component of cytoplasmic side of plasma membrane;cytoplasmic vesicle;extracellular exosome
- Molecular function
- protein binding;phosphatidylinositol-4,5-bisphosphate binding