VPS52
Basic information
Region (hg38): 6:33250272-33272047
Previous symbols: [ "SACM2L" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (64 variants)
- not_provided (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the VPS52 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000022553.6. 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 | 2 | |||||
| missense | 65 | 65 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 66 | 0 | 2 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| VPS52 | protein_coding | protein_coding | ENST00000445902 | 20 | 21776 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000389 | 1.00 | 125708 | 0 | 40 | 125748 | 0.000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.50 | 286 | 432 | 0.662 | 0.0000264 | 4671 |
| Missense in Polyphen | 81 | 139.29 | 0.58152 | 1526 | ||
| Synonymous | 1.60 | 134 | 160 | 0.839 | 0.00000854 | 1461 |
| Loss of Function | 4.30 | 15 | 46.7 | 0.321 | 0.00000292 | 461 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000481 | 0.000460 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.000370 | 0.000370 |
| European (Non-Finnish) | 0.000135 | 0.000132 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000367 | 0.000229 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Acts as component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). The GARP complex is required for the maintenance of the cycling of mannose 6-phosphate receptors between the TGN and endosomes, this cycling is necessary for proper lysosomal sorting of acid hydrolases such as CTSD (PubMed:15878329, PubMed:18367545). Acts as component of the EARP complex that is involved in endocytic recycling. The EARP complex associates with Rab4-positive endosomes and promotes recycling of internalized transferrin receptor (TFRC) to the plasma membrane (PubMed:25799061). {ECO:0000269|PubMed:15878329, ECO:0000269|PubMed:18367545, ECO:0000269|PubMed:25799061}.;
- Pathway
- Vesicle-mediated transport;Membrane Trafficking;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic
(Consensus)
Intolerance Scores
- loftool
- 0.241
- rvis_EVS
- -0.51
- rvis_percentile_EVS
- 21.56
Haploinsufficiency Scores
- pHI
- 0.300
- hipred
- Y
- hipred_score
- 0.627
- ghis
- 0.543
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.961
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Vps52
- Phenotype
- growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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; embryo phenotype;
Gene ontology
- Biological process
- Golgi to vacuole transport;lysosomal transport;ectodermal cell differentiation;protein transport;endocytic recycling;retrograde transport, endosome to Golgi;embryonic ectodermal digestive tract development
- Cellular component
- GARP complex;Golgi apparatus;cytosol;endosome membrane;membrane;trans-Golgi network membrane;perinuclear region of cytoplasm;recycling endosome;EARP complex
- Molecular function
- protein binding;Rab GTPase binding;syntaxin binding