VPS37B

gene
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Also known as FLJ12750

Summary

VPS37B (VPS37B subunit of ESCRT-I, HGNC:25754) is a protein-coding gene on chromosome 12q24.31, encoding Vacuolar protein sorting-associated protein 37B (Q9H9H4). Component of the ESCRT-I complex, a regulator of vesicular trafficking process.

Enables calcium-dependent protein binding activity. Predicted to be involved in protein targeting to membrane; protein targeting to vacuole; and ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway. Located in endosome membrane; midbody; and plasma membrane. Part of ESCRT I complex.

Source: NCBI Gene 79720 — RefSeq curated summary.

At a glance

  • GWAS associations: 13
  • Clinical variants (ClinVar): 54 total
  • MANE Select transcript: NM_024667

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25754
Approved symbolVPS37B
NameVPS37B subunit of ESCRT-I
Location12q24.31
Locus typegene with protein product
StatusApproved
AliasesFLJ12750
Ensembl geneENSG00000139722
Ensembl biotypeprotein_coding
OMIM610037
Entrez79720

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 retained_intron

ENST00000267202, ENST00000371248, ENST00000535765, ENST00000543590, ENST00000852158

RefSeq mRNA: 1 — MANE Select: NM_024667 NM_024667

CCDS: CCDS9239

Canonical transcript exons

ENST00000267202 — 4 exons

ExonStartEnd
ENSE00000939889122870890122871061
ENSE00000939890122868480122868562
ENSE00001314131122865330122867607
ENSE00002244083122895952122896124

Expression profiles

Bgee: expression breadth ubiquitous, 273 present calls, max score 96.76.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 39.5065 / max 1026.3619, expressed in 1811 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
13386239.50651811

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
lower esophagus mucosaUBERON:003583496.76gold quality
sural nerveUBERON:001548896.37gold quality
ventricular zoneUBERON:000305394.86gold quality
oocyteCL:000002394.82gold quality
esophagus mucosaUBERON:000246994.73gold quality
cartilage tissueUBERON:000241894.52gold quality
olfactory segment of nasal mucosaUBERON:000538694.51gold quality
secondary oocyteCL:000065594.11gold quality
mucosa of transverse colonUBERON:000499193.92gold quality
pancreatic ductal cellCL:000207993.33gold quality
body of stomachUBERON:000116192.82gold quality
palpebral conjunctivaUBERON:000181292.81gold quality
granulocyteCL:000009492.72gold quality
minor salivary glandUBERON:000183092.58gold quality
amniotic fluidUBERON:000017392.41gold quality
esophagus squamous epitheliumUBERON:000692092.33gold quality
oral cavityUBERON:000016792.10gold quality
epithelium of esophagusUBERON:000197692.06gold quality
mouth mucosaUBERON:000372991.91gold quality
ganglionic eminenceUBERON:000402391.70gold quality
saliva-secreting glandUBERON:000104491.69gold quality
esophagusUBERON:000104391.46gold quality
transverse colonUBERON:000115791.40gold quality
bloodUBERON:000017891.24gold quality
left lobe of thyroid glandUBERON:000112091.11gold quality
right lobe of thyroid glandUBERON:000111990.86gold quality
stomachUBERON:000094590.83gold quality
upper lobe of left lungUBERON:000895290.71gold quality
squamous epitheliumUBERON:000691490.23gold quality
upper lobe of lungUBERON:000894890.20gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes11.62

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

86 targeting VPS37B, 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-3163100.0077.238605
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-1213699.9872.815713
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-365899.9673.874379
HSA-MIR-452599.9464.38675
HSA-MIR-5010-5P99.9464.11705
HSA-MIR-454-3P99.9174.011925
HSA-MIR-130A-3P99.9073.311861
HSA-MIR-130B-3P99.9073.271850
HSA-MIR-301A-3P99.9073.151839
HSA-MIR-301B-3P99.9073.191836
HSA-MIR-366699.9073.241833
HSA-MIR-429599.9073.111838
HSA-MIR-345-3P99.8970.231421
HSA-MIR-124-3P99.8973.743043
HSA-MIR-506-3P99.8973.553057

Literature-anchored findings (GeneRIF, showing 1)

  • VPS37B and appeared to interact with ALG-2 in a stronger manner than TSG101 does. (PMID:23924735)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriovps37baENSDARG00000039319
danio_reriovps37bbENSDARG00000101143
mus_musculusVps37bENSMUSG00000066278
rattus_norvegicusVps37bENSRNOG00000001086
drosophila_melanogasterVps37BFBGN0037299

Paralogs (3): VPS37A (ENSG00000155975), VPS37C (ENSG00000167987), VPS37D (ENSG00000176428)

Protein

Protein identifiers

Vacuolar protein sorting-associated protein 37BQ9H9H4 (reviewed: Q9H9H4)

Alternative names: ESCRT-I complex subunit VPS37B

All UniProt accessions (3): Q9H9H4, F5H1F6, F5H4M0

UniProt curated annotations — full annotation on UniProt →

Function. Component of the ESCRT-I complex, a regulator of vesicular trafficking process. Required for the sorting of endocytic ubiquitinated cargos into multivesicular bodies. May be involved in cell growth and differentiation.

Subunit / interactions. Component of the ESCRT-I complex (endosomal sorting complex required for transport I) which consists of TSG101, VPS28, a VPS37 protein (VPS37A to -D) and MVB12A or MVB12B in a 1:1:1:1 stoichiometry. Interacts with TSG101, VPS28, MVB12A and MVB12B. Component of the ESCRT-I complex (endosomal sorting complex required for transport I) which consists of TSG101, VPS28, a VPS37 protein (VPS37A to -D) and UBAP1 in a 1:1:1:1 stoichiometry. Interacts with CEP55. Interacts with IST1.

Subcellular location. Late endosome membrane.

Tissue specificity. Widely expressed. Expressed in macrophages and lymphocytes.

Similarity. Belongs to the VPS37 family.

RefSeq proteins (1): NP_078943* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR009851Mod_rDomain
IPR029012Helix_hairpin_bin_sfHomologous_superfamily
IPR037202ESCRT_assembly_domHomologous_superfamily

Pfam: PF07200

UniProt features (10 total): region of interest 3, compositionally biased region 2, helix 2, chain 1, domain 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
6VMEX-RAY DIFFRACTION2.19

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H9H4-F176.420.45

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 (1): 218

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-162588Budding and maturation of HIV virion
R-HSA-174490Membrane binding and targetting of GAG proteins
R-HSA-917729Endosomal Sorting Complex Required For Transport (ESCRT)
R-HSA-9610379HCMV Late Events
R-HSA-9615710Late endosomal microautophagy

MSigDB gene sets: 317 (showing top): ATF_B, REACTOME_ENDOSOMAL_SORTING_COMPLEX_REQUIRED_FOR_TRANSPORT_ESCRT, GOBP_ENDOSOME_ORGANIZATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_VESICLE_ORGANIZATION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOBP_PROTEIN_TARGETING, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, GOBP_VACUOLAR_TRANSPORT, CREBP1_Q2, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_MACROAUTOPHAGY

GO Biological Process (11): protein targeting to membrane (GO:0006612), protein targeting to vacuole (GO:0006623), macroautophagy (GO:0016236), viral release from host cell (GO:0019076), multivesicular body assembly (GO:0036258), viral budding via host ESCRT complex (GO:0039702), ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162), protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043328), membrane fission (GO:0090148), positive regulation of viral budding via host ESCRT complex (GO:1903774), protein transport (GO:0015031)

GO Molecular Function (2): calcium-dependent protein binding (GO:0048306), protein binding (GO:0005515)

GO Cellular Component (9): ESCRT I complex (GO:0000813), cytoplasm (GO:0005737), endosome (GO:0005768), plasma membrane (GO:0005886), endosome membrane (GO:0010008), midbody (GO:0030496), late endosome membrane (GO:0031902), extracellular exosome (GO:0070062), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-5 pathways:

CategoryPathways
Late Phase of HIV Life Cycle1
Synthesis And Processing Of GAG, GAGPOL Polyproteins1
Membrane Trafficking1
HCMV Infection1
Autophagy1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
protein targeting2
intracellular protein transport2
protein localization to vacuole2
establishment of protein localization to vacuole2
endosome membrane2
establishment of protein localization to membrane1
vacuolar transport1
autophagosome assembly1
autophagy1
viral process1
viral life cycle1
exit from host cell1
multivesicular body organization1
organelle assembly1
viral budding1
ubiquitin-dependent protein catabolic process1
protein catabolic process in the vacuole1
multivesicular body sorting pathway1
late endosome to vacuole transport via multivesicular body sorting pathway1
ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway1
membrane organization1
viral budding via host ESCRT complex1
regulation of viral budding via host ESCRT complex1
positive regulation of viral life cycle1
transport1
intracellular protein localization1
establishment of protein localization1
calcium ion binding1
protein binding1
binding1
ESCRT complex1
membrane protein complex1
intracellular anatomical structure1
endomembrane system1
cytoplasmic vesicle1
membrane1
cell periphery1
endosome1
cytoplasmic vesicle membrane1

Protein interactions and networks

STRING

539 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
VPS37BVPS28Q9UK41984
VPS37BTSG101Q99816949
VPS37BVPS4AQ9UN37912
VPS37BMVB12AQ96EY5833
VPS37BMVB12BQ9H7P6711
VPS37BCHMP3Q9Y3E7663
VPS37BA0A140T963A0A140T963663
VPS37BVPS25Q9BRG1643
VPS37BCHMP1AQ9HD42639
VPS37BCHMP5Q9NZZ3617
VPS37BVPS36Q86VN1593
VPS37BCHMP6Q96FZ7588
VPS37BCHMP1BQ7LBR1573
VPS37BCHMP2AO43633560
VPS37BUBAP1Q9NZ09537

IntAct

171 interactions, top by confidence:

ABTypeScore
CEP55TSG101psi-mi:“MI:0914”(association)0.970
VPS28VPS37Bpsi-mi:“MI:0915”(physical association)0.890
VPS37BVPS28psi-mi:“MI:0915”(physical association)0.890
CEP55VPS37Cpsi-mi:“MI:0914”(association)0.800
VPS37BSMARCD1psi-mi:“MI:0915”(physical association)0.780
VPS37BSH3YL1psi-mi:“MI:0915”(physical association)0.780
SMARCD1VPS37Bpsi-mi:“MI:0915”(physical association)0.780
SH3YL1VPS37Bpsi-mi:“MI:0915”(physical association)0.780
TSG101VPS37Cpsi-mi:“MI:0914”(association)0.780
GRB2WIPF3psi-mi:“MI:0914”(association)0.730
VPS37BNCK2psi-mi:“MI:0915”(physical association)0.720
BYSLVPS37Bpsi-mi:“MI:0915”(physical association)0.720
UBASH3BVPS37Bpsi-mi:“MI:0915”(physical association)0.720
VPS37BBYSLpsi-mi:“MI:0915”(physical association)0.720
VPS37BUBASH3Bpsi-mi:“MI:0915”(physical association)0.720

BioGRID (108): VPS37B (Two-hybrid), VPS37B (Two-hybrid), VPS37B (Two-hybrid), VPS37B (Two-hybrid), VPS37B (Two-hybrid), VPS37B (Two-hybrid), VPS37B (Two-hybrid), VPS37B (Two-hybrid), VPS37B (Two-hybrid), VPS37B (Two-hybrid), VPS37B (Two-hybrid), VPS37B (Two-hybrid), UBASH3B (Two-hybrid), FBF1 (Two-hybrid), VPS37B (Affinity Capture-MS)

ESM2 similar proteins: A0JPN4, A2A9T0, A5D8V6, A6ND36, A6QQJ8, A7MCY6, E9Q2Z1, O14529, O54714, O70260, O88902, P70298, P98175, Q07912, Q0IIJ3, Q13227, Q13625, Q148V8, Q15025, Q15942, Q3SZL6, Q3U564, Q3UIL6, Q499E4, Q5BJU7, Q5D1E7, Q5D1E8, Q5NVG8, Q5R9T2, Q5RBV9, Q5U2X5, Q5XIA0, Q61140, Q62415, Q62523, Q63767, Q6DG50, Q6IQ23, Q810I0, Q8CG79

Diamond homologs: A5D8V6, Q5R9T2, Q810I0, Q86XT2, Q8R0J7, Q8R105, Q9H9H4, Q9SCP9, Q8CHS8, Q8NEZ2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 74 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
Endosomal Sorting Complex Required For Transport (ESCRT)853.6×6e-10
Budding and maturation of HIV virion644.5×4e-07
Late endosomal microautophagy741.5×4e-08
HCMV Late Events712.5×1e-04

GO biological processes:

GO termPartnersFoldFDR
protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway8133.8×2e-13
multivesicular body assembly866.9×5e-11
viral budding via host ESCRT complex563.7×1e-06
membrane fission958.7×8e-12
ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway651.8×2e-07
macroautophagy830.6×3e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance51
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1134 predictions. Top by Δscore:

VariantEffectΔscore
12:122867604:TGTT:Tacceptor_gain1.0000
12:122867605:GTT:Gacceptor_gain1.0000
12:122867606:TT:Tacceptor_gain1.0000
12:122867607:TCT:Tacceptor_loss1.0000
12:122867608:C:CCacceptor_gain1.0000
12:122868563:C:CCacceptor_gain1.0000
12:122870885:GTTAC:Gdonor_loss1.0000
12:122870886:TTACC:Tdonor_loss1.0000
12:122870887:TACCT:Tdonor_loss1.0000
12:122870889:C:CGdonor_loss1.0000
12:122870908:T:Cdonor_gain1.0000
12:122870937:T:Adonor_gain1.0000
12:122871061:TCT:Tacceptor_loss1.0000
12:122871062:C:CCacceptor_gain1.0000
12:122871062:C:CGacceptor_loss1.0000
12:122871063:T:Aacceptor_loss1.0000
12:122895946:GCTCA:Gdonor_loss1.0000
12:122895947:CTCA:Cdonor_loss1.0000
12:122895948:TCA:Tdonor_loss1.0000
12:122895949:CAC:Cdonor_loss1.0000
12:122895950:A:Cdonor_loss1.0000
12:122895950:ACCT:Adonor_gain1.0000
12:122895951:CCTC:Cdonor_gain1.0000
12:122895953:T:TAdonor_gain1.0000
12:122867603:ATGTT:Aacceptor_gain0.9900
12:122867605:GTTCT:Gacceptor_gain0.9900
12:122868490:T:TAdonor_gain0.9900
12:122868559:CTGT:Cacceptor_gain0.9900
12:122870892:A:ACdonor_gain0.9900
12:122870893:A:Cdonor_gain0.9900

AlphaMissense

1818 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:122867537:C:GR146P0.999
12:122868517:A:GL110P0.999
12:122867498:A:GL159P0.998
12:122867519:C:GR152P0.998
12:122867560:G:CF138L0.998
12:122867560:G:TF138L0.998
12:122867561:A:GF138S0.998
12:122867562:A:GF138L0.998
12:122870994:A:GL60P0.998
12:122867516:C:GR153P0.997
12:122870934:A:GL80P0.997
12:122871007:C:GA56P0.997
12:122896010:A:GL18P0.997
12:122867550:A:CY142D0.996
12:122867591:A:GF128S0.996
12:122868520:A:GL109P0.996
12:122867526:G:CH150D0.995
12:122867529:C:GA149P0.995
12:122868512:C:GA112P0.995
12:122871015:C:GR53P0.995
12:122896001:A:GL21P0.995
12:122871006:G:TA56E0.994
12:122871009:A:GL55P0.994
12:122871027:A:GL49P0.994
12:122868503:C:GA115P0.993
12:122870996:G:CN59K0.993
12:122870996:G:TN59K0.993
12:122871017:G:CN52K0.993
12:122871017:G:TN52K0.993
12:122867601:C:GA125P0.992

dbSNP variants (sampled 300 via entrez): RS1000037591 (12:122881894 C>T), RS1000090174 (12:122874683 T>C), RS1000119167 (12:122871930 G>A), RS1000163742 (12:122875029 T>G), RS1000344487 (12:122867910 G>A), RS1000399748 (12:122874127 T>C), RS1000491154 (12:122864834 C>A,G,T), RS1000609864 (12:122880478 A>C,G,T), RS1000690911 (12:122865520 C>T), RS1000726176 (12:122870497 C>T), RS1001006671 (12:122885765 G>C), RS1001144473 (12:122895488 C>T), RS1001165589 (12:122892575 C>A), RS1001261428 (12:122892237 A>C), RS1001682194 (12:122881807 TA>T,TAA)

Disease associations

OMIM: gene MIM:610037 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

13 associations (top):

StudyTraitp-value
GCST007277_17Tourette syndrome2.000000e-06
GCST90020024_249A body shape index3.000000e-08
GCST90020024_428A body shape index3.000000e-08
GCST90020025_33Waist-to-hip ratio adjusted for BMI8.000000e-11
GCST90020025_401Waist-to-hip ratio adjusted for BMI5.000000e-09
GCST90020025_402Waist-to-hip ratio adjusted for BMI7.000000e-11
GCST90020025_41Waist-to-hip ratio adjusted for BMI8.000000e-11
GCST90020027_1210Waist-hip index4.000000e-11
GCST90020027_1243Waist-hip index6.000000e-11
GCST90020027_1253Waist-hip index2.000000e-08
GCST90020028_1249Hip circumference adjusted for BMI2.000000e-11
GCST90020028_1258Hip circumference adjusted for BMI2.000000e-11
GCST90020029_361Waist circumference adjusted for body mass index4.000000e-10

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0007789BMI-adjusted waist circumference
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0008039BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

52 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Tobacco Smoke Pollutionaffects expression, increases expression4
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression3
(+)-JQ1 compounddecreases expression2
Cyclosporineincreases expression2
aristolochic acid Iincreases expression1
triphenyl phosphateaffects expression1
bisphenol Aaffects methylation1
beta-lapachoneincreases expression1
cobaltous chlorideincreases expression1
perfluorooctanoic aciddecreases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
aflatoxin B2decreases methylation1
cupric chlorideincreases expression1
4-aminophenylarsenoxideaffects binding, decreases reaction1
isobutyl alcoholaffects cotreatment, increases abundance, increases expression1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic aciddecreases expression1
perfluorohexanesulfonic aciddecreases expression1
erucylphospho-N,N,N-trimethylpropylammoniumincreases expression1
abrineincreases expression1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)increases expression1
PCI 5002affects cotreatment, increases expression1
Sunitinibdecreases expression1
Arsenic Trioxidedecreases reaction, affects binding1
Acetaminophenincreases expression1
Air Pollutantsaffects expression, increases abundance1
Arsenicincreases abundance, increases expression, affects cotreatment1

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.