UVRAG
UV radiation resistance associated, the group of C2 domain containing|PIK3C3 complex subunits
Basic information
Region (hg38): 11:75815210-76144232
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (95 variants)
- not_provided (5 variants)
- Prostate_cancer (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the UVRAG gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003369.4. 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 | 2 | |||||
| missense | 94 | 97 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 94 | 4 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| UVRAG | protein_coding | protein_coding | ENST00000356136 | 15 | 328028 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.989 | 0.0106 | 125735 | 0 | 13 | 125748 | 0.0000517 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.49 | 289 | 369 | 0.782 | 0.0000205 | 4535 |
| Missense in Polyphen | 80 | 120.51 | 0.66385 | 1395 | ||
| Synonymous | 0.610 | 132 | 141 | 0.935 | 0.00000783 | 1376 |
| Loss of Function | 4.76 | 5 | 35.7 | 0.140 | 0.00000189 | 442 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000177 | 0.000177 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000442 | 0.0000439 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Versatile protein that is involved in regulation of different cellular pathways implicated in membrane trafficking. Involved in regulation of the COPI-dependent retrograde transport from Golgi and the endoplasmic reticulum by associating with the NRZ complex; the function is dependent on its binding to phosphatidylinositol 3-phosphate (PtdIns(3)P) (PubMed:24056303). During autophagy acts as regulatory subunit of the alternative PI3K complex II (PI3KC3-C2) that mediates formation of phosphatidylinositol 3-phosphate and is believed to be involved in maturation of autophagosomes and endocytosis. Activates lipid kinase activity of PIK3C3. Involved in the regulation of degradative endocytic trafficking and cytokinesis, and in regulation of ATG9A transport from the Golgi to the autophagosome; the functions seems to implicate its association with PI3KC3-C2 (PubMed:16799551, PubMed:20643123, PubMed:24056303). Involved in maturation of autophagosomes and degradative endocytic trafficking independently of BECN1 but depending on its association with a class C Vps complex (possibly the HOPS complex); the association is also proposed to promote autophagosome recruitment and activation of Rab7 and endosome-endosome fusion events (PubMed:18552835). Enhances class C Vps complex (possibly HOPS complex) association with a SNARE complex and promotes fusogenic SNARE complex formation during late endocytic membrane fusion (PubMed:24550300). In case of negative-strand RNA virus infection is required for efficient virus entry, promotes endocytic transport of virions and is implicated in a VAMP8-specific fusogenic SNARE complex assembly (PubMed:24550300). {ECO:0000269|PubMed:18552835, ECO:0000269|PubMed:20643123, ECO:0000269|PubMed:24056303, ECO:0000305}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving UVRAG has been observed in a patient with heterotaxy (left-right axis malformation). Inversion Inv(11)(q13.5;q25). {ECO:0000269|PubMed:10798355}.;
- Pathway
- Autophagy - animal - Homo sapiens (human);Nanoparticle triggered autophagic cell death;Senescence and Autophagy in Cancer
(Consensus)
Recessive Scores
- pRec
- 0.0998
Intolerance Scores
- loftool
- 0.482
- rvis_EVS
- -0.37
- rvis_percentile_EVS
- 28.16
Haploinsufficiency Scores
- pHI
- 0.198
- hipred
- Y
- hipred_score
- 0.735
- ghis
- 0.539
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.999
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Uvrag
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; muscle 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); immune system phenotype;
Zebrafish Information Network
- Gene name
- uvrag
- Affected structure
- melanocyte
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- DNA repair;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;autophagy;spindle organization;chromosome segregation;centrosome cycle;regulation of cytokinesis;receptor catabolic process;SNARE complex assembly;viral entry into host cell;maintenance of Golgi location;regulation of protein serine/threonine kinase activity;multivesicular body sorting pathway;double-strand break repair via classical nonhomologous end joining;positive regulation of autophagosome maturation
- Cellular component
- chromosome, centromeric region;cytoplasm;lysosome;early endosome;late endosome;endoplasmic reticulum;centrosome;midbody;HOPS complex;phagocytic vesicle;DNA-dependent protein kinase complex
- Molecular function
- SNARE binding;protein binding;SH3 domain binding