SNX5
sorting nexin 5, the group of PX-BAR domain containing|Sorting nexins|Small nucleolar RNA protein coding host genes
Basic information
Region (hg38): 20:17941597-17968980
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 SNX5 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 | 23 | 23 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 23 | 0 | 0 |
Variants in SNX5
This is a list of pathogenic ClinVar variants found in the SNX5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-17942377-C-G | not specified | Uncertain significance (Oct 20, 2023) | ||
| 20-17947501-C-T | not specified | Uncertain significance (Aug 27, 2024) | ||
| 20-17947533-T-C | not specified | Uncertain significance (Dec 01, 2022) | ||
| 20-17947537-G-T | not specified | Uncertain significance (Feb 13, 2024) | ||
| 20-17947575-C-T | not specified | Uncertain significance (May 31, 2023) | ||
| 20-17947588-G-C | not specified | Uncertain significance (Mar 06, 2023) | ||
| 20-17947590-G-A | not specified | Uncertain significance (Feb 05, 2024) | ||
| 20-17947608-T-C | not specified | Uncertain significance (Jan 19, 2024) | ||
| 20-17947615-T-C | not specified | Uncertain significance (Jun 10, 2024) | ||
| 20-17947630-G-A | not specified | Uncertain significance (Oct 12, 2021) | ||
| 20-17947642-G-C | not specified | Uncertain significance (Mar 20, 2023) | ||
| 20-17947645-C-G | not specified | Uncertain significance (Aug 21, 2023) | ||
| 20-17948892-T-C | not specified | Uncertain significance (Nov 18, 2022) | ||
| 20-17948904-T-C | not specified | Uncertain significance (May 26, 2024) | ||
| 20-17948906-T-C | not specified | Uncertain significance (Jun 22, 2021) | ||
| 20-17948919-A-T | not specified | Uncertain significance (Jun 17, 2024) | ||
| 20-17948925-G-A | not specified | Uncertain significance (Dec 15, 2022) | ||
| 20-17949101-T-C | not specified | Uncertain significance (Nov 29, 2024) | ||
| 20-17950198-T-C | not specified | Uncertain significance (Aug 26, 2024) | ||
| 20-17950307-C-T | not specified | Uncertain significance (Dec 04, 2024) | ||
| 20-17950309-T-C | not specified | Uncertain significance (Apr 26, 2024) | ||
| 20-17950344-T-C | not specified | Uncertain significance (Dec 18, 2023) | ||
| 20-17952618-T-C | not specified | Uncertain significance (Sep 08, 2024) | ||
| 20-17952621-C-T | not specified | Uncertain significance (Aug 10, 2021) | ||
| 20-17954093-C-T | not specified | Uncertain significance (Jun 28, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SNX5 | protein_coding | protein_coding | ENST00000377768 | 13 | 27383 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00145 | 0.997 | 125710 | 0 | 38 | 125748 | 0.000151 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.139 | 204 | 210 | 0.973 | 0.0000108 | 2690 |
| Missense in Polyphen | 58 | 70.846 | 0.81868 | 961 | ||
| Synonymous | -0.575 | 84 | 77.6 | 1.08 | 0.00000417 | 725 |
| Loss of Function | 2.81 | 9 | 23.8 | 0.379 | 0.00000132 | 298 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000514 | 0.000514 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000489 | 0.000489 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000106 | 0.000105 |
| Middle Eastern | 0.000489 | 0.000489 |
| South Asian | 0.000196 | 0.000196 |
| 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 3,4-bisphosphate (PtdIns(3,4)P2) (PubMed:15561769). 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). Does not have in vitro vesicle-to-membrane remodeling activity (PubMed:23085988). Involved in retrograde transport of lysosomal enzyme receptor IGF2R (PubMed:17148574, PubMed:18596235). May function as link between endosomal transport vesicles and dynactin (Probable). Plays a role in the internalization of EGFR after EGF stimulation (Probable). Involved in EGFR endosomal sorting and degradation; the function involves PIP5K1C isoform 3 and is retromer-independent (PubMed:23602387). Together with PIP5K1C isoform 3 facilitates HGS interaction with ubiquitinated EGFR, which initiates EGFR sorting to intraluminal vesicles (ILVs) of the multivesicular body for subsequent lysosomal degradation (Probable). Involved in E-cadherin sorting and degradation; inhibits PIP5K1C isoform 3-mediated E-cadherin degradation (PubMed:24610942). Plays a role in macropinocytosis (PubMed:18854019, PubMed:21048941). {ECO:0000269|PubMed:18854019, ECO:0000269|PubMed:21048941, ECO:0000269|PubMed:24610942, ECO:0000303|PubMed:15561769, ECO:0000303|PubMed:19619496, ECO:0000303|PubMed:23085988}.;
- Pathway
- Endocytosis - Homo sapiens (human);Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking;EGFR1
(Consensus)
Recessive Scores
- pRec
- 0.208
Intolerance Scores
- loftool
- 0.812
- rvis_EVS
- -0.25
- rvis_percentile_EVS
- 35.99
Haploinsufficiency Scores
- pHI
- 0.110
- hipred
- Y
- hipred_score
- 0.745
- ghis
- 0.602
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.997
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Snx5
- Phenotype
- growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; respiratory system phenotype; pigmentation phenotype; hematopoietic system 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
- snx5
- Affected structure
- Muller cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- intracellular protein transport;pinocytosis;epidermal growth factor catabolic process;regulation of macroautophagy;positive regulation of renal sodium excretion;retrograde transport, endosome to Golgi;negative regulation of blood pressure
- Cellular component
- ruffle;phagocytic cup;cytosol;brush border;cytoplasmic vesicle membrane;retromer complex;retromer, tubulation complex;extrinsic component of cytoplasmic side of plasma membrane;extrinsic component of endosome membrane;early endosome membrane;macropinocytic cup;tubular endosome
- Molecular function
- protein binding;phosphatidylinositol-5-phosphate binding;D1 dopamine receptor binding;dynactin binding;phosphatidylinositol binding;cadherin binding;protein heterodimerization activity;phosphatidylinositol-4-phosphate binding;phosphatidylinositol-3,5-bisphosphate binding