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GeneBe

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): 6:33250271-33272047

Previous symbols: [ "SACM2L" ]

Links

ENSG00000223501NCBI:6293OMIM:603443HGNC:10518Uniprot:Q8N1B4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VPS52 gene.

  • Inborn genetic diseases (28 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.

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
clinvar
2
missense
29
clinvar
29
nonsense
1
clinvar
1
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
?
0
non coding
?
1
clinvar
1
Total 0 0 30 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
6-33251615-C-T Inborn genetic diseases Uncertain significance (Feb 28, 2023)2491523
6-33263846-C-T Inborn genetic diseases Uncertain significance (Aug 12, 2022)2306840
6-33264061-T-C Inborn genetic diseases Uncertain significance (Sep 27, 2022)2313715
6-33264073-C-T Inborn genetic diseases Uncertain significance (Dec 21, 2022)2214531
6-33264399-C-A Inborn genetic diseases Uncertain significance (May 26, 2022)2291092
6-33264472-G-C Inborn genetic diseases Uncertain significance (Jul 14, 2022)2222458
6-33264791-G-A Inborn genetic diseases Uncertain significance (Nov 09, 2021)2260323
6-33264879-C-T Inborn genetic diseases Uncertain significance (Sep 27, 2022)2410175
6-33264910-T-A Benign (Apr 10, 2018)782824
6-33266641-G-T Inborn genetic diseases Uncertain significance (Oct 06, 2021)2253739
6-33266665-G-A Benign (Apr 10, 2018)770362
6-33266672-A-G Inborn genetic diseases Uncertain significance (Sep 12, 2023)2597299
6-33266677-G-A Benign (Jun 06, 2017)775237
6-33267243-G-C Inborn genetic diseases Uncertain significance (Feb 07, 2023)2482140
6-33267268-T-C Inborn genetic diseases Uncertain significance (Nov 21, 2022)2408850
6-33267871-C-G Inborn genetic diseases Uncertain significance (Dec 14, 2022)2334961
6-33267874-C-T Inborn genetic diseases Uncertain significance (Jan 04, 2022)2269879
6-33267881-C-T Inborn genetic diseases Uncertain significance (May 24, 2023)2519198
6-33267986-T-C Inborn genetic diseases Uncertain significance (Oct 12, 2021)2206163
6-33268139-G-C Inborn genetic diseases Uncertain significance (Apr 03, 2023)2532267
6-33268507-G-A Inborn genetic diseases Uncertain significance (Apr 08, 2023)2552931
6-33268513-G-A Inborn genetic diseases Uncertain significance (Aug 30, 2021)2247519
6-33268516-C-A Inborn genetic diseases Uncertain significance (Sep 28, 2022)2384171
6-33268576-C-T Inborn genetic diseases Uncertain significance (Sep 01, 2021)2342916
6-33268590-T-C Inborn genetic diseases Uncertain significance (Jul 06, 2021)2317155

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
VPS52protein_codingprotein_codingENST00000445902 2021776
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0003891.001257080401257480.000159
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.502864320.6620.00002644671
Missense in Polyphen81139.290.581521526
Synonymous1.601341600.8390.000008541461
Loss of Function4.301546.70.3210.00000292461

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004810.000460
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.0003700.000370
European (Non-Finnish)0.0001350.000132
Middle Eastern0.0001090.000109
South Asian0.0003670.000229
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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