HOMER3

gene
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Also known as HOMER-3

Summary

HOMER3 (homer scaffold protein 3, HGNC:17514) is a protein-coding gene on chromosome 19p13.11, encoding Homer protein homolog 3 (Q9NSC5). Postsynaptic density scaffolding protein.

This gene encodes a member of the HOMER family of postsynaptic density scaffolding proteins that share a similar domain structure consisting of an N-terminal Enabled/vasodilator-stimulated phosphoprotein homology 1 domain which mediates protein-protein interactions, and a carboxy-terminal coiled-coil domain and two leucine zipper motifs that are involved in self-oligomerization. The encoded protein binds numerous other proteins including group I metabotropic glutamate receptors, inositol 1,4,5-trisphosphate receptors and amyloid precursor proteins and has been implicated in diverse biological functions such as neuronal signaling, T-cell activation and trafficking of amyloid beta peptides. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 9454 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 84 total
  • MANE Select transcript: NM_004838

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17514
Approved symbolHOMER3
Namehomer scaffold protein 3
Location19p13.11
Locus typegene with protein product
StatusApproved
AliasesHOMER-3
Ensembl geneENSG00000051128
Ensembl biotypeprotein_coding
OMIM604800
Entrez9454

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 18 protein_coding, 2 retained_intron

ENST00000221222, ENST00000392351, ENST00000433218, ENST00000539827, ENST00000542541, ENST00000594439, ENST00000594794, ENST00000595756, ENST00000596482, ENST00000599097, ENST00000599808, ENST00000600077, ENST00000861160, ENST00000861161, ENST00000861162, ENST00000936392, ENST00000936393, ENST00000971943, ENST00000971944, ENST00000971945

RefSeq mRNA: 4 — MANE Select: NM_004838 NM_001145721, NM_001145722, NM_001145724, NM_004838

CCDS: CCDS12391, CCDS46022, CCDS46023

Canonical transcript exons

ENST00000392351 — 10 exons

ExonStartEnd
ENSE000011135231892920318929634
ENSE000011226101893430318934410
ENSE000011829081893872818938884
ENSE000012236411893835318938484
ENSE000015115491893896918939049
ENSE000023015581894105118941217
ENSE000035208951893292418933045
ENSE000035424041893197618932132
ENSE000035626581893150918931625
ENSE000036087571893132518931411

Expression profiles

Bgee: expression breadth ubiquitous, 277 present calls, max score 97.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.9560 / max 292.2226, expressed in 1750 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
18011727.29041747
1801161.3913869
1801150.5449363
1801140.4006213
1801130.3288159

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cerebellar vermisUBERON:000472097.29gold quality
right hemisphere of cerebellumUBERON:001489096.54gold quality
C1 segment of cervical spinal cordUBERON:000646996.30gold quality
spleenUBERON:000210696.04gold quality
cerebellar cortexUBERON:000212995.47gold quality
hindlimb stylopod muscleUBERON:000425295.40gold quality
cerebellar hemisphereUBERON:000224595.38gold quality
spinal cordUBERON:000224095.26gold quality
gastrocnemiusUBERON:000138895.24gold quality
cerebellumUBERON:000203795.00gold quality
metanephros cortexUBERON:001053394.80gold quality
muscle of legUBERON:000138394.52gold quality
inferior vagus X ganglionUBERON:000536393.91gold quality
stromal cell of endometriumCL:000225593.64gold quality
ganglionic eminenceUBERON:000402393.17gold quality
right lobe of thyroid glandUBERON:000111993.11gold quality
left lobe of thyroid glandUBERON:000112093.06gold quality
muscle organUBERON:000163092.74gold quality
monocyteCL:000057692.68gold quality
paraflocculusUBERON:000535192.60gold quality
thyroid glandUBERON:000204692.16gold quality
mononuclear cellCL:000084291.94gold quality
leukocyteCL:000073891.50gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451191.24gold quality
ascending aortaUBERON:000149691.02gold quality
thoracic aortaUBERON:000151590.91gold quality
skin of legUBERON:000151190.54gold quality
endocervixUBERON:000045890.49gold quality
right adrenal gland cortexUBERON:003582790.18gold quality
gluteal muscleUBERON:000200090.17gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-8271yes15.77
E-CURD-114yes10.17
E-ANND-3yes7.60

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CEBPA

miRNA regulators (miRDB)

13 targeting HOMER3, 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-22-3P99.9368.13917
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-568099.9169.833421
HSA-MIR-806799.8669.592260
HSA-MIR-6764-5P99.7567.892304
HSA-MIR-1915-3P99.5866.791988
HSA-MIR-376A-3P99.0669.171128
HSA-MIR-376B-3P99.0669.171128
HSA-MIR-3928-5P98.5067.48980
HSA-MIR-6806-3P98.5067.31980
HSA-MIR-6773-5P97.0464.30595
HSA-MIR-6724-5P96.4163.11507
HSA-MIR-4743-5P88.0864.3191

Literature-anchored findings (GeneRIF, showing 10)

  • Homer-3 may be involved in the regulation of SRE activation in T cells via interaction between its EVH1 domain and C/EBP beta. (PMID:14645007)
  • Fat1 exhibit co-localisation with Homer-3 in cellular protrusions and at the plasma membrane of HeLa cells (PMID:16979624)
  • study found that Homer2 and Homer3 are negative regulators of T cell activation; this is achieved through binding of nuclear factor of activated T cells (NFAT) and by competing with calcineurin (PMID:18218901)
  • Homer3 specifically associates with a novel ubiquitin-like domain in the I kappa B kinase (IKK) beta subunit of the IKK complex. (PMID:20693425)
  • Loss of Homer3 is associated with acute myeloid leukemia. (PMID:23725168)
  • Interaction of the protein with amyloid precursor protein is regulated by calcium homeostasis. (PMID:24792907)
  • Homer3 acts as a scaffold that spatially organizes actin assembly to support neutrophil polarity and motility downstream of GPCR activation. (PMID:25739453)
  • HOMER3 facilitates growth factor-mediated beta-Catenin tyrosine phosphorylation and activation to promote metastasis in triple negative breast cancer. (PMID:33407765)
  • Glycoproteomics identifies HOMER3 as a potentially targetable biomarker triggered by hypoxia and glucose deprivation in bladder cancer. (PMID:34108014)
  • HOMER3 promotes liver hepatocellular carcinoma cancer progression by -upregulating EZH2 and mediating miR-361/GPNMB axis. (PMID:38266459)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriohomer3bENSDARG00000010789
danio_reriohomer3aENSDARG00000102532
mus_musculusHomer3ENSMUSG00000003573
rattus_norvegicusHomer3ENSRNOG00000020229

Paralogs (2): HOMER2 (ENSG00000103942), HOMER1 (ENSG00000152413)

Protein

Protein identifiers

Homer protein homolog 3Q9NSC5 (reviewed: Q9NSC5)

All UniProt accessions (5): Q9NSC5, M0QYF9, M0QZN1, M0R2T8, M0R2U7

UniProt curated annotations — full annotation on UniProt →

Function. Postsynaptic density scaffolding protein. Binds and cross-links cytoplasmic regions of GRM1, GRM5, ITPR1, DNM3, RYR1, RYR2, SHANK1 and SHANK3. By physically linking GRM1 and GRM5 with ER-associated ITPR1 receptors, it aids the coupling of surface receptors to intracellular calcium release. Isoforms can be differently regulated and may play an important role in maintaining the plasticity at glutamatergic synapses. Negatively regulates T cell activation by inhibiting the calcineurin-NFAT pathway. Acts by competing with calcineurin/PPP3CA for NFAT protein binding, hence preventing NFAT activation by PPP3CA.

Subunit / interactions. Tetramer. Isoform 1 and isoform 2 encode coiled-coil structures that mediate homo- and heteromultimerization. Interacts with NFATC2; interaction is calcium independent; interaction competes with PPP3CA for NFATC2 binding; interaction is reduced by AKT activation. Interacts with NFATC1 and NFATC4. Interacts with SHANK1; forms a high-order complex at least composed of SHANK1 and HOMER3; the complex formation is regulated by CAMK2A-mediated phosphorylation.

Subcellular location. Cytoplasm. Postsynaptic density. Synapse.

Domain organisation. The WH1 domain interacts with the PPXXF motif in GRM1, GRM5, RYR1, RYR2, ITPR1, SHANK 1 and SHANK3.

Similarity. Belongs to the Homer family.

Isoforms (5)

UniProt IDNamesCanonical?
Q9NSC5-11, 3ayes
Q9NSC5-22
Q9NSC5-33, 3c
Q9NSC5-44, 3d
Q9NSC5-55

RefSeq proteins (4): NP_001139193, NP_001139194, NP_001139196, NP_004829* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000697WH1/EVH1_domDomain
IPR011993PH-like_dom_sfHomologous_superfamily
IPR044100Homer_EVH1Domain
IPR045027HomerFamily

Pfam: PF00568

UniProt features (36 total): mutagenesis site 8, strand 8, splice variant 6, turn 3, region of interest 2, helix 2, coiled-coil region 2, modified residue 2, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
2P8VX-RAY DIFFRACTION1.85
3CVFX-RAY DIFFRACTION2.9

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NSC5-F183.470.62

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): 120, 159

Mutagenesis-validated functional residues (8):

PositionPhenotype
22does not affect interaction with nfatc2. decreases interaction with nfatc2; when associated with 53-l–s-56. decreases i
30–31markedly decreases interaction with nfatc2; when associated with s-43 and 53-l–s-56. markedly decreases interaction wit
36does not affect interaction with nfatc2; when associated with a-38 and a-52. attenuates inhibition by akt; when associat
38does not affect interaction with nfatc2; when associated with a-36 and a-52. attenuates inhibition by akt; when associat
43does not affect interaction with nfatc2. decreases interaction with nfatc2; when associated with n-22 and 53-l–s-56. ma
52does not affect interaction with nfatc2; when associated with a-36 and a-38. attenuates inhibition by akt; when associat
53–56decreases interaction with nfatc2. decreases interaction with nfatc2; when associated with n-22. decreases interaction w
54decreases interaction with nfatc2.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-6794361Neurexins and neuroligins

MSigDB gene sets: 192 (showing top): TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP, MULLIGHAN_NPM1_SIGNATURE_3_UP, GOBP_REGULATION_OF_CALCIUM_MEDIATED_SIGNALING, GOBP_REGULATION_OF_SYNAPTIC_TRANSMISSION_GLUTAMATERGIC, GOBP_PROTEIN_TARGETING, DARWICHE_SKIN_TUMOR_PROMOTER_UP, DARWICHE_PAPILLOMA_RISK_LOW_UP, DARWICHE_PAPILLOMA_RISK_HIGH_UP, CROONQUIST_NRAS_SIGNALING_UP, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, GOBP_G_PROTEIN_COUPLED_GLUTAMATE_RECEPTOR_SIGNALING_PATHWAY, GOBP_MONOATOMIC_CATION_TRANSPORT, GOBP_CELL_CELL_SIGNALING, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINDED_IN_ERYTHROCYTE_UP

GO Biological Process (6): protein targeting (GO:0006605), G protein-coupled glutamate receptor signaling pathway (GO:0007216), negative regulation of interleukin-2 production (GO:0032703), regulation of synaptic transmission, glutamatergic (GO:0051966), negative regulation of calcineurin-NFAT signaling cascade (GO:0070885), regulation of store-operated calcium entry (GO:2001256)

GO Molecular Function (4): protein domain specific binding (GO:0019904), G protein-coupled glutamate receptor binding (GO:0035256), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (8): cytoplasm (GO:0005737), cytosol (GO:0005829), plasma membrane (GO:0005886), postsynaptic density (GO:0014069), dendrite (GO:0030425), basal part of cell (GO:0045178), glutamatergic synapse (GO:0098978), synapse (GO:0045202)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Protein-protein interactions at synapses1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
protein binding2
establishment of protein localization1
G protein-coupled receptor signaling pathway1
glutamate receptor signaling pathway1
G protein-coupled glutamate receptor activity1
negative regulation of cytokine production1
interleukin-2 production1
regulation of interleukin-2 production1
synaptic transmission, glutamatergic1
modulation of chemical synaptic transmission1
calcineurin-NFAT signaling cascade1
regulation of calcineurin-NFAT signaling cascade1
negative regulation of calcineurin-mediated signaling1
store-operated calcium entry1
regulation of calcium ion transport1
G protein-coupled receptor binding1
glutamate receptor binding1
binding1
intracellular anatomical structure1
cytoplasm1
membrane1
cell periphery1
asymmetric synapse1
postsynaptic specialization1
neuron projection1
dendritic tree1
synapse1
cell junction1

Protein interactions and networks

STRING

984 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
HOMER3SHANK1Q9Y566917
HOMER3GRM1Q13255902
HOMER3ITPR1Q14643898
HOMER3DLGAP1P78335883
HOMER3GRM5P41594851
HOMER3DLG4P78352736
HOMER3SHANK3Q9BYB0712
HOMER3SYNGAP1Q96PV0664
HOMER3ARHGAP26Q9UNA1602
HOMER3NCDNQ9UBB6595
HOMER3ACTN1P12814590
HOMER3HOMER2Q9NSB8587
HOMER3SHANK2Q9UPX8583
HOMER3DNERQ8NFT8580
HOMER3LGI1O95970572

IntAct

415 interactions, top by confidence:

ABTypeScore
HOMER1HOMER3psi-mi:“MI:0915”(physical association)0.870
MOSHOMER3psi-mi:“MI:0915”(physical association)0.790
HOMER3MOSpsi-mi:“MI:0915”(physical association)0.790
HOMER3PKN1psi-mi:“MI:0915”(physical association)0.780
EAF1HOMER3psi-mi:“MI:0915”(physical association)0.780
HOMER3EAF1psi-mi:“MI:0915”(physical association)0.780
PKN1HOMER3psi-mi:“MI:0915”(physical association)0.780
HOMER3ABI2psi-mi:“MI:0915”(physical association)0.740
ABI2HOMER3psi-mi:“MI:0915”(physical association)0.740
HOMER3HOMER3psi-mi:“MI:0915”(physical association)0.740
HOMER3EIF3Dpsi-mi:“MI:0915”(physical association)0.720
USP2HOMER3psi-mi:“MI:0915”(physical association)0.720
HOMER3PSMA1psi-mi:“MI:0915”(physical association)0.720
HOMER3SNRPFpsi-mi:“MI:0915”(physical association)0.720
HOMER3PPP1R18psi-mi:“MI:0915”(physical association)0.720
EIF3DHOMER3psi-mi:“MI:0915”(physical association)0.720

BioGRID (213): HOMER3 (Two-hybrid), HOMER3 (Two-hybrid), HOMER3 (Two-hybrid), HOMER3 (Two-hybrid), HOMER3 (Two-hybrid), HOMER3 (Two-hybrid), HOMER3 (Two-hybrid), HOMER3 (Two-hybrid), HOMER3 (Two-hybrid), HOMER1 (Two-hybrid), POM121 (Two-hybrid), ABI2 (Two-hybrid), NEBL (Two-hybrid), EAF1 (Two-hybrid), PPP1R18 (Two-hybrid)

ESM2 similar proteins: A0A0D1E2P6, A0A0D2XVZ5, A0A0P0VG31, A0A0P1AAU8, A0A287B8J2, A2WYG9, A4QP73, B9EHT4, B9F2Y7, D0NCC1, J9VKM5, O08788, O59739, P0C7L7, P0CP26, P0CP27, P14725, P28023, P39742, P82874, P92792, Q10MW6, Q13217, Q14203, Q149L6, Q27968, Q28I38, Q54M21, Q54NS3, Q58DR2, Q5JJI4, Q5JNB5, Q5R686, Q5R6H3, Q5ZI13, Q6PCJ1, Q6YUL8, Q7ZXQ8, Q8TBM8, Q91YW3

Diamond homologs: O88801, Q2KJ56, Q86YM7, Q99JP6, Q9NSB8, Q9NSC5, Q9QWW1, Q9Z214, Q9Z2X5, Q9Z2Y3, Q5TJ65, P50551, P70460, Q2TA49

SIGNOR signaling

3 interactions.

AEffectBMechanism
CAMK2A“down-regulates activity”HOMER3phosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance68
Likely benign2
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

1281 predictions. Top by Δscore:

VariantEffectΔscore
19:18929493:G:Cdonor_gain1.0000
19:18929570:T:TAdonor_gain1.0000
19:18929630:AGGTC:Aacceptor_gain1.0000
19:18929633:TC:Tacceptor_gain1.0000
19:18929634:CC:Cacceptor_gain1.0000
19:18929635:C:CCacceptor_gain1.0000
19:18929640:A:Tacceptor_gain1.0000
19:18931409:CTC:Cacceptor_gain1.0000
19:18931504:CTCA:Cdonor_loss1.0000
19:18931505:TCA:Tdonor_loss1.0000
19:18931505:TCACC:Tdonor_loss1.0000
19:18931506:CA:Cdonor_loss1.0000
19:18931506:CAC:Cdonor_loss1.0000
19:18931507:A:ACdonor_gain1.0000
19:18931507:ACCTG:Adonor_loss1.0000
19:18931508:C:Adonor_loss1.0000
19:18931508:C:CCdonor_gain1.0000
19:18931622:CCAC:Cacceptor_gain1.0000
19:18931623:CACC:Cacceptor_gain1.0000
19:18931624:ACC:Aacceptor_loss1.0000
19:18931625:CCTG:Cacceptor_loss1.0000
19:18931626:C:CAacceptor_loss1.0000
19:18931626:C:CCacceptor_gain1.0000
19:18931626:CTGTA:Cacceptor_loss1.0000
19:18931970:CCTCA:Cdonor_loss1.0000
19:18931971:CTCA:Cdonor_loss1.0000
19:18931972:TCACC:Tdonor_loss1.0000
19:18931973:CAC:Cdonor_loss1.0000
19:18931973:CACC:Cdonor_loss1.0000
19:18931974:A:ACdonor_gain1.0000

AlphaMissense

2330 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:18934396:G:CF106L1.000
19:18934396:G:TF106L1.000
19:18934397:A:GF106S1.000
19:18934398:A:GF106L1.000
19:18934408:A:CF102L1.000
19:18934408:A:TF102L1.000
19:18934409:A:GF102S1.000
19:18934410:A:GF102L1.000
19:18938377:A:CF93L1.000
19:18938377:A:TF93L1.000
19:18938378:A:GF93S1.000
19:18938379:A:GF93L1.000
19:18938384:A:GL91P1.000
19:18938384:A:TL91Q1.000
19:18938387:C:TG90D1.000
19:18938388:C:GG90R1.000
19:18938391:A:CY89D1.000
19:18938393:A:TV88D1.000
19:18938412:C:GD82H1.000
19:18938416:C:AW80C1.000
19:18938416:C:GW80C1.000
19:18938417:C:GW80S1.000
19:18938418:A:GW80R1.000
19:18938418:A:TW80R1.000
19:18938423:C:TG78E1.000
19:18938424:C:AG78W1.000
19:18938424:C:GG78R1.000
19:18938424:C:TG78R1.000
19:18938425:G:CF77L1.000
19:18938425:G:TF77L1.000

dbSNP variants (sampled 300 via entrez): RS1000062098 (19:18928985 C>A), RS1000208428 (19:18936798 G>A), RS1000262151 (19:18936538 T>C), RS1000374083 (19:18930961 T>G), RS1000418128 (19:18934825 A>G), RS1000481184 (19:18941974 G>A), RS1000789075 (19:18934601 G>C), RS1000838409 (19:18939832 C>A,T), RS1000891583 (19:18931140 G>A), RS1000931303 (19:18940043 G>A), RS1001088873 (19:18940736 CAGT>C), RS1001243172 (19:18942289 C>A,G), RS1001540152 (19:18940565 G>A), RS1001720369 (19:18940488 C>A,T), RS1002072452 (19:18928992 A>C,G)

Disease associations

OMIM: gene MIM:604800 | disease phenotypes: MIM:614622

GenCC curated gene-disease

Mondo (1): keratoconus 5 (MONDO:0013830)

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression, increases methylation3
Benzo(a)pyrenedecreases methylation, increases expression2
Estradiolaffects cotreatment, decreases expression, increases expression2
Silicon Dioxideincreases expression2
Tobacco Smoke Pollutionincreases expression, affects expression2
FR900359increases phosphorylation1
methyleugenolincreases expression1
triphenyl phosphateaffects expression1
glycidyl methacrylateincreases expression1
beta-lapachonedecreases expression1
sodium arseniteincreases expression1
cupric chlorideincreases expression1
arsenic disulfidedecreases expression1
2-palmitoylglycerolincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
abrineincreases expression1
LDN 193189affects cotreatment, increases expression1
(+)-JQ1 compounddecreases expression1
Temozolomideincreases expression1
Arsenic Trioxideaffects reaction, decreases expression1
Acetaminophenincreases expression1
Air Pollutantsaffects expression, increases abundance1
Arsenicaffects methylation1
Caffeinedecreases phosphorylation1
Dactinomycinincreases expression1
Doxorubicindecreases expression1
Leaddecreases expression1
Lithiumdecreases expression1
Methyl Methanesulfonateincreases expression1
N-Nitrosopyrrolidineincreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): keratoconus 5