SNX4
Basic information
Region (hg38): 3:125446650-125520202
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (52 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003794.4. 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 | 0 | |||||
| missense | 52 | 52 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 52 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SNX4 | protein_coding | protein_coding | ENST00000251775 | 14 | 73547 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 5.68e-8 | 0.992 | 125698 | 0 | 49 | 125747 | 0.000195 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.887 | 190 | 228 | 0.835 | 0.0000111 | 2941 |
| Missense in Polyphen | 39 | 49.148 | 0.79352 | 610 | ||
| Synonymous | -0.827 | 85 | 75.8 | 1.12 | 0.00000355 | 782 |
| Loss of Function | 2.45 | 17 | 31.9 | 0.533 | 0.00000190 | 358 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000274 | 0.000272 |
| Ashkenazi Jewish | 0.000298 | 0.000298 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.000271 | 0.000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000263 | 0.000229 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in several stages of intracellular trafficking. Plays a role in recycling endocytosed transferrin receptor and prevent its degradation. {ECO:0000269|PubMed:17994011}.;
- Pathway
- Endocytosis - Homo sapiens (human);TGF_beta_Receptor
(Consensus)
Recessive Scores
- pRec
- 0.145
Intolerance Scores
- loftool
- 0.814
- rvis_EVS
- -0.58
- rvis_percentile_EVS
- 18.44
Haploinsufficiency Scores
- pHI
- 0.380
- hipred
- Y
- hipred_score
- 0.718
- ghis
- 0.696
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.641
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Snx4
- Phenotype
Gene ontology
- Biological process
- protein transport;endocytic recycling;positive regulation of histamine secretion by mast cell
- Cellular component
- cytoplasm;cytoplasmic dynein complex;plasma membrane;membrane;SNARE complex;early endosome membrane;protein-containing complex
- Molecular function
- epidermal growth factor receptor binding;insulin receptor binding;protein binding;phosphatidylinositol binding;transferrin receptor binding;leptin receptor binding