VPS52
gene geneOn this page
Also known as ARE1
Summary
VPS52 (VPS52 subunit of GARP complex, HGNC:10518) is a protein-coding gene on chromosome 6p21.32, encoding Vacuolar protein sorting-associated protein 52 homolog (Q8N1B4). Acts as a component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). It is a selective cancer dependency (DepMap: 30.3% of cell lines).
This gene encodes a protein that is similar to the yeast suppressor of actin mutations 2 gene. The yeast protein forms a subunit of the tetrameric Golgi-associated retrograde protein complex that is involved in vesicle trafficking from from both early and late endosomes, back to the trans-Golgi network. This gene is located on chromosome 6 in a head-to-head orientation with the gene encoding ribosomal protein S18. Alternative splicing results in multiple transcript variants.
Source: NCBI Gene 6293 — RefSeq curated summary.
At a glance
- Gene–disease (curated): complex neurodevelopmental disorder with or without congenital anomalies (Moderate, GenCC)
- GWAS associations: 2
- Clinical variants (ClinVar): 99 total
- Cancer dependency (DepMap): dependent in 30.3% of screened cell lines
- MANE Select transcript:
NM_022553
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:10518 |
| Approved symbol | VPS52 |
| Name | VPS52 subunit of GARP complex |
| Location | 6p21.32 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | ARE1 |
| Ensembl gene | ENSG00000223501 |
| Ensembl biotype | protein_coding |
| OMIM | 603443 |
| Entrez | 6293 |
Gene structure
Transcript identifiers
Ensembl transcripts: 23 — 14 protein_coding, 6 protein_coding_CDS_not_defined, 3 retained_intron
ENST00000445902, ENST00000461743, ENST00000463486, ENST00000464425, ENST00000471309, ENST00000478934, ENST00000482399, ENST00000493379, ENST00000493674, ENST00000495755, ENST00000495981, ENST00000865493, ENST00000865494, ENST00000865495, ENST00000865496, ENST00000865497, ENST00000865498, ENST00000865499, ENST00000920311, ENST00000954722, ENST00000954723, ENST00000954724, ENST00000954725
RefSeq mRNA: 4 — MANE Select: NM_022553
NM_001289174, NM_001289175, NM_001289176, NM_022553
CCDS: CCDS4770
Canonical transcript exons
ENST00000383210 — 0 exons
Expression profiles
Bgee: expression breadth ubiquitous, 134 present calls, max score 97.02.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.1921 / max 87.0869, expressed in 1811 samples.
FANTOM5 promoters (4 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 73111 | 12.0368 | 1782 |
| 73110 | 5.5958 | 1705 |
| 73112 | 0.4149 | 205 |
| 73109 | 0.1445 | 64 |
Top tissues by expression
134 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| right lobe of thyroid gland | UBERON:0001119 | 97.02 | gold quality |
| right uterine tube | UBERON:0001302 | 97.00 | gold quality |
| pituitary gland | UBERON:0000007 | 96.78 | gold quality |
| metanephros cortex | UBERON:0010533 | 96.67 | gold quality |
| right adrenal gland cortex | UBERON:0035827 | 96.60 | gold quality |
| left lobe of thyroid gland | UBERON:0001120 | 96.59 | gold quality |
| right adrenal gland | UBERON:0001233 | 96.53 | gold quality |
| thyroid gland | UBERON:0002046 | 96.46 | gold quality |
| right hemisphere of cerebellum | UBERON:0014890 | 96.44 | gold quality |
| spleen | UBERON:0002106 | 96.38 | gold quality |
| adenohypophysis | UBERON:0002196 | 96.37 | gold quality |
| small intestine Peyer’s patch | UBERON:0003454 | 96.19 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 96.09 | gold quality |
| cerebellar cortex | UBERON:0002129 | 96.08 | gold quality |
| cerebellum | UBERON:0002037 | 96.05 | gold quality |
| left adrenal gland cortex | UBERON:0035825 | 95.98 | gold quality |
| left adrenal gland | UBERON:0001234 | 95.97 | gold quality |
| right ovary | UBERON:0002118 | 95.97 | gold quality |
| fundus of stomach | UBERON:0001160 | 95.94 | gold quality |
| skin of abdomen | UBERON:0001416 | 95.92 | gold quality |
| body of pancreas | UBERON:0001150 | 95.90 | gold quality |
| left ovary | UBERON:0002119 | 95.86 | gold quality |
| tibial nerve | UBERON:0001323 | 95.85 | gold quality |
| zone of skin | UBERON:0000014 | 95.83 | gold quality |
| skin of leg | UBERON:0001511 | 95.82 | gold quality |
| body of stomach | UBERON:0001161 | 95.73 | gold quality |
| lower esophagus mucosa | UBERON:0035834 | 95.71 | gold quality |
| apex of heart | UBERON:0002098 | 95.66 | gold quality |
| minor salivary gland | UBERON:0001830 | 95.62 | gold quality |
| small intestine | UBERON:0002108 | 95.61 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 3.83 |
Regulation
Is transcription factor: no
Upstream regulators (CollecTRI, top): AR, NFE2L2
miRNA regulators (miRDB)
28 targeting VPS52, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-4725-3P | 99.96 | 69.53 | 2520 |
| HSA-MIR-6780B-5P | 99.96 | 69.60 | 2562 |
| HSA-MIR-6772-5P | 99.94 | 67.01 | 577 |
| HSA-MIR-4493 | 99.90 | 66.48 | 977 |
| HSA-MIR-4271 | 99.88 | 68.32 | 2244 |
| HSA-MIR-4668-5P | 99.79 | 70.58 | 3782 |
| HSA-MIR-4255 | 99.72 | 67.70 | 1541 |
| HSA-MIR-1827 | 99.63 | 68.57 | 3265 |
| HSA-MIR-4753-5P | 99.54 | 68.51 | 1356 |
| HSA-MIR-671-5P | 99.52 | 67.11 | 1277 |
| HSA-MIR-3147 | 99.52 | 66.34 | 388 |
| HSA-MIR-6165 | 99.44 | 67.12 | 1389 |
| HSA-MIR-548V | 99.29 | 69.47 | 1157 |
| HSA-MIR-892C-5P | 99.16 | 70.56 | 2116 |
| HSA-MIR-6768-3P | 99.14 | 67.38 | 1319 |
| HSA-MIR-6506-5P | 99.04 | 65.66 | 1386 |
| HSA-MIR-1304-5P | 98.90 | 68.58 | 1054 |
| HSA-MIR-619-5P | 98.57 | 64.97 | 1988 |
| HSA-MIR-4664-5P | 98.17 | 65.07 | 1020 |
| HSA-MIR-4494 | 97.86 | 64.93 | 850 |
| HSA-MIR-6783-5P | 97.67 | 67.21 | 1528 |
| HSA-MIR-526B-5P | 97.41 | 67.99 | 1074 |
| HSA-MIR-342-5P | 97.25 | 64.10 | 817 |
| HSA-MIR-3972 | 97.19 | 66.46 | 808 |
| HSA-MIR-1202 | 97.19 | 66.43 | 827 |
| HSA-MIR-4513 | 95.04 | 67.06 | 727 |
| HSA-MIR-6855-3P | 95.04 | 66.57 | 725 |
| HSA-MIR-6765-5P | 94.51 | 62.65 | 164 |
Functional genomics
DepMap (CRISPR cell-line fitness): dependent in 30.3% of screened cell lines.
Literature-anchored findings (GeneRIF, showing 7)
- Golgi associated retrograde protein complex, consisting of the Vps52, Vps53, and Vps54 proteins, shows significant conservation between various species but diversification and specialization result in important differences in human cells. (PMID:15878329)
- Missorting of cathepsin D in GARP-depleted cells results from accumulation of recycling MPRs in a population of light, small vesicles downstream of endosomes. (PMID:18367545)
- Golgi-associated retrograde protein orchestrates retrograde transport from endosomes to the trans-Golgi network by promoting vesicle tethering and assembly of SNARE complexes in consecutive, independent steps.[Golgi associated retrograde protein] (PMID:19620288)
- our data indicate that cisplatin resistance in HOCCs is partially attributable to their high expression of p62, which plays an important role in preventing ROS stress-induced apoptosis by regulating the Keap1-Nrf2-ARE signaling pathway. (PMID:25269472)
- These data demonstrate that the beneficial properties of SFN extend beyond activation of the KEAP1-Nrf2-ARE system and warrant further interrogation given the current use of this agent in multiple clinical trials (PMID:27889639)
- Loss of heterozygosity and stop-gain mutation of VPS52 were found in gastric cancer. (PMID:28791438)
- The Sac2 operates upstream of granule docking, since loss of Sac2 prevented granule tethering to the plasma membrane and resulted in both reduced granule density and number of exocytic events. (PMID:31533953)
Cross-species orthologs
5 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | vps52 | ENSDARG00000099258 |
| mus_musculus | Vps52 | ENSMUSG00000024319 |
| rattus_norvegicus | Vps52 | ENSRNOG00000000470 |
| drosophila_melanogaster | Vps52 | FBGN0031710 |
| caenorhabditis_elegans | WBGENE00007059 |
Protein
Protein identifiers
Vacuolar protein sorting-associated protein 52 homolog — Q8N1B4 (reviewed: Q8N1B4)
Alternative names: SAC2 suppressor of actin mutations 2-like protein
All UniProt accessions (3): Q8N1B4, E9PI03, Q4VXZ2
UniProt curated annotations — full annotation on UniProt →
Function. Acts as a 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. Acts as a 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.
Subunit / interactions. Component of the Golgi-associated retrograde protein (GARP) complex, also called VFT (VPS fifty-three) complex, composed of VPS51, VPS52, VPS53 and VPS54. Component of the endosome-associated retrograde protein (EARP) complex, composed of VPS51, VPS52, VPS53 and VPS50/Syndetin. EIPR1 interacts with both EARP and GARP complexes and mediates the recruitment of the GARP complex to the trans-Golgi network. Interacts with RAB6A and STX10. Interacts with BLTP3B.
Subcellular location. Golgi apparatus. trans-Golgi network membrane. Endosome membrane. Recycling endosome.
Similarity. Belongs to the VPS52 family.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q8N1B4-1 | 1 | yes |
| Q8N1B4-2 | 2 |
RefSeq proteins (4): NP_001276103, NP_001276104, NP_001276105, NP_072047* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR007258 | Vps52 | Family |
| IPR048319 | Vps52_CC | Domain |
| IPR048361 | Vps52_C | Domain |
Pfam: PF04129, PF20655
UniProt features (8 total): coiled-coil region 2, modified residue 2, initiator methionine 1, chain 1, splice variant 1, sequence conflict 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q8N1B4-F1 | 86.10 | 0.61 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Post-translational modifications (2): 2, 355
Function
Pathways and Gene Ontology
Reactome pathways
1 pathways
| ID | Pathway |
|---|---|
| R-HSA-6811440 | Retrograde transport at the Trans-Golgi-Network |
MSigDB gene sets: 191 (showing top):
GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, GCM_MAP4K4, FREAC2_01, GOBP_LYSOSOMAL_TRANSPORT, GCM_GSPT1, GCANCTGNY_MYOD_Q6, MORF_HDAC1, GOBP_PROTEIN_TARGETING, GOBP_VACUOLAR_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_ORGANIC_HYDROXY_COMPOUND_TRANSPORT, GOBP_DIGESTIVE_SYSTEM_DEVELOPMENT, GOBP_ECTODERM_DEVELOPMENT, MORF_SKP1A
GO Biological Process (9): protein targeting (GO:0006605), Golgi to vacuole transport (GO:0006896), lysosomal transport (GO:0007041), ectodermal cell differentiation (GO:0010668), protein transport (GO:0015031), endocytic recycling (GO:0032456), retrograde transport, endosome to Golgi (GO:0042147), embryonic ectodermal digestive tract development (GO:0048611), vesicle-mediated cholesterol transport (GO:0090119)
GO Molecular Function (2): syntaxin binding (GO:0019905), protein binding (GO:0005515)
GO Cellular Component (12): GARP complex (GO:0000938), Golgi apparatus (GO:0005794), cytosol (GO:0005829), endosome membrane (GO:0010008), membrane (GO:0016020), trans-Golgi network membrane (GO:0032588), perinuclear region of cytoplasm (GO:0048471), recycling endosome (GO:0055037), presynapse (GO:0098793), postsynapse (GO:0098794), EARP complex (GO:1990745), endosome (GO:0005768)
Reactome top-level categories
Rollup of top-1 pathways:
| Category | Pathways |
|---|---|
| Intra-Golgi and retrograde Golgi-to-ER traffic | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 5 |
| cytoplasm | 3 |
| establishment of protein localization | 2 |
| vacuolar transport | 2 |
| intercellular transport | 2 |
| endosomal transport | 2 |
| cytosolic transport | 2 |
| cytoplasmic vesicle | 2 |
| endomembrane system | 2 |
| endosome | 2 |
| synapse | 2 |
| post-Golgi vesicle-mediated transport | 1 |
| ectoderm development | 1 |
| cell differentiation | 1 |
| transport | 1 |
| intracellular protein localization | 1 |
| vesicle-mediated transport to the plasma membrane | 1 |
| ectodermal digestive tract development | 1 |
| embryonic digestive tract development | 1 |
| vesicle-mediated transport | 1 |
| intracellular cholesterol transport | 1 |
| SNARE binding | 1 |
| binding | 1 |
| Golgi apparatus | 1 |
| vesicle tethering complex | 1 |
| intracellular membrane-bounded organelle | 1 |
| cytoplasmic vesicle membrane | 1 |
| bounding membrane of organelle | 1 |
| trans-Golgi network | 1 |
| organelle membrane | 1 |
| protein-containing complex | 1 |
| recycling endosome | 1 |
Protein interactions and networks
STRING
1328 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| VPS52 | VPS53 | Q5VIR6 | 998 |
| VPS52 | VPS54 | Q9P1Q0 | 997 |
| VPS52 | VPS51 | Q9UID3 | 997 |
| VPS52 | VPS50 | Q96JG6 | 887 |
| VPS52 | SOAT2 | O75908 | 856 |
| VPS52 | RPS18 | P25232 | 846 |
| VPS52 | COG3 | Q96JB2 | 832 |
| VPS52 | SOAT1 | P35610 | 792 |
| VPS52 | STX16 | O14662 | 771 |
| VPS52 | COG6 | Q9Y2V7 | 758 |
| VPS52 | EXOC1 | Q9NV70 | 715 |
| VPS52 | VTI1A | Q96AJ9 | 708 |
| VPS52 | RAB6A | P20340 | 694 |
| VPS52 | VAMP4 | O75379 | 671 |
| VPS52 | EXOC7 | Q9UPT5 | 671 |
IntAct
497 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| VPS50 | VPS53 | psi-mi:“MI:0914”(association) | 0.840 |
| VPS52 | VPS50 | psi-mi:“MI:0915”(physical association) | 0.830 |
| TXLNA | VPS52 | psi-mi:“MI:0915”(physical association) | 0.780 |
| VPS52 | RNF41 | psi-mi:“MI:0915”(physical association) | 0.780 |
| VPS52 | TBC1D22B | psi-mi:“MI:0915”(physical association) | 0.780 |
| VPS52 | TXLNA | psi-mi:“MI:0915”(physical association) | 0.780 |
| RNF41 | VPS52 | psi-mi:“MI:0915”(physical association) | 0.780 |
| TBC1D22B | VPS52 | psi-mi:“MI:0915”(physical association) | 0.780 |
| PSMC5 | PSMD11 | psi-mi:“MI:0914”(association) | 0.730 |
| VPS52 | USP2 | psi-mi:“MI:0915”(physical association) | 0.720 |
| VPS52 | DDX6 | psi-mi:“MI:0915”(physical association) | 0.720 |
| MFAP1 | VPS52 | psi-mi:“MI:0915”(physical association) | 0.720 |
| VPS52 | WTAP | psi-mi:“MI:0915”(physical association) | 0.720 |
| TSTD2 | VPS52 | psi-mi:“MI:0915”(physical association) | 0.720 |
| VPS52 | PPP1R18 | psi-mi:“MI:0915”(physical association) | 0.720 |
| EPM2AIP1 | VPS52 | psi-mi:“MI:0915”(physical association) | 0.720 |
| GOLGA1 | VPS52 | psi-mi:“MI:0915”(physical association) | 0.720 |
| TSSK3 | VPS52 | psi-mi:“MI:0915”(physical association) | 0.720 |
| TXN2 | VPS52 | psi-mi:“MI:0915”(physical association) | 0.720 |
| AIRIM | VPS52 | psi-mi:“MI:0915”(physical association) | 0.720 |
| TRAF6 | VPS52 | psi-mi:“MI:0915”(physical association) | 0.720 |
| ATP6V1D | VPS52 | psi-mi:“MI:0915”(physical association) | 0.720 |
| USP2 | VPS52 | psi-mi:“MI:0915”(physical association) | 0.720 |
| DDX6 | VPS52 | psi-mi:“MI:0915”(physical association) | 0.720 |
| VPS52 | MFAP1 | psi-mi:“MI:0915”(physical association) | 0.720 |
BioGRID (283): VPS52 (Two-hybrid), VPS52 (Two-hybrid), VPS52 (Two-hybrid), VPS52 (Two-hybrid), VPS52 (Two-hybrid), VPS52 (Two-hybrid), VPS52 (Two-hybrid), VPS52 (Two-hybrid), VPS52 (Two-hybrid), VPS52 (Two-hybrid), TEAD4 (Two-hybrid), TPM3 (Two-hybrid), TRAF6 (Two-hybrid), LMO4 (Two-hybrid), STX11 (Two-hybrid)
ESM2 similar proteins: A1A4I4, A2SXS5, A6QQ47, B2DCZ9, O00255, O08908, O55166, O75146, O88559, P70268, Q0P5I0, Q0VCR8, Q155U0, Q16512, Q29RB1, Q2KJ58, Q3MHG0, Q3MII6, Q3SZI7, Q3UVL4, Q4V9Y0, Q505L3, Q5R7R6, Q5TJF0, Q5ZJ25, Q63433, Q63788, Q68FF6, Q68FP9, Q69Z89, Q6PB44, Q6ZT62, Q865S3, Q8BI71, Q8BZQ7, Q8C190, Q8C754, Q8N1B4, Q8R1U1, Q8R3I3
Diamond homologs: G5EFV8, O55166, Q5TJF0, Q8C754, Q8N1B4, Q94KD3, Q9FVV6
SIGNOR signaling
1 interactions.
| A | Effect | B | Mechanism |
|---|---|---|---|
| RNF41 | “down-regulates quantity by destabilization” | VPS52 | ubiquitination |
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 81 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.
Reactome pathways:
| Pathway | Partners | Fold | FDR |
|---|---|---|---|
| Retrograde transport at the Trans-Golgi-Network | 5 | 22.0× | 1e-03 |
| AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) | 5 | 19.4× | 1e-03 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| endocytic recycling | 7 | 27.1× | 3e-06 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
99 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 67 |
| Likely benign | 0 |
| Benign | 3 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
3326 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 6:33251855:CATA:C | donor_loss | 1.0000 |
| 6:33251856:ATACC:A | donor_loss | 1.0000 |
| 6:33251857:TACC:T | donor_loss | 1.0000 |
| 6:33251858:A:C | donor_loss | 1.0000 |
| 6:33251859:C:G | donor_loss | 1.0000 |
| 6:33251968:ATTCC:A | acceptor_loss | 1.0000 |
| 6:33251969:TTCC:T | acceptor_loss | 1.0000 |
| 6:33251970:TCCT:T | acceptor_loss | 1.0000 |
| 6:33251971:CCTGG:C | acceptor_loss | 1.0000 |
| 6:33251973:T:G | acceptor_loss | 1.0000 |
| 6:33263545:CGCTC:C | acceptor_gain | 1.0000 |
| 6:33263547:CTC:C | acceptor_gain | 1.0000 |
| 6:33263548:TC:T | acceptor_gain | 1.0000 |
| 6:33263548:TCCT:T | acceptor_loss | 1.0000 |
| 6:33263549:CC:C | acceptor_gain | 1.0000 |
| 6:33263550:C:CC | acceptor_gain | 1.0000 |
| 6:33263550:CT:C | acceptor_loss | 1.0000 |
| 6:33263786:G:C | donor_gain | 1.0000 |
| 6:33263828:T:TA | donor_gain | 1.0000 |
| 6:33263881:T:C | acceptor_loss | 1.0000 |
| 6:33264398:C:A | donor_gain | 1.0000 |
| 6:33264801:C:A | donor_gain | 1.0000 |
| 6:33266616:C:CT | acceptor_gain | 1.0000 |
| 6:33267646:AAGG:A | donor_gain | 1.0000 |
| 6:33267736:CATA:C | acceptor_gain | 1.0000 |
| 6:33267740:C:CC | acceptor_gain | 1.0000 |
| 6:33267859:CCTTA:C | donor_loss | 1.0000 |
| 6:33267860:CTTAC:C | donor_loss | 1.0000 |
| 6:33267862:TAC:T | donor_loss | 1.0000 |
| 6:33267863:ACCTG:A | donor_loss | 1.0000 |
AlphaMissense
0 scored. Top likely-pathogenic:
dbSNP variants (sampled 300 via entrez): RS1000532472 (6:33257018 G>T), RS1000730962 (6:33264492 C>G,T), RS1000779401 (6:33250292 A>G), RS1000807229 (6:33269923 A>C), RS1001184413 (6:33264132 C>G), RS1001799027 (6:33255919 G>C,T), RS1001899236 (6:33263939 G>A), RS1002011 (6:33250460 G>A), RS1002076048 (6:33270403 T>G), RS1002583131 (6:33259973 A>C,T), RS1002628716 (6:33260961 T>C), RS1002696843 (6:33273466 GTCT>G,GTCTTCT), RS1002727320 (6:33267014 G>A), RS1002733868 (6:33267625 G>A), RS1002807468 (6:33273686 C>T)
Disease associations
OMIM: gene MIM:603443 | disease phenotypes:
GenCC curated gene-disease
| Disease | Classification | Inheritance |
|---|---|---|
| complex neurodevelopmental disorder with or without congenital anomalies | Moderate | Autosomal recessive |
Mondo (1): complex neurodevelopmental disorder with or without congenital anomalies (MONDO:0100465)
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
2 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST004521_287 | Autism spectrum disorder or schizophrenia | 5.000000e-08 |
| GCST005951_153 | Body mass index | 5.000000e-09 |
EFO canonical traits (1, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004340 | body mass index |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
36 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | decreases expression, affects expression, affects cotreatment | 6 |
| bisphenol A | decreases expression | 2 |
| Benzo(a)pyrene | affects methylation, decreases methylation | 2 |
| bisphenol F | affects cotreatment, increases expression | 1 |
| dicrotophos | increases expression | 1 |
| sodium arsenite | decreases expression | 1 |
| butyraldehyde | decreases expression | 1 |
| tetrabromobisphenol A | decreases expression | 1 |
| benzo(e)pyrene | decreases methylation | 1 |
| aflatoxin B2 | decreases methylation | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| perfluorooctane sulfonic acid | increases expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, decreases expression | 1 |
| ICG 001 | increases expression | 1 |
| 2,2’,4,4’-tetrabromodiphenyl ether | increases expression | 1 |
| dorsomorphin | decreases expression, affects cotreatment | 1 |
| pentabrominated diphenyl ether 100 | increases expression | 1 |
| hexabrominated diphenyl ether 153 | increases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| Vorinostat | decreases expression | 1 |
| Acetaminophen | decreases expression | 1 |
| Arsenic | affects methylation | 1 |
| Cisplatin | affects response to substance | 1 |
| Dexamethasone | affects cotreatment, increases expression | 1 |
| Fluorouracil | decreases expression | 1 |
| Indomethacin | affects cotreatment, increases expression | 1 |
| Ivermectin | decreases expression | 1 |
| Methapyrilene | decreases methylation | 1 |
| Thiram | decreases expression | 1 |
| Tretinoin | increases expression | 1 |
Cellosaurus cell lines
2 cell lines: 2 cancer cell line
First 10 cell lines (id-ordered, not curated):
| Cellosaurus | Name | Category | Sex |
|---|---|---|---|
| CVCL_TX68 | HAP1 VPS52 (-) 1 | Cancer cell line | Male |
| CVCL_TX69 | HAP1 VPS52 (-) 2 | Cancer cell line | Male |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
- Associated diseases: complex neurodevelopmental disorder with or without congenital anomalies
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): complex neurodevelopmental disorder with or without congenital anomalies