UVRAG

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

Basic information

Region (hg38): 11:75815209-76144232

Links

ENSG00000198382 ∙ NCBI:7405 ∙ OMIM:602493 ∙ HGNC:12640 ∙ Uniprot:Q9P2Y5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (36 variants)
• not provided (5 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.

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	1	2
missense			36	1		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	36	2	1

Variants in UVRAG

This is a list of pathogenic ClinVar variants found in the UVRAG region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-75815459-C-T		not specified	Uncertain significance (May 30, 2023)
11-75815510-C-A		not specified	Uncertain significance (Apr 07, 2022)
11-75851914-C-T		not specified	Uncertain significance (May 11, 2022)
11-75851970-C-T		not specified	Uncertain significance (Dec 27, 2022)
11-75851976-T-C		not specified	Uncertain significance (Nov 12, 2021)
11-75851994-T-C		not specified	Uncertain significance (Dec 21, 2023)
11-75879912-A-G		not specified	Uncertain significance (Feb 03, 2022)
11-75879948-G-A		not specified	Uncertain significance (Dec 21, 2022)
11-75879982-A-T		not specified	Uncertain significance (Dec 06, 2022)
11-75888831-T-G		not specified	Uncertain significance (Aug 21, 2023)
11-75888896-A-G		Malignant tumor of prostate	Uncertain significance (-)
11-75888910-A-C			Likely benign (May 31, 2018)
11-75911978-A-G		not specified	Uncertain significance (Mar 29, 2023)
11-75912008-C-T		not specified	Uncertain significance (Jan 27, 2022)
11-75912020-G-A		not specified	Uncertain significance (Mar 22, 2023)
11-75912042-A-G			Benign (May 31, 2018)
11-75961485-C-T		not specified	Uncertain significance (Feb 03, 2022)
11-75961542-A-G		not specified	Uncertain significance (Jul 19, 2023)
11-75983387-A-G		not specified	Uncertain significance (Jan 23, 2024)
11-75983402-T-C		not specified	Uncertain significance (Feb 14, 2024)
11-75983418-T-G		not specified	Uncertain significance (Dec 03, 2021)
11-75983435-G-A		not specified	Uncertain significance (Nov 13, 2023)
11-75983444-C-T		not specified	Uncertain significance (Aug 21, 2023)
11-75983445-G-A		not specified	Uncertain significance (Dec 30, 2023)
11-75983504-C-G		not specified	Uncertain significance (May 04, 2022)

GnomAD

Source: gnomAD

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: 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

	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