SNX1
sorting nexin 1, the group of PX-BAR domain containing|Sorting nexins
Basic information
Region (hg38): 15:64094123-64146090
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 SNX1 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 | 42 | 42 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 42 | 0 | 0 |
Variants in SNX1
This is a list of pathogenic ClinVar variants found in the SNX1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 15-64096045-C-T | not specified | Uncertain significance (Nov 26, 2024) | ||
| 15-64096053-C-G | not specified | Uncertain significance (Feb 27, 2023) | ||
| 15-64096059-C-T | not specified | Uncertain significance (Jun 22, 2021) | ||
| 15-64096092-G-A | not specified | Uncertain significance (Feb 15, 2023) | ||
| 15-64096101-G-A | not specified | Uncertain significance (Apr 05, 2023) | ||
| 15-64096105-G-A | not specified | Uncertain significance (Mar 07, 2023) | ||
| 15-64096120-C-G | not specified | Uncertain significance (Dec 30, 2024) | ||
| 15-64096155-A-G | not specified | Uncertain significance (Oct 12, 2021) | ||
| 15-64112625-G-T | not specified | Uncertain significance (Sep 04, 2024) | ||
| 15-64112631-A-T | not specified | Uncertain significance (Dec 28, 2024) | ||
| 15-64112666-C-T | not specified | Uncertain significance (Dec 02, 2022) | ||
| 15-64112681-G-A | not specified | Uncertain significance (May 12, 2024) | ||
| 15-64118122-A-G | not specified | Uncertain significance (Jan 09, 2024) | ||
| 15-64118125-G-A | not specified | Uncertain significance (Apr 20, 2023) | ||
| 15-64118182-C-G | not specified | Uncertain significance (Sep 23, 2023) | ||
| 15-64118219-C-T | not specified | Uncertain significance (Apr 18, 2024) | ||
| 15-64118233-A-G | not specified | Uncertain significance (Jan 07, 2022) | ||
| 15-64118828-T-G | not specified | Uncertain significance (Oct 27, 2022) | ||
| 15-64118845-G-A | not specified | Uncertain significance (Dec 07, 2021) | ||
| 15-64123508-G-A | not specified | Uncertain significance (Jun 30, 2024) | ||
| 15-64126084-C-G | not specified | Uncertain significance (Jan 19, 2025) | ||
| 15-64126148-T-C | not specified | Uncertain significance (Jul 02, 2024) | ||
| 15-64126185-T-A | not specified | Uncertain significance (May 27, 2022) | ||
| 15-64127206-T-C | not specified | Uncertain significance (Oct 20, 2021) | ||
| 15-64127213-C-A | not specified | Uncertain significance (Jan 26, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SNX1 | protein_coding | protein_coding | ENST00000261889 | 15 | 51968 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.932 | 0.0682 | 125736 | 0 | 11 | 125747 | 0.0000437 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.804 | 267 | 307 | 0.871 | 0.0000170 | 3654 |
| Missense in Polyphen | 92 | 128.67 | 0.71501 | 1513 | ||
| Synonymous | 0.326 | 112 | 116 | 0.962 | 0.00000640 | 1034 |
| Loss of Function | 4.29 | 5 | 30.6 | 0.163 | 0.00000149 | 352 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.0000440 | 0.0000439 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in several stages of intracellular trafficking. Interacts with membranes containing phosphatidylinositol 3- phosphate (PtdIns(3P)) or phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2) (PubMed:12198132). Acts in part as component of the retromer membrane-deforming SNX-BAR subcomplex. The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX-BAR subcomplex functions to deform the donor membrane into a tubular profile called endosome-to-TGN transport carrier (ETC) (Probable). Can sense membrane curvature and has in vitro vesicle- to-membrane remodeling activity (PubMed:19816406, PubMed:23085988). Involved in retrograde endosome-to-TGN transport of lysosomal enzyme receptors (IGF2R, M6PR and SORT1) and Shiginella dysenteria toxin stxB. Plays a role in targeting ligand-activated EGFR to the lysosomes for degradation after endocytosis from the cell surface and release from the Golgi (PubMed:12198132, PubMed:15498486, PubMed:17550970, PubMed:17101778, PubMed:18088323, PubMed:21040701). Involvement in retromer-independent endocytic trafficking of P2RY1 and lysosomal degradation of protease-activated receptor-1/F2R (PubMed:16407403, PubMed:20070609). Promotes KALRN- and RHOG-dependent but retromer- independent membrane remodeling such as lamellipodium formation; the function is dependent on GEF activity of KALRN (PubMed:20604901). Required for endocytosis of DRD5 upon agonist stimulation but not for basal receptor trafficking (PubMed:23152498). {ECO:0000269|PubMed:12198132, ECO:0000269|PubMed:15498486, ECO:0000269|PubMed:16407403, ECO:0000269|PubMed:17101778, ECO:0000269|PubMed:17550970, ECO:0000269|PubMed:18088323, ECO:0000269|PubMed:19816406, ECO:0000269|PubMed:20070609, ECO:0000269|PubMed:20604901, ECO:0000269|PubMed:21040701, ECO:0000269|PubMed:23085988, ECO:0000269|PubMed:23152498, ECO:0000303|PubMed:15498486}.;
- Pathway
- Endocytosis - Homo sapiens (human);TGF_beta_Receptor;Posttranslational regulation of adherens junction stability and dissassembly;PAR1-mediated thrombin signaling events
(Consensus)
Recessive Scores
- pRec
- 0.0962
Intolerance Scores
- loftool
- 0.484
- rvis_EVS
- -0.51
- rvis_percentile_EVS
- 21.56
Haploinsufficiency Scores
- pHI
- 0.759
- hipred
- Y
- hipred_score
- 0.739
- ghis
- 0.611
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.745
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Snx1
- 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); embryo 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); normal phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- intracellular protein transport;receptor internalization;early endosome to Golgi transport;retrograde transport, endosome to Golgi;positive regulation of protein catabolic process;lamellipodium morphogenesis
- Cellular component
- cytoplasm;lysosome;endosome;Golgi apparatus;cytosol;endosome membrane;membrane;lamellipodium;retromer complex;retromer, tubulation complex;early endosome membrane;vesicle;protein-containing complex;intracellular membrane-bounded organelle
- Molecular function
- epidermal growth factor receptor binding;insulin receptor binding;protein binding;phosphatidylinositol binding;identical protein binding;protein homodimerization activity;cadherin binding;protein heterodimerization activity;transferrin receptor binding;leptin receptor binding