SNX3
sorting nexin 3, the group of Sorting nexins
Basic information
Region (hg38): 6:108211221-108261246
Links
Phenotypes
GenCC
Source:
- MMEP syndrome (Limited), mode of inheritance: AD
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 SNX3 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 | 2 | |||||
| missense | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 2 | 0 |
Variants in SNX3
This is a list of pathogenic ClinVar variants found in the SNX3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-108212170-T-C | Likely benign (Jan 31, 2018) | |||
| 6-108214563-A-C | not specified | Uncertain significance (Oct 06, 2021) | ||
| 6-108222963-T-C | not specified | Uncertain significance (Jan 16, 2024) | ||
| 6-108260792-C-T | not specified | Uncertain significance (May 26, 2023) | ||
| 6-108260826-A-G | SNX3-related disorder | Likely benign (Jan 14, 2021) | ||
| 6-108260842-T-G | not specified | Uncertain significance (Dec 22, 2023) | ||
| 6-108260899-G-C | not specified | Uncertain significance (Jul 26, 2022) | ||
| 6-108260911-G-C | not specified | Uncertain significance (Feb 28, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SNX3 | protein_coding | protein_coding | ENST00000230085 | 4 | 50039 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.249 | 0.725 | 125735 | 0 | 7 | 125742 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.73 | 44 | 90.1 | 0.488 | 0.00000476 | 1060 |
| Missense in Polyphen | 11 | 35.626 | 0.30876 | 423 | ||
| Synonymous | -1.13 | 44 | 35.5 | 1.24 | 0.00000191 | 310 |
| Loss of Function | 1.86 | 2 | 7.52 | 0.266 | 3.99e-7 | 87 |
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) | 0.0000178 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000165 | 0.000163 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Phosphoinositide-binding protein required for multivesicular body formation. Specifically binds phosphatidylinositol 3-phosphate (PtdIns(P3)). Also can bind phosphatidylinositol 4-phosphate (PtdIns(P4)), phosphatidylinositol 5-phosphate (PtdIns(P5)) and phosphatidylinositol 3,5-biphosphate (PtdIns(3,5)P2) (By similarity). Plays a role in protein transport between cellular compartments. Together with RAB7A facilitates endosome membrane association of the retromer cargo-selective subcomplex (CSC/VPS). May in part act as component of the SNX3-retromer complex which mediates the retrograde endosome-to-TGN transport of WLS distinct from the SNX-BAR retromer pathway (PubMed:21725319, PubMed:24344282). Promotes stability and cell surface expression of epithelial sodium channel (ENAC) subunits SCNN1A and SCNN1G (By similarity). Not involved in EGFR degradation. Involved in the regulation of phagocytosis in dendritic cells possibly by regulating EEA1 recruitment to the nascent phagosomes (PubMed:23237080). Involved in iron homeostasis through regulation of endocytic recycling of the transferrin receptor TFRC presumably by delivering the transferrin:transferrin receptor complex to recycling endosomes; the function may involve the CSC retromer subcomplex (By similarity). In the case of Salmonella enterica infection plays arole in maturation of the Salmonella-containing vacuole (SCV) and promotes recruitment of LAMP1 to SCVs (PubMed:20482551). {ECO:0000250|UniProtKB:O70492, ECO:0000269|PubMed:11433298, ECO:0000269|PubMed:18767904, ECO:0000269|PubMed:21725319, ECO:0000269|PubMed:23237080, ECO:0000269|PubMed:24344282, ECO:0000305|PubMed:21725319}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving SNX3 has been found in patients with syndromic microphthalmia. Translocation t(6;13)(q21;q12). {ECO:0000269|PubMed:12471201}.;
- Pathway
- Endocytosis - Homo sapiens (human);Signaling by WNT;Signal Transduction;Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination;WNT ligand biogenesis and trafficking
(Consensus)
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- loftool
- 0.251
- rvis_EVS
- 0.12
- rvis_percentile_EVS
- 62.38
Haploinsufficiency Scores
- pHI
- 0.570
- hipred
- Y
- hipred_score
- 0.800
- ghis
- 0.566
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Snx3
- 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);
Zebrafish Information Network
- Gene name
- snx3
- Affected structure
- nucleate erythrocyte
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- response to bacterium;membrane invagination;positive regulation of neuron projection development;protein transport;Wnt signaling pathway;protein deubiquitination;protein to membrane docking;regulation of Wnt signaling pathway;negative regulation of protein catabolic process;negative regulation of viral entry into host cell;negative regulation of phagocytosis;negative regulation of protein transport;intralumenal vesicle formation;negative regulation of early endosome to late endosome transport
- Cellular component
- cytoplasm;early endosome;cytosol;endosome membrane;clathrin-coated vesicle;retromer complex;early endosome membrane;early phagosome;extracellular exosome
- Molecular function
- protein binding;phosphatidylinositol-5-phosphate binding;protein phosphatase binding;phosphatidylinositol-3-phosphate binding;phosphatidylinositol-4-phosphate binding;phosphatidylinositol-3,5-bisphosphate binding