SNX33

gene
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Also known as MGC32065SH3PXD3CSNX30

Summary

SNX33 (sorting nexin 33, HGNC:28468) is a protein-coding gene on chromosome 15q24.2, encoding Sorting nexin-33 (Q8WV41). Plays a role in the reorganization of the cytoskeleton, endocytosis and cellular vesicle trafficking via its interactions with membranes, WASL, DNM1 and DNM2.

The protein encoded by this gene is involved in cytoskeletal reorganization, vesicle trafficking, endocytosis, and mitosis. The encoded protein is essential for the creation of the cleavage furrow during mitosis and for completion of mitosis. Two transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 257364 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 86 total
  • MANE Select transcript: NM_153271

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28468
Approved symbolSNX33
Namesorting nexin 33
Location15q24.2
Locus typegene with protein product
StatusApproved
AliasesMGC32065, SH3PXD3C, SNX30
Ensembl geneENSG00000173548
Ensembl biotypeprotein_coding
OMIM619107
Entrez257364

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000308527, ENST00000569152

RefSeq mRNA: 2 — MANE Select: NM_153271 NM_001318146, NM_153271

CCDS: CCDS10283

Canonical transcript exons

ENST00000308527 — 2 exons

ExonStartEnd
ENSE000012083987564791275650573
ENSE000018768927565696275662301

Expression profiles

Bgee: expression breadth ubiquitous, 249 present calls, max score 96.35.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.1258 / max 73.9449, expressed in 1694 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1478198.69091633
1478181.43491050

Top tissues by expression

255 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
pancreatic ductal cellCL:000207996.35gold quality
lower esophagus mucosaUBERON:003583495.17gold quality
tendon of biceps brachiiUBERON:000818895.01gold quality
esophagus mucosaUBERON:000246990.68gold quality
cardiac muscle of right atriumUBERON:000337990.66silver quality
parotid glandUBERON:000183190.65gold quality
right coronary arteryUBERON:000162590.55gold quality
popliteal arteryUBERON:000225090.48gold quality
tibial arteryUBERON:000761090.46gold quality
aortaUBERON:000094790.31gold quality
descending thoracic aortaUBERON:000234590.27gold quality
ascending aortaUBERON:000149690.24gold quality
thoracic aortaUBERON:000151590.21gold quality
stromal cell of endometriumCL:000225590.02gold quality
ectocervixUBERON:001224989.46gold quality
vaginaUBERON:000099688.91gold quality
skin of legUBERON:000151188.90gold quality
esophagusUBERON:000104388.89gold quality
body of pancreasUBERON:000115088.88gold quality
endocervixUBERON:000045888.70gold quality
upper arm skinUBERON:000426388.70silver quality
right ovaryUBERON:000211888.28gold quality
skin of abdomenUBERON:000141688.11gold quality
left ovaryUBERON:000211988.03gold quality
apex of heartUBERON:000209887.82gold quality
left coronary arteryUBERON:000162687.76gold quality
esophagogastric junction muscularis propriaUBERON:003584187.72gold quality
subcutaneous adipose tissueUBERON:000219087.58gold quality
mucosa of stomachUBERON:000119987.52gold quality
zone of skinUBERON:000001487.51gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes8.26

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

63 targeting SNX33, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-3065-3P99.8770.251407
HSA-MIR-477999.8666.501583
HSA-MIR-132199.8465.301811
HSA-MIR-473999.8465.251832
HSA-MIR-4756-5P99.8464.981809
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-4713-5P99.7867.801794
HSA-MIR-6763-5P99.7664.681767
HSA-MIR-3150A-3P99.7664.441640
HSA-MIR-431999.7669.832586
HSA-MIR-6764-5P99.7567.892304
HSA-MIR-430699.7270.503630
HSA-MIR-3059-5P99.7069.932491
HSA-MIR-317599.6566.302031
HSA-MIR-4690-5P99.6566.24813
HSA-MIR-1915-3P99.5866.791988
HSA-MIR-486-3P99.5166.821901
HSA-MIR-608199.4866.071446
HSA-MIR-6722-3P99.4567.621919

Literature-anchored findings (GeneRIF, showing 7)

  • identifies SNX33 as a new endocytic protein, which modulates amyloid precursor protein endocytosis and APP alpha-secretase cleavage, and demonstrates that the rate of APP endocytosis is a major control factor for APP alpha-secretase cleavage (PMID:18353773)
  • SNX33 interferes with cellular PrP formation by modulation of PrP shedding (PMID:18419754)
  • SNX33 plays a role in maintaining cell shape and cell cycle progression through its interaction with WASp (PMID:19487689)
  • Alternative splicing of ADAM15 regulates its interactions with cellular SH3 proteins SNX33 and nephrocystin (PMID:19718658)
  • study identifies critical amino acids within the BAR domains of SNX9 and SNX33 as determinants for the specificity of BAR domain-mediated interactions and suggests that SNX9 and SNX33 have distinct molecular functions. (PMID:20964629)
  • The sorting nexin 9 (SNX9) subfamily members - SNX9, SNX18 and SNX33 - are required for progression and completion of mitosis. (PMID:22718350)
  • [Donepezil Reduces Amyloid Precursor Protein Endocytosis by Resulting from Increase in the Expression of Sorting Nexin Protein 33]. (PMID:34078793)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriosnx33ENSDARG00000014954
mus_musculusSnx33ENSMUSG00000032733
rattus_norvegicusSnx33ENSRNOG00000017382
drosophila_melanogasterSnx1FBGN0031534
drosophila_melanogasterSnx6FBGN0032005
caenorhabditis_elegansWBGENE00004927
caenorhabditis_elegansWBGENE00013354

Paralogs (15): SNX11 (ENSG00000002919), SNX1 (ENSG00000028528), SNX10 (ENSG00000086300), SNX5 (ENSG00000089006), SNX8 (ENSG00000106266), SNX3 (ENSG00000112335), SNX4 (ENSG00000114520), SNX6 (ENSG00000129515), SNX9 (ENSG00000130340), SNX12 (ENSG00000147164), SNX30 (ENSG00000148158), SNX7 (ENSG00000162627), SNX32 (ENSG00000172803), SNX18 (ENSG00000178996), SNX2 (ENSG00000205302)

Protein

Protein identifiers

Sorting nexin-33Q8WV41 (reviewed: Q8WV41)

Alternative names: SH3 and PX domain-containing protein 3

All UniProt accessions (2): Q8WV41, H3BPR3

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in the reorganization of the cytoskeleton, endocytosis and cellular vesicle trafficking via its interactions with membranes, WASL, DNM1 and DNM2. Acts both during interphase and at the end of mitotic cell divisions. Required for efficient progress through mitosis and cytokinesis. Required for normal formation of the cleavage furrow at the end of mitosis. Modulates endocytosis of cell-surface proteins, such as APP and PRNP; this then modulates the secretion of APP and PRNP peptides. Promotes membrane tubulation (in vitro). May promote the formation of macropinosomes.

Subunit / interactions. Homodimer (via BAR domain). Interacts with ADAM15. Interacts with FASLG. Interacts (via SH3 domain) with DNM1 and DNM2. Interacts with WASL. Interacts with FCHSD1 (via the F-BAR domain).

Subcellular location. Cytoplasm. Cytosol. Membrane. Cytoplasmic vesicle membrane.

Tissue specificity. Detected in heart and pancreas.

Post-translational modifications. Phosphorylated.

Domain organisation. The PX and BAR domains mediate association with membranes and are required for membrane tubulation.

Similarity. Belongs to the sorting nexin family.

RefSeq proteins (2): NP_001305075, NP_695003* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001452SH3_domainDomain
IPR001683PX_domDomain
IPR014536Snx9_famFamily
IPR019497Sorting_nexin_WASP-bd-domDomain
IPR027267AH/BAR_dom_sfHomologous_superfamily
IPR036028SH3-like_dom_sfHomologous_superfamily
IPR036871PX_dom_sfHomologous_superfamily
IPR037427SNX33_BARDomain

Pfam: PF00787, PF10456, PF14604

UniProt features (30 total): helix 14, strand 7, domain 3, modified residue 2, chain 1, turn 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
4AKVX-RAY DIFFRACTION2.65

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8WV41-F182.620.66

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): 77, 92

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 368 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, GOBP_MITOTIC_CYTOKINESIS, GGGACCA_MIR133A_MIR133B, GOBP_REGULATION_OF_AUTOPHAGY, GOBP_PINOCYTOSIS, GOBP_ENDOSOME_ORGANIZATION, GOBP_VACUOLE_ORGANIZATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOBP_VESICLE_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_VACUOLE_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_PROTEIN_LOCALIZATION, GOBP_PLASMA_MEMBRANE_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS

GO Biological Process (17): mitotic cytokinesis (GO:0000281), intracellular protein transport (GO:0006886), endocytosis (GO:0006897), endosome organization (GO:0007032), endosomal transport (GO:0016197), protein import (GO:0017038), cleavage furrow formation (GO:0036089), macropinocytosis (GO:0044351), negative regulation of endocytosis (GO:0045806), positive regulation of membrane protein ectodomain proteolysis (GO:0051044), plasma membrane tubulation (GO:0097320), negative regulation of protein localization to cell surface (GO:2000009), positive regulation of protein localization to cell surface (GO:2000010), mitotic cell cycle (GO:0000278), positive regulation of catabolic process (GO:0009896), protein transport (GO:0015031), cell division (GO:0051301)

GO Molecular Function (3): phosphatidylinositol binding (GO:0035091), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (6): cytosol (GO:0005829), plasma membrane (GO:0005886), membrane (GO:0016020), cytoplasmic vesicle membrane (GO:0030659), cytoplasmic vesicle (GO:0031410), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
cytoskeleton-dependent cytokinesis2
intracellular protein localization2
protein transport2
intracellular transport2
vesicle-mediated transport2
protein localization to cell surface2
regulation of protein localization to cell surface2
cytoplasm2
mitotic cell cycle1
mitotic cell cycle process1
vesicle budding from membrane1
membrane invagination1
import into cell1
endomembrane system organization1
vesicle organization1
cytokinetic process1
plasma membrane invagination1
pinocytosis1
endocytosis1
regulation of endocytosis1
negative regulation of transport1
negative regulation of cellular component organization1
membrane protein ectodomain proteolysis1
positive regulation of protein catabolic process1
positive regulation of proteolysis1
regulation of membrane protein ectodomain proteolysis1
plasma membrane organization1
negative regulation of protein localization1
positive regulation of protein localization1
cell cycle1
mitotic nuclear division1
catabolic process1
positive regulation of metabolic process1
regulation of catabolic process1
transport1
establishment of protein localization1
cellular process1
anion binding1
protein binding1

Protein interactions and networks

STRING

754 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SNX33ENC1O14682642
SNX33SNX12Q9UMY4638
SNX33SNX32Q86XE0637
SNX33SNX6Q9UNH7631
SNX33SNX17Q15036610
SNX33SNX15Q9NRS6608
SNX33SNX5Q9Y5X3585
SNX33SNX4O95219559
SNX33CIBAR2Q6ZTR7519
SNX33GPR85P60893515
SNX33DNM1Q05193513
SNX33BACE1P56817505
SNX33SNX27Q96L92500
SNX33AMPHP49418487
SNX33SNX11Q9Y5W9477

IntAct

122 interactions, top by confidence:

ABTypeScore
ANKRD54TULP3psi-mi:“MI:0914”(association)0.930
FASLGSNX33psi-mi:“MI:0915”(physical association)0.780
DNM2DNM1psi-mi:“MI:0914”(association)0.740
KBTBD7METTL15psi-mi:“MI:0914”(association)0.730
ADAM15SNX33psi-mi:“MI:0407”(direct interaction)0.710
ADAM15SNX33psi-mi:“MI:0915”(physical association)0.710
SNX33NAF1psi-mi:“MI:0915”(physical association)0.670
NAA10SNX33psi-mi:“MI:0915”(physical association)0.670
YWHAGSNX33psi-mi:“MI:0915”(physical association)0.670
DNM2SNX33psi-mi:“MI:0915”(physical association)0.670
GPR156PLD2psi-mi:“MI:0914”(association)0.640
FASLGPRMT2psi-mi:“MI:0914”(association)0.640
SDC2PDPK1psi-mi:“MI:0914”(association)0.640
NCKIPSDGEMIN2psi-mi:“MI:0914”(association)0.640
PPP2R3AWTIPpsi-mi:“MI:0914”(association)0.640
DNM1SNX33psi-mi:“MI:0915”(physical association)0.640
SNX33DNM1psi-mi:“MI:0915”(physical association)0.640
SNX33SNX33psi-mi:“MI:0915”(physical association)0.590
SNX33SNX9psi-mi:“MI:0915”(physical association)0.590

BioGRID (83): SNX33 (Affinity Capture-MS), SNX33 (Affinity Capture-MS), SNX33 (Affinity Capture-MS), SNX33 (Affinity Capture-MS), SNX33 (Affinity Capture-MS), SNX33 (Affinity Capture-MS), SNX33 (Affinity Capture-MS), SNX33 (Affinity Capture-MS), SNX33 (Affinity Capture-MS), SNX33 (Affinity Capture-MS), SNX33 (Affinity Capture-MS), SNX33 (Affinity Capture-MS), SNX33 (Affinity Capture-MS), SNX33 (Affinity Capture-MS), SNX33 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B7YDZ4, B1H267, I1RXT2, O14243, O60107, O74960, O94447, P0CR58, P0CR59, P0CR62, P0CR63, P0CR64, P0CR65, P32912, P32913, P40531, P40959, P47057, Q09746, Q10253, Q28GP7, Q3ZBM5, Q4PHC3, Q4VAA7, Q4WQI6, Q522W5, Q5B797, Q5R613, Q6C238, Q6C9X0, Q6CGJ5, Q6CHY6, Q6CTQ0, Q6CUC4, Q6FPT9, Q6NRL2, Q6P8X1, Q759T1, Q75B65, Q75C43

Diamond homologs: A1A4L0, O14120, O60107, O60493, O70492, O70493, O94291, O95219, P0C220, P0CR60, P0CR61, P40959, Q04053, Q08DD7, Q1RMH8, Q28GP7, Q2KHV6, Q2U4K2, Q3MPQ4, Q4I1H6, Q4P1V3, Q4PHC3, Q4VAA7, Q4WWS3, Q4WZF1, Q59TN9, Q5A748, Q5AD77, Q5AZC9, Q5R4C2, Q5R5V1, Q5R7A7, Q5R9A9, Q5U211, Q6BIS2, Q6BZE1, Q6C2S9, Q6CHY6, Q6CUC4, Q6CWX3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 80 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:

PathwayPartnersFoldFDR
Degradation of the extracellular matrix616.1×3e-04
Extracellular matrix organization1115.8×3e-08

GO biological processes:

GO termPartnersFoldFDR
receptor-mediated endocytosis516.1×2e-03
endocytosis811.0×2e-04
cell migration76.2×7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

86 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance81
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

627 predictions. Top by Δscore:

VariantEffectΔscore
15:75657196:GCAT:Gdonor_gain1.0000
15:75657200:G:GGdonor_gain1.0000
15:75648098:T:Gdonor_gain0.9900
15:75650572:AGG:Adonor_loss0.9900
15:75650573:GGT:Gdonor_loss0.9900
15:75650575:T:Adonor_loss0.9900
15:75656956:T:Gacceptor_gain0.9900
15:75656958:CCA:Cacceptor_loss0.9900
15:75656960:A:AGacceptor_gain0.9900
15:75656961:G:Aacceptor_loss0.9900
15:75656961:G:GGacceptor_gain0.9900
15:75656961:GGC:Gacceptor_gain0.9900
15:75657197:C:Tdonor_gain0.9900
15:75656955:A:AGacceptor_gain0.9800
15:75656956:T:TAacceptor_gain0.9800
15:75656960:AGGC:Aacceptor_gain0.9800
15:75656961:GGCG:Gacceptor_gain0.9800
15:75656961:GGCGC:Gacceptor_gain0.9800
15:75648310:T:TAdonor_gain0.9700
15:75648423:AGT:Adonor_gain0.9700
15:75656950:T:TAacceptor_gain0.9700
15:75648102:GTGT:Gdonor_gain0.9600
15:75648265:G:Cdonor_gain0.9600
15:75656955:AT:Aacceptor_gain0.9600
15:75647912:G:Adonor_gain0.9500
15:75648082:T:Adonor_gain0.9500
15:75648133:GGGTC:Gdonor_gain0.9500
15:75648134:GGTCG:Gdonor_gain0.9500
15:75648335:T:TAdonor_gain0.9500
15:75650411:G:GCacceptor_gain0.9500

AlphaMissense

3859 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:75649133:T:CF11L1.000
15:75649135:T:AF11L1.000
15:75649135:T:GF11L1.000
15:75649214:T:AW38R1.000
15:75649214:T:CW38R1.000
15:75649248:G:AG49E1.000
15:75649658:T:CF186L1.000
15:75649660:C:AF186L1.000
15:75649660:C:GF186L1.000
15:75649769:T:AW223R1.000
15:75649769:T:CW223R1.000
15:75649771:G:CW223C1.000
15:75649771:G:TW223C1.000
15:75649826:A:GK242E1.000
15:75649828:A:CK242N1.000
15:75649828:A:TK242N1.000
15:75649830:T:CF243S1.000
15:75649841:A:GK247E1.000
15:75649842:A:TK247I1.000
15:75649843:A:CK247N1.000
15:75649843:A:TK247N1.000
15:75649847:T:GY249D1.000
15:75649856:T:CY252H1.000
15:75649856:T:GY252D1.000
15:75649898:C:AR266S1.000
15:75649898:C:GR266G1.000
15:75649901:T:CY267H1.000
15:75649901:T:GY267D1.000
15:75649904:A:GK268E1.000
15:75649905:A:TK268I1.000

dbSNP variants (sampled 300 via entrez): RS1000117540 (15:75648477 AC>A), RS1000185994 (15:75660997 G>A), RS1000813448 (15:75659719 C>G), RS1001179303 (15:75654209 C>A), RS1001270659 (15:75647419 A>C), RS1001408101 (15:75658055 T>C), RS1001488948 (15:75652264 C>T), RS1001500411 (15:75651895 T>G), RS1001618212 (15:75646294 C>T), RS1001754537 (15:75658504 C>T), RS1002355191 (15:75656885 C>T), RS1002755378 (15:75647774 T>A,C,G), RS1002989227 (15:75646246 T>G), RS1003117886 (15:75652537 G>A), RS1003303485 (15:75657488 C>A,T)

Disease associations

OMIM: gene MIM:619107 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST007876_30Estimated glomerular filtration rate3.000000e-25

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, affects expression4
FR900359increases phosphorylation1
pirinixic acidaffects binding, increases activity, increases expression1
manganese chlorideincreases abundance, increases expression1
potassium chromate(VI)decreases expression1
coumarindecreases phosphorylation1
CGP 52608increases reaction, affects binding1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
bisphenol Sdecreases methylation1
jinfukangaffects cotreatment, increases expression1
Sunitinibdecreases expression1
Caffeineaffects phosphorylation1
Calcitriolincreases expression, affects cotreatment1
Cisplatinaffects cotreatment, increases expression1
Doxorubicindecreases expression1
Estradioldecreases expression1
Manganeseincreases abundance, increases expression1
Oxygenincreases expression1
Smokedecreases expression1
Testosteroneaffects cotreatment, increases expression1
Tobacco Smoke Pollutionincreases expression1
Urethanedecreases expression1
Antirheumatic Agentsincreases expression1
Copper Sulfatedecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.