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VPS37D

gene
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Also known as MGC35352

Summary

VPS37D (VPS37D subunit of ESCRT-I, HGNC:18287) is a protein-coding gene on chromosome 7q11.23, encoding Vacuolar protein sorting-associated protein 37D (Q86XT2). Component of the ESCRT-I complex, a regulator of vesicular trafficking process.

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 extracellular exosome. Part of ESCRT I complex.

Source: NCBI Gene 155382 — RefSeq curated summary.

At a glance

  • GWAS associations: 8
  • Clinical variants (ClinVar): 64 total
  • Phenotypes (HPO): 186
  • MANE Select transcript: NM_001077621

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18287
Approved symbolVPS37D
NameVPS37D subunit of ESCRT-I
Location7q11.23
Locus typegene with protein product
StatusApproved
AliasesMGC35352
Ensembl geneENSG00000176428
Ensembl biotypeprotein_coding
OMIM610039
Entrez155382

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000324941, ENST00000451519, ENST00000903466, ENST00000965880

RefSeq mRNA: 1 — MANE Select: NM_001077621 NM_001077621

CCDS: CCDS43596

Canonical transcript exons

ENST00000324941 — 4 exons

ExonStartEnd
ENSE000012280647366941973669590
ENSE000012280757367002073670102
ENSE000012280867366783173668096
ENSE000013334727367101473672110

Expression profiles

Bgee: expression breadth ubiquitous, 180 present calls, max score 89.90.

FANTOM5 (CAGE): breadth broad, TPM avg 0.5531 / max 7.8349, expressed in 330 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
790110.5531330

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
pancreatic ductal cellCL:000207989.90silver quality
cortical plateUBERON:000534386.58gold quality
nasal cavity epitheliumUBERON:000538485.95gold quality
ganglionic eminenceUBERON:000402385.94gold quality
kidney epitheliumUBERON:000481985.84gold quality
upper arm skinUBERON:000426383.84gold quality
epithelial cell of pancreasCL:000008383.18gold quality
cerebellar vermisUBERON:000472083.11silver quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099181.57gold quality
ventricular zoneUBERON:000305380.69gold quality
endothelial cellCL:000011580.14silver quality
vena cavaUBERON:000408780.02gold quality
ventral tegmental areaUBERON:000269179.89silver quality
renal medullaUBERON:000036279.71gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047379.62gold quality
prefrontal cortexUBERON:000045179.61gold quality
pericardiumUBERON:000240779.45silver quality
anterior cingulate cortexUBERON:000983578.85gold quality
adult mammalian kidneyUBERON:000008278.71gold quality
lateral nuclear group of thalamusUBERON:000273678.66gold quality
lateral globus pallidusUBERON:000247678.56silver quality
substantia nigra pars compactaUBERON:000196578.29silver quality
neocortexUBERON:000195078.11gold quality
frontal cortexUBERON:000187077.91gold quality
nucleus accumbensUBERON:000188277.91gold quality
cortex of kidneyUBERON:000122577.62gold quality
right frontal lobeUBERON:000281077.58gold quality
pharyngeal mucosaUBERON:000035577.41gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450277.34gold quality
heart right ventricleUBERON:000208077.33gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no0.60

Regulation

Is transcription factor: no

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriovps37dENSDARG00000097055
mus_musculusVps37dENSMUSG00000043614
rattus_norvegicusVps37dENSRNOG00000048699
drosophila_melanogasterVps37BFBGN0037299

Paralogs (3): VPS37B (ENSG00000139722), VPS37A (ENSG00000155975), VPS37C (ENSG00000167987)

Protein

Protein identifiers

Vacuolar protein sorting-associated protein 37D — Q86XT2 (reviewed: Q86XT2)

Alternative names: ESCRT-I complex subunit VPS37D, Williams-Beuren syndrome chromosomal region 24 protein

All UniProt accessions (2): Q86XT2, C9JYT9

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 and MVB12A. 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.

Subcellular location. Late endosome membrane.

Disease relevance. VPS37D is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region.

Similarity. Belongs to the VPS37 family.

RefSeq proteins (1): NP_001071089* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR009851Mod_rDomain

Pfam: PF07200

UniProt features (4 total): chain 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q86XT2-F181.370.61

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: 545 (showing top): GSE45365_NK_CELL_VS_BCELL_DN, REACTOME_ENDOSOMAL_SORTING_COMPLEX_REQUIRED_FOR_TRANSPORT_ESCRT, GOBP_ENDOSOME_ORGANIZATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN, GOBP_VESICLE_ORGANIZATION, GOBP_PROTEIN_TARGETING, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_VACUOLAR_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_MACROAUTOPHAGY, GOBP_PROTEIN_TARGETING_TO_MEMBRANE, REACTOME_HIV_INFECTION

GO Biological Process (9): protein targeting to membrane (GO:0006612), protein targeting to vacuole (GO:0006623), macroautophagy (GO:0016236), 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), protein transport (GO:0015031)

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

GO Cellular Component (6): ESCRT I complex (GO:0000813), endosome membrane (GO:0010008), late endosome membrane (GO:0031902), extracellular exosome (GO:0070062), endosome (GO:0005768), 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
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
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
transport1
intracellular protein localization1
establishment of protein localization1
binding1
ESCRT complex1
membrane protein complex1
endosome1
cytoplasmic vesicle membrane1
bounding membrane of organelle1
late endosome1
extracellular vesicle1
endomembrane system1
cytoplasmic vesicle1
cellular anatomical structure1

Protein interactions and networks

STRING

477 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
VPS37DVPS28Q9UK41795
VPS37DTSG101Q99816658
VPS37DMVB12AQ96EY5652
VPS37DMVB12BQ9H7P6592
VPS37DUBAP1Q9NZ09583
VPS37DVPS36Q86VN1544
VPS37DSNF8Q96H20462
VPS37DCHMP3Q9Y3E7460
VPS37DA0A140T963A0A140T963460
VPS37DVPS25Q9BRG1455
VPS37DCHMP4CQ96CF2444
VPS37DTMEM270Q6UE05426
VPS37DCHMP2AO43633416
VPS37DGTF2IRD1Q9UHL9413
VPS37DOR11L1Q8NGX0400

IntAct

18 interactions, top by confidence:

ABTypeScore
VPS37DARMC7psi-mi:“MI:0915”(physical association)0.560
VPS37DCRTAPpsi-mi:“MI:0914”(association)0.530
CEP55VPS37Dpsi-mi:“MI:0915”(physical association)0.370
TRAF2UMAD1psi-mi:“MI:0914”(association)0.350
RBCK1UMAD1psi-mi:“MI:0914”(association)0.350
SHARPINMAP3K7psi-mi:“MI:0914”(association)0.350
VPS28DCAF6psi-mi:“MI:0914”(association)0.350
VPS28PRPF6psi-mi:“MI:0914”(association)0.350
VPS37DRPSA2psi-mi:“MI:0914”(association)0.350
CACYBPVPS37Cpsi-mi:“MI:0914”(association)0.350
CAPRIN1SDCBPpsi-mi:“MI:0914”(association)0.350
EIF4A1SNAP23psi-mi:“MI:0914”(association)0.350
CSDE1VPS37Cpsi-mi:“MI:0914”(association)0.350
ARMC7VPS37Dpsi-mi:“MI:0915”(physical association)0.000

BioGRID (26): VPS37D (Affinity Capture-MS), ACAD8 (Affinity Capture-MS), TSG101 (Affinity Capture-MS), CRTAP (Affinity Capture-MS), SAV1 (Affinity Capture-MS), P3H1 (Affinity Capture-MS), AASS (Affinity Capture-MS), KIAA1279 (Affinity Capture-MS), VPS37D (Affinity Capture-MS), VPS37D (Affinity Capture-MS), VPS37D (Affinity Capture-MS), VPS37D (Affinity Capture-MS), VPS37D (Two-hybrid), P3H1 (Affinity Capture-MS), CRTAP (Affinity Capture-MS)

ESM2 similar proteins: A0A8I5KY20, A2A9T0, A2IDD5, B0BNK9, B8ZZ34, C9JI98, C9JLR9, F5GYI3, O18734, P0CG25, P84157, Q0IIA6, Q0PHV7, Q0X0E2, Q13387, Q1RMK9, Q2M3D2, Q2TAM9, Q3ZCQ3, Q4VA45, Q673H1, Q69YZ2, Q6NS60, Q6P6N5, Q6PJ61, Q7Z6J2, Q80ZJ8, Q810I0, Q86SX3, Q86UD0, Q86XT2, Q8BNN1, Q8IUW3, Q8N4Y2, Q8N6N2, Q8QZV0, Q8R4T5, Q8TF61, Q8VCR9, Q8WXF8

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance53
Likely benign6
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

749 predictions. Top by Δscore:

VariantEffectΔscore
7:73668092:GGAAG:Gdonor_gain1.0000
7:73668093:G:GTdonor_gain1.0000
7:73668094:A:Tdonor_gain1.0000
7:73669415:GCA:Gacceptor_loss1.0000
7:73669417:A:AGacceptor_gain1.0000
7:73669418:G:GAacceptor_gain1.0000
7:73669418:GT:Gacceptor_gain1.0000
7:73669418:GTT:Gacceptor_gain1.0000
7:73669418:GTTCC:Gacceptor_gain1.0000
7:73669555:TGGCC:Tdonor_gain1.0000
7:73669556:GGCCG:Gdonor_gain1.0000
7:73669589:GG:Gdonor_gain1.0000
7:73669590:GG:Gdonor_gain1.0000
7:73669591:G:GGdonor_gain1.0000
7:73669591:GTGA:Gdonor_loss1.0000
7:73671006:C:Aacceptor_gain1.0000
7:73668055:G:GTdonor_gain0.9900
7:73668096:GGTAG:Gdonor_loss0.9900
7:73668097:GTA:Gdonor_loss0.9900
7:73668098:T:Adonor_loss0.9900
7:73669418:GTTC:Gacceptor_gain0.9900
7:73669598:C:Tdonor_gain0.9900
7:73669905:GAAAC:Gdonor_gain0.9900
7:73670010:T:TAacceptor_gain0.9900
7:73671007:G:Aacceptor_gain0.9900
7:73671012:A:ACacceptor_loss0.9900
7:73671012:A:AGacceptor_gain0.9900
7:73671013:G:GAacceptor_gain0.9900
7:73669588:TGG:Tdonor_gain0.9800
7:73669589:GGG:Gdonor_gain0.9800

AlphaMissense

1573 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:73668038:T:CL27P0.999
7:73668047:T:CL30P0.999
7:73669474:C:AA65D0.999
7:73669525:T:CL82P0.999
7:73669546:T:CL89P0.999
7:73668038:T:AL27H0.998
7:73669463:C:AN61K0.998
7:73669463:C:GN61K0.998
7:73669473:G:CA65P0.998
7:73669484:C:AN68K0.998
7:73669484:C:GN68K0.998
7:73669486:T:CL69P0.998
7:73671123:T:CL168P0.998
7:73668050:T:CL31P0.997
7:73669441:G:CR54P0.997
7:73671059:T:CF147L0.997
7:73671061:C:AF147L0.997
7:73671061:C:GF147L0.997
7:73669504:T:CL75P0.996
7:73669527:G:CA83P0.996
7:73671071:T:CF151L0.996
7:73671073:C:AF151L0.996
7:73671073:C:GF151L0.996
7:73671113:G:CA165P0.996
7:73668068:T:CL37P0.995
7:73669482:A:GN68D0.995
7:73671060:T:CF147S0.995
7:73671105:G:CR162P0.995
7:73668088:A:CS44R0.994
7:73668090:C:AS44R0.994

dbSNP variants (sampled 300 via entrez): RS1000079310 (7:73671877 A>G,T), RS1000293803 (7:73666573 C>T), RS1000560888 (7:73672242 C>T), RS1000594615 (7:73667509 G>A), RS1000623786 (7:73668311 C>T), RS1002265169 (7:73669329 C>G,T), RS1002585874 (7:73670336 G>A), RS1002642620 (7:73663411 G>A), RS1002764670 (7:73664692 C>A), RS1002937467 (7:73664487 C>A), RS1004332603 (7:73669035 A>G), RS1004534163 (7:73670306 C>G,T), RS1004601114 (7:73669264 G>A), RS1004672384 (7:73664676 G>A), RS1005073232 (7:73670052 G>A,T)

Disease associations

OMIM: gene MIM:610039 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

186 total (30 of 186 shown, HPO-id order):

HPOTerm
HP:0000010Recurrent urinary tract infections
HP:0000014Abnormality of the bladder
HP:0000015Bladder diverticulum
HP:0000023Inguinal hernia
HP:0000025Functional abnormality of male internal genitalia
HP:0000028Cryptorchidism
HP:0000044Hypogonadotropic hypogonadism
HP:0000075Renal duplication
HP:0000076Vesicoureteral reflux
HP:0000083Renal insufficiency
HP:0000089Renal hypoplasia
HP:0000093Proteinuria
HP:0000121Nephrocalcinosis
HP:0000125Pelvic kidney
HP:0000147Polycystic ovaries
HP:0000154Wide mouth
HP:0000158Macroglossia
HP:0000179Thick lower lip vermilion
HP:0000212Gingival overgrowth
HP:0000232Everted lower lip vermilion
HP:0000252Microcephaly
HP:0000275Narrow face
HP:0000280Coarse facial features
HP:0000286Epicanthus
HP:0000307Pointed chin
HP:0000337Broad forehead
HP:0000343Long philtrum
HP:0000347Micrognathia
HP:0000348High forehead
HP:0000358Posteriorly rotated ears

GWAS associations

8 associations (top):

StudyTraitp-value
GCST001905_7Hypertriglyceridemia2.000000e-06
GCST002650_8Coffee consumption (cups per day)3.000000e-11
GCST005983_23Serum uric acid levels4.000000e-09
GCST005988_8Serum albumin levels2.000000e-09
GCST006019_1Gamma glutamyl transferase levels1.000000e-21
GCST010725_13Malaria8.000000e-06
GCST010725_74Malaria6.000000e-06
GCST010725_91Malaria7.000000e-06

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0004530triglyceride measurement
EFO:0004330coffee consumption
EFO:0006782cups of coffee per day measurement
EFO:0004761uric acid measurement
EFO:0004532serum gamma-glutamyl transferase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

ChemicalActions (top 5)PubMed papers
trichostatin Aaffects cotreatment, decreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
bisphenol Aincreases expression1
sodium arsenateincreases abundance, increases expression1
S-(1,2-dichlorovinyl)cysteinedecreases expression, affects response to substance, increases expression, affects cotreatment1
beta-methylcholineaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
nutlin 3affects cotreatment, increases expression1
dorsomorphinaffects cotreatment, decreases expression1
(+)-JQ1 compounddecreases expression1
Rosiglitazonedecreases expression1
Resveratrolaffects cotreatment, decreases expression1
Temozolomidedecreases expression1
Arsenicincreases abundance, increases expression1
Benzo(a)pyreneaffects methylation1
Camptothecinincreases expression1
Dactinomycinaffects cotreatment, increases expression1
Estradioldecreases expression1
Lipopolysaccharidesincreases expression, affects cotreatment, decreases expression, affects response to substance1
Niclosamideincreases expression1
Plant Extractsaffects cotreatment, decreases expression1
Tobacco Smoke Pollutionincreases expression1
Valproic Acidaffects expression1
Okadaic Aciddecreases 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.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 75

This page pulls from 75 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot