UVRAG

UV radiation resistance associated, the group of C2 domain containing|PIK3C3 complex subunits

Basic information

Region (hg38): 11:75815210-76144232

Links

ENSG00000198382NCBI:7405OMIM:602493HGNC:12640Uniprot:Q9P2Y5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UVRAG gene.

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: . 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.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
1
clinvar
1
clinvar
2
missense
65
clinvar
1
clinvar
66
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 65 2 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
UVRAGprotein_codingprotein_codingENST00000356136 15328028
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9890.01061257350131257480.0000517
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.492893690.7820.00002054535
Missense in Polyphen80120.510.663851395
Synonymous0.6101321410.9350.000007831376
Loss of Function4.76535.70.1400.00000189442

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001770.000177
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00004420.0000439
Middle Eastern0.00005440.0000544
South Asian0.00006530.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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