SNX9
sorting nexin 9, the group of PX-BAR domain containing|Sorting nexins
Basic information
Region (hg38): 6:157700387-157945077
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (44 variants)
- not_provided (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016224.5. 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 | 1 | |||||
| missense | 42 | 44 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 42 | 3 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SNX9 | protein_coding | protein_coding | ENST00000392185 | 18 | 121814 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.706 | 0.294 | 125720 | 0 | 28 | 125748 | 0.000111 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.82 | 237 | 330 | 0.718 | 0.0000178 | 3939 |
| Missense in Polyphen | 97 | 161.36 | 0.60116 | 1952 | ||
| Synonymous | 1.42 | 96 | 115 | 0.832 | 0.00000666 | 1057 |
| Loss of Function | 4.62 | 8 | 39.2 | 0.204 | 0.00000199 | 456 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000327 | 0.0000327 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.000462 | 0.000462 |
| European (Non-Finnish) | 0.000151 | 0.000132 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| 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. Promotes internalization of TNFR. Promotes degradation of EGFR after EGF signaling. Stimulates the GTPase activity of DNM1. Promotes DNM1 oligomerization. Promotes activation of the Arp2/3 complex by WASL, and thereby plays a role in the reorganization of the F- actin cytoskeleton. Binds to membranes enriched in phosphatidylinositol 4,5-bisphosphate and promotes membrane tubulation. Has lower affinity for membranes enriched in phosphatidylinositol 3-phosphate. {ECO:0000269|PubMed:11799118, ECO:0000269|PubMed:12952949, ECO:0000269|PubMed:15703209, ECO:0000269|PubMed:17609109, ECO:0000269|PubMed:17948057, ECO:0000269|PubMed:18388313, ECO:0000269|PubMed:20427313, ECO:0000269|PubMed:21048941, ECO:0000269|PubMed:22718350}.;
- Pathway
- EGF-Ncore;Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis
(Consensus)
Recessive Scores
- pRec
- 0.180
Intolerance Scores
- loftool
- 0.737
- rvis_EVS
- -0.13
- rvis_percentile_EVS
- 43.91
Haploinsufficiency Scores
- pHI
- 0.173
- hipred
- Y
- hipred_score
- 0.756
- ghis
- 0.556
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.974
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Snx9
- Phenotype
Gene ontology
- Biological process
- mitotic cytokinesis;intracellular protein transport;endocytosis;receptor-mediated endocytosis;endosomal transport;positive regulation of protein oligomerization;cleavage furrow formation;positive regulation of GTPase activity;positive regulation of protein kinase activity;positive regulation of membrane protein ectodomain proteolysis;lipid tube assembly;membrane organization;plasma membrane tubulation
- Cellular component
- ruffle;cytoplasm;trans-Golgi network;cytosol;plasma membrane;clathrin-coated vesicle;cytoplasmic vesicle membrane;extrinsic component of cytoplasmic side of plasma membrane;cytoplasmic vesicle;extracellular exosome
- Molecular function
- protein binding;1-phosphatidylinositol binding;ubiquitin protein ligase binding;phosphatidylinositol binding;identical protein binding;protein homodimerization activity;cadherin binding;Arp2/3 complex binding