VPS26B

gene
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Also known as MGC10485Pep8b

Summary

VPS26B (VPS26 retromer complex component B, HGNC:28119) is a protein-coding gene on chromosome 11q25, encoding Vacuolar protein sorting-associated protein 26B (Q4G0F5). Acts as a component of the retromer cargo-selective complex (CSC).

Predicted to be involved in intracellular protein transport and retrograde transport, endosome to Golgi. Predicted to act upstream of or within cellular response to type II interferon. Predicted to be located in early endosome and late endosome. Predicted to be part of retromer complex. Predicted to be active in glutamatergic synapse; postsynaptic early endosome; and postsynaptic recycling endosome.

Source: NCBI Gene 112936 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 31 total — 1 pathogenic
  • Druggable target: yes
  • MANE Select transcript: NM_052875

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28119
Approved symbolVPS26B
NameVPS26 retromer complex component B
Location11q25
Locus typegene with protein product
StatusApproved
AliasesMGC10485, Pep8b
Ensembl geneENSG00000151502
Ensembl biotypeprotein_coding
OMIM610027
Entrez112936

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 7 protein_coding, 3 retained_intron, 2 nonsense_mediated_decay

ENST00000281187, ENST00000525095, ENST00000525918, ENST00000527586, ENST00000530402, ENST00000531741, ENST00000532160, ENST00000860204, ENST00000860205, ENST00000911842, ENST00000911843, ENST00000957932

RefSeq mRNA: 1 — MANE Select: NM_052875 NM_052875

CCDS: CCDS8495

Canonical transcript exons

ENST00000281187 — 6 exons

ExonStartEnd
ENSE00001000001134244938134245080
ENSE00001099786134234897134235053
ENSE00001194641134224671134225345
ENSE00001279598134245444134247788
ENSE00003570973134239991134240155
ENSE00003584878134243119134243294

Expression profiles

Bgee: expression breadth ubiquitous, 248 present calls, max score 96.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.3895 / max 126.8866, expressed in 1816 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
11769929.00961816
1177000.3799168

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534396.44gold quality
right hemisphere of cerebellumUBERON:001489095.91gold quality
cerebellar hemisphereUBERON:000224595.69gold quality
upper arm skinUBERON:000426395.63gold quality
cerebellar cortexUBERON:000212995.62gold quality
embryoUBERON:000092295.02gold quality
ganglionic eminenceUBERON:000402395.02gold quality
cerebellumUBERON:000203794.87gold quality
granulocyteCL:000009494.78gold quality
right frontal lobeUBERON:000281094.64gold quality
prefrontal cortexUBERON:000045194.60gold quality
skin of legUBERON:000151193.94gold quality
Brodmann (1909) area 9UBERON:001354093.84gold quality
skin of abdomenUBERON:000141693.74gold quality
anterior cingulate cortexUBERON:000983593.69gold quality
right uterine tubeUBERON:000130293.64gold quality
body of pancreasUBERON:000115093.31gold quality
nucleus accumbensUBERON:000188293.06gold quality
stromal cell of endometriumCL:000225592.94gold quality
frontal cortexUBERON:000187092.89gold quality
body of uterusUBERON:000985392.87gold quality
dorsolateral prefrontal cortexUBERON:000983492.82gold quality
neocortexUBERON:000195092.73gold quality
caudate nucleusUBERON:000187392.66gold quality
islet of LangerhansUBERON:000000692.47gold quality
zone of skinUBERON:000001492.23gold quality
muscle layer of sigmoid colonUBERON:003580592.22gold quality
left ovaryUBERON:000211992.18gold quality
putamenUBERON:000187492.12gold quality
pancreasUBERON:000126492.03gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.82

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

125 targeting VPS26B, 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-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-188-3P100.0068.761240
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-453499.9966.581907
HSA-MIR-186-5P99.9970.833707
HSA-MIR-6759-5P99.9966.54785
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-314899.9775.066478
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-365899.9673.874379
HSA-MIR-570-3P99.9672.414910
HSA-MIR-808299.9567.271170
HSA-MIR-96-5P99.9572.802140
HSA-MIR-6768-5P99.9267.361942
HSA-MIR-1213399.9271.822006
HSA-MIR-1271-5P99.9171.991972
HSA-MIR-6783-3P99.8967.922059
HSA-MIR-1343-3P99.8966.781815
HSA-MIR-605-3P99.8869.221833
HSA-MIR-6780A-5P99.8866.692776

Literature-anchored findings (GeneRIF, showing 2)

  • Colocalization of Vps26 paralogues with different endosomally located Rab proteins shows prolonged association of Vps26B-retromer with maturing endosomes relative to Vps26A-retromer. (PMID:21920005)
  • Authors propose that PAR-2 plasma membrane repopulation is regulated by Vps26B-retromer, describing a potential novel role for this complex. (PMID:26113136)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriovps26bENSDARG00000015823
danio_reriovps26blENSDARG00000055433
mus_musculusVps26bENSMUSG00000031988
rattus_norvegicusVps26bENSRNOG00000047235
drosophila_melanogasterVps26FBGN0014411
caenorhabditis_elegansWBGENE00006931

Paralogs (2): VPS26A (ENSG00000122958), VPS26C (ENSG00000157538)

Protein

Protein identifiers

Vacuolar protein sorting-associated protein 26BQ4G0F5 (reviewed: Q4G0F5)

Alternative names: Vesicle protein sorting 26B

All UniProt accessions (3): Q4G0F5, A0A0D9SFQ6, H0YCI7

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a component of the retromer cargo-selective complex (CSC). The CSC is believed to be the core functional component of retromer or respective retromer complex variants acting to prevent missorting of selected transmembrane cargo proteins into the lysosomal degradation pathway. The recruitment of the CSC to the endosomal membrane involves RAB7A and SNX3. The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX3-retromer mediates the retrograde transport of WLS distinct from the SNX-BAR retromer pathway. The SNX27-retromer is believed to be involved in endosome-to-plasma membrane trafficking and recycling of a broad spectrum of cargo proteins. The CSC seems to act as recruitment hub for other proteins, such as the WASH complex and TBC1D5. May be involved in retrograde transport of SORT1 but not of IGF2R. Acts redundantly with VSP26A in SNX-27 mediated endocytic recycling of SLC2A1/GLUT1.

Subunit / interactions. Component of the heterotrimeric retromer cargo-selective complex (CSC), also described as vacuolar protein sorting VPS subcomplex (VPS,) formed by VPS26 (VPS26A or VPS26B), VPS29 and VPS35. The CSC has a highly elongated structure with VPS26 and VPS29 binding independently at opposite distal ends of VPS35 as central platform. The CSC is believed to associate with variable sorting nexins to form functionally distinct retromer complex variants. The originally described retromer complex (also called SNX-BAR retromer) is a pentamer containing the CSC and a heterodimeric membrane-deforming subcomplex formed between SNX1 or SNX2 and SNX5 or SNX6 (also called SNX-BAR subcomplex); the respective CSC and SNX-BAR subcomplexes associate with low affinity. The CSC associates with SNX3 to form a SNX3-retromer complex. The CSC associates with SNX27, the WASH complex and the SNX-BAR subcomplex to form the SNX27-retromer complex. Interacts with VPS29, VPS35, TBC1D5, GOLPH3, SNX27.

Subcellular location. Cytoplasm. Membrane. Early endosome. Late endosome.

Similarity. Belongs to the VPS26 family.

RefSeq proteins (1): NP_443107* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR014752Arrestin-like_C_sfHomologous_superfamily
IPR028934Vps26-relatedFamily

Pfam: PF03643

UniProt features (5 total): modified residue 3, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q4G0F5-F187.110.76

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 (3): 302, 304, 319

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 219 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, GSE45365_NK_CELL_VS_CD8_TCELL_DN, GOBP_REGULATION_OF_AUTOPHAGY, GCM_GSPT1, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_RESPONSE_TO_PEPTIDE, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, AP2_Q3, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOBP_MACROAUTOPHAGY, YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_UP, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_REGULATION_OF_CELLULAR_LOCALIZATION

GO Biological Process (6): intracellular protein transport (GO:0006886), regulation of macroautophagy (GO:0016241), retrograde transport, endosome to Golgi (GO:0042147), cellular response to type II interferon (GO:0071346), regulation of neurotransmitter receptor localization to postsynaptic specialization membrane (GO:0098696), protein transport (GO:0015031)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (12): endosome (GO:0005768), early endosome (GO:0005769), late endosome (GO:0005770), cytosol (GO:0005829), retromer complex (GO:0030904), retromer, cargo-selective complex (GO:0030906), phagocytic vesicle (GO:0045335), postsynaptic recycling endosome (GO:0098837), postsynaptic early endosome (GO:0098842), glutamatergic synapse (GO:0098978), cytoplasm (GO:0005737), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
intracellular protein localization2
endomembrane system2
endosome2
membrane protein complex2
postsynapse2
postsynaptic endosome2
protein transport1
intracellular transport1
regulation of autophagy1
macroautophagy1
intercellular transport1
endosomal transport1
cytosolic transport1
response to type II interferon1
cellular response to cytokine stimulus1
regulation of biological quality1
neurotransmitter receptor localization to postsynaptic specialization membrane1
regulation of protein localization to synapse1
regulation of receptor localization to synapse1
regulation of protein localization to cell periphery1
regulation of protein localization to membrane1
transport1
establishment of protein localization1
binding1
cytoplasmic vesicle1
cytoplasm1
retromer complex1
endocytic vesicle1
recycling endosome1
early endosome1
synapse1
intracellular anatomical structure1

Protein interactions and networks

STRING

1184 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
VPS26BVPS35Q96QK1999
VPS26BVPS29Q9UBQ0997
VPS26BSNX27Q96L92913
VPS26BSNX1Q13596892
VPS26BSNX2P82862854
VPS26BSNX3O60493788
VPS26BSNX5Q9Y5X3731
VPS26BTBC1D5Q92609702
VPS26BSNX6Q9UNH7678
VPS26BSNX32Q86XE0598
VPS26BSNX4O95219569
VPS26BSNX17Q15036548
VPS26BENTR1Q96C92543
VPS26BDNAJC13O75165523
VPS26BWASHC1A8K0Z3518

IntAct

64 interactions, top by confidence:

ABTypeScore
VPS26BVPS35psi-mi:“MI:0915”(physical association)0.910
TBC1D5VPS26Apsi-mi:“MI:0914”(association)0.810
VPS29VPS26Cpsi-mi:“MI:0914”(association)0.760
VPS29VPS26Bpsi-mi:“MI:0914”(association)0.730
NPLOC4VPS26Bpsi-mi:“MI:0915”(physical association)0.560
VPS26BNPLOC4psi-mi:“MI:0915”(physical association)0.560
VPS26AVPS26Bpsi-mi:“MI:0914”(association)0.530
TRMOSTAT5Bpsi-mi:“MI:0914”(association)0.530
KXD1HIP1psi-mi:“MI:0914”(association)0.530
ZFC3H1HNRNPCL1psi-mi:“MI:0914”(association)0.530
SNX3VPS26Apsi-mi:“MI:0914”(association)0.530
PNMA2CCDC85Cpsi-mi:“MI:0914”(association)0.530
VPS35SPAG9psi-mi:“MI:0914”(association)0.530
VPS26BABCD1psi-mi:“MI:0914”(association)0.350
VPS26BKIF1Bpsi-mi:“MI:0914”(association)0.350
E6PLOD2psi-mi:“MI:0914”(association)0.350
VPS26BCFAP410psi-mi:“MI:0914”(association)0.350
ZFC3H1ANKHD1psi-mi:“MI:0914”(association)0.350
MRM1KIAA0391psi-mi:“MI:0914”(association)0.350
LOXL3MSI1psi-mi:“MI:0914”(association)0.350
ENGIGKV2-28psi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350

BioGRID (127): VPS26B (Affinity Capture-RNA), VPS26B (Affinity Capture-RNA), VPS26B (Affinity Capture-RNA), VPS26B (Affinity Capture-MS), VPS29 (Affinity Capture-MS), VPS35 (Affinity Capture-MS), NEK1 (Affinity Capture-MS), SUPT5H (Affinity Capture-MS), ATE1 (Affinity Capture-MS), TBC1D5 (Affinity Capture-MS), C21orf2 (Affinity Capture-MS), BTBD9 (Affinity Capture-MS), SNX27 (Affinity Capture-MS), VPS26B (Affinity Capture-MS), VPS26B (Co-fractionation)

ESM2 similar proteins: A0A7J6K9S4, A5PF44, C4R360, C5DL84, C5DRZ0, O01258, O17972, O45782, O75436, P30647, P40335, P40336, P53179, Q02331, Q09219, Q0VD53, Q10243, Q17388, Q18268, Q19829, Q28HT6, Q4G0F5, Q55CA0, Q5BKM4, Q5R436, Q5RAV3, Q68F29, Q6AY86, Q6CTM7, Q6DFB9, Q6DFU4, Q6DH23, Q6DTM3, Q6FWV1, Q6IRD0, Q6PAW0, Q6PB19, Q6PBN2, Q6TNP8, Q754G2

Diamond homologs: O01258, O75436, P40335, P40336, Q0VD53, Q10243, Q28HT6, Q4G0F5, Q55CA0, Q5BKM4, Q5R436, Q68F29, Q6AY86, Q6DFB9, Q6DFU4, Q6DH23, Q6IRD0, Q6TNP8, Q7ZV03, Q8C0E2, Q8I4T1, Q9FJD0, Q9T091, Q9W552

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 60 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.

GO biological processes:

GO termPartnersFoldFDR
endocytic recycling636.5×5e-06
retrograde transport, endosome to Golgi628.0×1e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance17
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
393778GRCh37/hg19 11q24.1-25(chr11:121501072-134868348)x1Pathogenic

SpliceAI

1162 predictions. Top by Δscore:

VariantEffectΔscore
11:134225341:GATCG:Gdonor_gain1.0000
11:134225343:TCGGT:Tdonor_loss1.0000
11:134225345:GGT:Gdonor_loss1.0000
11:134225346:G:Cdonor_loss1.0000
11:134225347:T:Gdonor_loss1.0000
11:134240137:T:Gdonor_gain1.0000
11:134240156:G:GGdonor_gain1.0000
11:134243116:CA:Cacceptor_loss1.0000
11:134243117:A:AGacceptor_gain1.0000
11:134243118:G:GAacceptor_gain1.0000
11:134243118:GA:Gacceptor_gain1.0000
11:134243118:GAT:Gacceptor_gain1.0000
11:134243118:GATA:Gacceptor_gain1.0000
11:134243118:GATAC:Gacceptor_gain1.0000
11:134243291:CGAG:Cdonor_loss1.0000
11:134243293:AG:Adonor_loss1.0000
11:134243294:GG:Gdonor_loss1.0000
11:134243295:G:Tdonor_loss1.0000
11:134243296:T:Adonor_loss1.0000
11:134244932:CTACA:Cacceptor_loss1.0000
11:134244933:TACA:Tacceptor_loss1.0000
11:134244936:A:AGacceptor_gain1.0000
11:134244936:A:Tacceptor_loss1.0000
11:134244937:G:GAacceptor_loss1.0000
11:134244937:G:GGacceptor_gain1.0000
11:134244937:GGA:Gacceptor_gain1.0000
11:134244937:GGAGA:Gacceptor_gain1.0000
11:134245077:GCAG:Gdonor_gain1.0000
11:134245079:AGG:Adonor_loss1.0000
11:134245080:GGTG:Gdonor_loss1.0000

AlphaMissense

2233 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:134225259:T:AV46D1.000
11:134225264:G:AG48R1.000
11:134225264:G:CG48R1.000
11:134225264:G:TG48W1.000
11:134225265:G:AG48E1.000
11:134225336:G:AG72R1.000
11:134225336:G:CG72R1.000
11:134225336:G:TG72W1.000
11:134225337:G:AG72E1.000
11:134225337:G:TG72V1.000
11:134234929:T:CF86L1.000
11:134234930:T:CF86S1.000
11:134234931:T:AF86L1.000
11:134234931:T:GF86L1.000
11:134234999:T:CF109S1.000
11:134235034:G:AG121R1.000
11:134235034:G:CG121R1.000
11:134235034:G:TG121W1.000
11:134235035:G:AG121E1.000
11:134235035:G:TG121V1.000
11:134235050:T:CL126P1.000
11:134235053:G:CR127P1.000
11:134239992:T:GY128D1.000
11:134240002:G:CR131P1.000
11:134240056:T:AV149D1.000
11:134240101:T:AM164K1.000
11:134240101:T:CM164T1.000
11:134240101:T:GM164R1.000
11:134240102:G:AM164I1.000
11:134240102:G:CM164I1.000

dbSNP variants (sampled 300 via entrez): RS1000236606 (11:134241395 G>A), RS1000388468 (11:134248228 G>A), RS1000444119 (11:134242710 G>C), RS1000731010 (11:134244493 C>T), RS1000814728 (11:134240957 T>G), RS1000894427 (11:134232137 C>T), RS1000953966 (11:134238724 T>C), RS1000983281 (11:134225633 G>A), RS1000988579 (11:134226876 A>G), RS1000996789 (11:134237189 T>C), RS1001144387 (11:134233225 G>A), RS1001186069 (11:134244250 T>A), RS1001490960 (11:134233465 T>C,G), RS1001551014 (11:134240623 A>G), RS1001554793 (11:134231798 C>A,T)

Disease associations

OMIM: gene MIM:610027 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST002701_37Verbal declarative memory2.000000e-06
GCST90000047_174Age at first sexual intercourse4.000000e-08

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004874memory performance
EFO:0006805word list delayed recall measurement
EFO:0009749age at first sexual intercourse measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067157 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects cotreatment, decreases expression, increases abundance4
Arsenicaffects methylation, affects cotreatment, decreases expression, increases abundance2
Benzo(a)pyrenedecreases expression, increases expression2
bisphenol Fincreases expression1
uranyl acetateaffects expression1
bisphenol Aincreases expression1
beta-lapachoneincreases expression1
manganese chloridedecreases expression, increases abundance, affects cotreatment1
coumarindecreases phosphorylation1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
ICG 001decreases expression1
abrinedecreases expression1
Fulvestrantdecreases methylation1
Air Pollutantsaffects expression, increases abundance1
Atrazineincreases expression1
Caffeinedecreases phosphorylation1
Diazinonincreases methylation1
Manganesedecreases expression, increases abundance, affects cotreatment1
Ozoneaffects expression, increases abundance1
Thiramdecreases expression1
Tobacco Smoke Pollutiondecreases methylation1
Tretinoinaffects cotreatment, decreases expression1
Uraniumaffects expression1
Valproic Aciddecreases methylation1
Aflatoxin B1decreases methylation1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5652812BindingBinding affinity to human VPS26B incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

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.