SNX6
sorting nexin 6, the group of PX-BAR domain containing|Sorting nexins
Basic information
Region (hg38): 14:34561093-34630160
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 SNX6 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 | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 5 | |||||
| Total | 0 | 0 | 18 | 0 | 0 |
Variants in SNX6
This is a list of pathogenic ClinVar variants found in the SNX6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 14-34563127-T-G | not specified | Uncertain significance (Jun 12, 2023) | ||
| 14-34563169-G-T | not specified | Uncertain significance (Aug 06, 2024) | ||
| 14-34567769-G-A | not specified | Uncertain significance (Apr 20, 2024) | ||
| 14-34567934-T-C | not specified | Uncertain significance (Aug 30, 2021) | ||
| 14-34575761-C-T | not specified | Uncertain significance (Jan 27, 2025) | ||
| 14-34581572-C-T | not specified | Uncertain significance (May 05, 2023) | ||
| 14-34581580-T-C | not specified | Uncertain significance (Dec 24, 2024) | ||
| 14-34586245-G-C | not specified | Uncertain significance (Jun 22, 2023) | ||
| 14-34586302-G-C | not specified | Uncertain significance (Jul 05, 2024) | ||
| 14-34586303-C-T | not specified | Uncertain significance (Jan 07, 2022) | ||
| 14-34593136-G-T | not specified | Uncertain significance (Nov 25, 2024) | ||
| 14-34593140-T-A | not specified | Uncertain significance (Apr 09, 2024) | ||
| 14-34593141-C-A | not specified | Uncertain significance (Apr 09, 2024) | ||
| 14-34597564-C-T | not specified | Uncertain significance (Jan 14, 2025) | ||
| 14-34608094-T-C | not specified | Uncertain significance (Dec 25, 2024) | ||
| 14-34608139-C-T | not specified | Uncertain significance (Oct 04, 2022) | ||
| 14-34630128-G-A | not specified | Uncertain significance (Aug 25, 2024) | ||
| 14-34630131-G-A | not specified | Uncertain significance (Mar 01, 2023) | ||
| 14-34630134-G-C | not specified | Uncertain significance (Jan 23, 2024) | ||
| 14-34630146-C-A | not specified | Uncertain significance (Nov 09, 2023) | ||
| 14-34630149-G-A | not specified | Uncertain significance (Dec 15, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SNX6 | protein_coding | protein_coding | ENST00000362031 | 14 | 69090 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.499 | 0.501 | 125729 | 0 | 9 | 125738 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.51 | 142 | 202 | 0.702 | 0.0000100 | 2723 |
| Missense in Polyphen | 31 | 56.296 | 0.55066 | 732 | ||
| Synonymous | -0.0756 | 74 | 73.2 | 1.01 | 0.00000373 | 753 |
| Loss of Function | 3.85 | 6 | 28.0 | 0.214 | 0.00000177 | 335 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000313 | 0.0000313 |
| Ashkenazi Jewish | 0.0000995 | 0.0000992 |
| East Asian | 0.000111 | 0.000109 |
| Finnish | 0.0000465 | 0.0000462 |
| European (Non-Finnish) | 0.0000266 | 0.0000264 |
| Middle Eastern | 0.000111 | 0.000109 |
| South Asian | 0.0000380 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in several stages of intracellular trafficking. Interacts with membranes phosphatidylinositol 3,4-bisphosphate and/or phosphatidylinositol 4,5-bisphosphate (Probable). Acts in part as component of the retromer membrane-deforming SNX-BAR subcomplex (PubMed:19935774). 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 endosome-to-TGN transport of lysosomal enzyme receptor IGF2R (PubMed:17148574). May function as link between transport vesicles and dynactin (Probable). Negatively regulates retrograde transport of BACE1 from the cell surface to the trans-Golgi network (PubMed:20354142). Involved in E-cadherin sorting and degradation; inhibits PIP5K1C isoform 3-mediated E-cadherin degradation (PubMed:24610942). In association with GIT1 involved in EGFR degradation. Promotes lysosomal degradation of CDKN1B (By similarity). May contribute to transcription regulation (Probable). {ECO:0000250|UniProtKB:Q6P8X1, ECO:0000269|PubMed:17148574, ECO:0000269|PubMed:19935774, ECO:0000269|PubMed:20354142, ECO:0000269|PubMed:23085988, ECO:0000269|PubMed:24610942, ECO:0000303|PubMed:19935774, ECO:0000303|PubMed:20830743, ECO:0000305}.;
- Pathway
- Endocytosis - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;TGF_beta_Receptor
(Consensus)
Recessive Scores
- pRec
- 0.0973
Intolerance Scores
- loftool
- 0.335
- rvis_EVS
- -0.23
- rvis_percentile_EVS
- 36.86
Haploinsufficiency Scores
- pHI
- 0.265
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.597
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.661
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Snx6
- Phenotype
Gene ontology
- Biological process
- intracellular protein transport;negative regulation of epidermal growth factor-activated receptor activity;regulation of macroautophagy;negative regulation of transforming growth factor beta receptor signaling pathway;retrograde transport, endosome to Golgi;negative regulation of transcription, DNA-templated;regulation of histamine secretion by mast cell
- Cellular component
- nucleus;cytoplasm;cytosol;retromer complex;retromer, tubulation complex;early endosome membrane;tubular endosome
- Molecular function
- protein binding;dynactin binding;phosphatidylinositol binding;protein homodimerization activity;protein heterodimerization activity