VPS52

VPS52 subunit of GARP complex, the group of Golgi associated retrograde protein (GARP) complex|Endosome-associated recycling protein (EARP) complex

Basic information

Region (hg38): 6:33250272-33272047

Previous symbols: [ "SACM2L" ]

Links

ENSG00000223501 ∙ NCBI:6293 ∙ OMIM:603443 ∙ HGNC:10518 ∙ Uniprot:Q8N1B4 ∙ 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 VPS52 gene.

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.

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					2	2
missense			36			36
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	37	0	3

Variants in VPS52

This is a list of pathogenic ClinVar variants found in the VPS52 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-33250929-G-A		not specified	Uncertain significance (Dec 16, 2023)
6-33251615-C-T		not specified	Uncertain significance (Feb 28, 2023)
6-33251892-C-T		not specified	Uncertain significance (Dec 09, 2023)
6-33263846-C-T		not specified	Uncertain significance (Aug 12, 2022)
6-33264061-T-C		not specified	Uncertain significance (Sep 27, 2022)
6-33264073-C-T		not specified	Uncertain significance (Dec 21, 2022)
6-33264102-A-C		not specified	Uncertain significance (Feb 06, 2024)
6-33264399-C-A		not specified	Uncertain significance (May 26, 2022)
6-33264472-G-C		not specified	Uncertain significance (Jul 14, 2022)
6-33264791-G-A		not specified	Uncertain significance (Nov 09, 2021)
6-33264879-C-T		not specified	Uncertain significance (Sep 27, 2022)
6-33264910-T-A			Benign (Apr 10, 2018)
6-33266561-G-A		not specified	Uncertain significance (May 30, 2024)
6-33266641-G-T		not specified	Uncertain significance (Oct 06, 2021)
6-33266665-G-A			Benign (Apr 10, 2018)
6-33266672-A-G		not specified	Uncertain significance (Sep 12, 2023)
6-33266677-G-A			Benign (Jun 06, 2017)
6-33267243-G-C		not specified	Uncertain significance (Feb 07, 2023)
6-33267268-T-C		not specified	Uncertain significance (Nov 21, 2022)
6-33267289-T-C		not specified	Uncertain significance (Jun 17, 2024)
6-33267871-C-G		not specified	Uncertain significance (Dec 14, 2022)
6-33267874-C-T		not specified	Uncertain significance (Jan 04, 2022)
6-33267881-C-T		not specified	Uncertain significance (May 24, 2023)
6-33267986-T-C		not specified	Uncertain significance (Oct 12, 2021)
6-33268139-G-C		not specified	Uncertain significance (Apr 03, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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