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HOMER2 homer scaffold protein 2 [ Homo sapiens (human) ]

Gene ID: 9455, updated on 3-Apr-2024

Summary

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Official Symbol
HOMER2provided by HGNC
Official Full Name
homer scaffold protein 2provided by HGNC
Primary source
HGNC:HGNC:17513
See related
Ensembl:ENSG00000103942 MIM:604799; AllianceGenome:HGNC:17513
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CPD; ACPD; DFNA68; VESL-2; HOMER-2
Summary
This gene encodes a member of the homer family of dendritic proteins. Members of this family regulate group 1 metabotrophic glutamate receptor function. The encoded protein is a postsynaptic density scaffolding protein. Alternative splicing results in multiple transcript variants. Two related pseudogenes have been identified on chromosome 14. [provided by RefSeq, Jun 2011]
Expression
Broad expression in prostate (RPKM 9.3), pancreas (RPKM 6.8) and 16 other tissues See more
Orthologs
mouse all
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Genomic context

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See HOMER2 in Genome Data Viewer
Location:
15q25.2
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (82834661..82986157, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (80701241..80850554, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (83517735..83621472, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene actin gamma 1 pseudogene 17 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9965 Neighboring gene MPRA-validated peak2404 silencer Neighboring gene small Cajal body-specific RNA 15 Neighboring gene small nucleolar RNA host gene 21 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:83450989-83451154 Neighboring gene fibronectin type III and SPRY domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9966 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6754 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6755 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6756 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:83501038-83502237 Neighboring gene WASP homolog associated with actin, golgi membranes and microtubules Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:83518553-83519328 Neighboring gene uncharacterized LOC105370928 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:83620722-83621222 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:83632148-83632648 Neighboring gene Sharpr-MPRA regulatory region 12194 Neighboring gene chromosome 15 open reading frame 40 Neighboring gene uncharacterized LOC124903542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9968 Neighboring gene RNA guanine-7 methyltransferase activating subunit Neighboring gene BTB domain containing 1 Neighboring gene fatty acid binding protein 5 pseudogene 8

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A Novel Truncating Mutation in HOMER2 Causes Nonsyndromic Progressive DFNA68 Hearing Loss in a Spanish Family. Lachgar M, et al. Genes (Basel), 2021 Mar 12. PMID 33809266, Free PMC Article
  2. Whole exome sequencing identified a second pathogenic variant in HOMER2 for autosomal dominant non-syndromic deafness. Lu X, et al. Clin Genet, 2018 Nov. PMID 30047143
  3. Overexpression of HOMER2 predicts better outcome in low-grade endometrioid endometrial adenocarcinoma. Mhawech-Fauceglia P, et al. Pathology, 2018 Aug. PMID 29891190, Free PMC Article
  4. Novel candidate colorectal cancer biomarkers identified by methylation microarray-based scanning. Mori Y, et al. Endocr Relat Cancer, 2011 Aug. PMID 21636702, Free PMC Article
  5. Recurrent microdeletions of 15q25.2 are associated with increased risk of congenital diaphragmatic hernia, cognitive deficits and possibly Diamond--Blackfan anaemia. Wat MJ, et al. J Med Genet, 2010 Nov. PMID 20921022, Free PMC Article

See all (46) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Identification and in vivo functional investigation of a HOMER2 nonstop variant causing hearing loss.
    Title: Identification and in vivo functional investigation of a HOMER2 nonstop variant causing hearing loss.
  2. A Novel Truncating Mutation in HOMER2 Causes Nonsyndromic Progressive DFNA68 Hearing Loss in a Spanish Family.
    Title: A Novel Truncating Mutation in HOMER2 Causes Nonsyndromic Progressive DFNA68 Hearing Loss in a Spanish Family.
  3. we have identified a distinct, novel insertion variant in HOMER2, which provides validating evidence that HOMER2 is indeed required for normal hearing. Its sequence alteration is responsible for late-onset, autosomal dominant, non-syndromic, SNHL in humans.
    Title: Whole exome sequencing identified a second pathogenic variant in HOMER2 for autosomal dominant non-syndromic deafness.
  4. that HOMER2 may be involved in tumourigenesis of endometrioid uterine tumours
    Title: Overexpression of HOMER2 predicts better outcome in low-grade endometrioid endometrial adenocarcinoma.
  5. Homer1 and Homer2 might be considered as novel diagnostic biomarkers for large-artery atherosclerosis stroke.
    Title: Diagnostic Potential of Differentially Expressed Homer1 and Homer2 in Ischemic Stroke.
  6. This study showed that HOMER2 (rs1256429; intronic, p = 8.7 x 10(1)) associated with Alzheimer disease.
    Title: Linking Genetics of Brain Changes to Alzheimer's Disease: Sparse Whole Genome Association Scan of Regional MRI Volumes in the ADNI and AddNeuroMed Cohorts.
  7. These data provide compelling evidence that HOMER2 is required for normal hearing and that its sequence alteration in humans leads to ADNSHL through a dominant-negative mode of action
    Title: HOMER2, a stereociliary scaffolding protein, is essential for normal hearing in humans and mice.
  8. monitored Homer1 and Homer2 expression and subcellular localization in skeletal muscle biopsies following 60 days of bedrest
    Title: Expression and regulation of Homer in human skeletal muscle during neuromuscular junction adaptation to disuse and exercise.
  9. Haplotypes of the HOMER 1 and 2 genes are unlikely to play a major role in the pathophysiology of alcohol dependence.
    Title: No association of alcohol dependence with HOMER 1 and 2 genetic variants.
  10. This study supports a role for HOMER2 gene in schizophrenia susceptibility.
    Title: Replicated genetic evidence supports a role for HOMER2 in schizophrenia.
Submit: New GeneRIF Correction See all GeneRIFs (13)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Autosomal dominant nonsyndromic hearing loss 68
MedGen: C4225240 OMIM: 616707 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables G protein-coupled glutamate receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables actin binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables synaptic receptor adaptor activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in G protein-coupled glutamate receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in behavioral response to cocaine IEA
Inferred from Electronic Annotation
more info
  
involved_in calcium-mediated signaling using intracellular calcium source IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of calcineurin-NFAT signaling cascade IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of interleukin-2 production IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of G protein-coupled receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of store-operated calcium entry IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in apical part of cell IEA
Inferred from Electronic Annotation
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in dendrite IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
  
located_in intracellular organelle ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in postsynaptic density IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in stereocilium tip ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
homer protein homolog 2
Names
cupidin
homer homolog 2
homer homolog 3
homer scaffolding protein 2
homer, neuronal immediate early gene, 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_029435.3 RefSeqGene

    Range
    38437..142174
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_004839.4 → NP_004830.2  homer protein homolog 2 isoform 1

    See identical proteins and their annotated locations for NP_004830.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1), also known as HOMER-2A, uses an alternate in-frame splice site in the central coding region, compared to variant 2, resulting in an isoform (1) that is shorter than isoform 2.
    Source sequence(s)
    BC012109
    Consensus CDS
    CCDS45336.1
    UniProtKB/TrEMBL
    A8K9Q7
    Related
    ENSP00000407634.2, ENST00000450735.7
    Conserved Domains (2) summary
    cd01206
    Location:3 → 111
    EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
    TIGR02168
    Location:93 → 322
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type

  2. NM_199330.3 → NP_955362.1  homer protein homolog 2 isoform 2

    See identical proteins and their annotated locations for NP_955362.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), also known as HOMER-2B, represents the longer transcript and encodes the longer isoform (2).
    Source sequence(s)
    BI666912, CB321822, Y19026
    Consensus CDS
    CCDS45334.1
    UniProtKB/Swiss-Prot
    O95269, O95349, Q9NSB6, Q9NSB7, Q9NSB8, Q9UNT7
    UniProtKB/TrEMBL
    A8K9Q7
    Related
    ENSP00000305632.8, ENST00000304231.12
    Conserved Domains (2) summary
    cd01206
    Location:3 → 111
    EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
    cl25732
    Location:93 → 333
    SMC_N; RecF/RecN/SMC N terminal domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    82834661..82986157 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047433359.1 → XP_047289315.1  homer protein homolog 2 isoform X7

  2. XM_047433356.1 → XP_047289312.1  homer protein homolog 2 isoform X5

  3. XM_011522232.3 → XP_011520534.1  homer protein homolog 2 isoform X1

    See identical proteins and their annotated locations for XP_011520534.1

    UniProtKB/TrEMBL
    A8K9Q7
    Conserved Domains (2) summary
    cd01206
    Location:13 → 121
    EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
    cl25732
    Location:103 → 343
    SMC_N; RecF/RecN/SMC N terminal domain

  4. XM_047433360.1 → XP_047289316.1  homer protein homolog 2 isoform X8

  5. XM_047433358.1 → XP_047289314.1  homer protein homolog 2 isoform X7

  6. XM_047433355.1 → XP_047289311.1  homer protein homolog 2 isoform X4

    UniProtKB/Swiss-Prot
    O95269, O95349, Q9NSB6, Q9NSB7, Q9NSB8, Q9UNT7

  7. XM_047433357.1 → XP_047289313.1  homer protein homolog 2 isoform X5

  8. XM_006720775.4 → XP_006720838.1  homer protein homolog 2 isoform X1

    See identical proteins and their annotated locations for XP_006720838.1

    UniProtKB/TrEMBL
    A8K9Q7
    Conserved Domains (2) summary
    cd01206
    Location:13 → 121
    EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
    cl25732
    Location:103 → 343
    SMC_N; RecF/RecN/SMC N terminal domain

  9. XM_005272449.5 → XP_005272506.1  homer protein homolog 2 isoform X6

    See identical proteins and their annotated locations for XP_005272506.1

    UniProtKB/TrEMBL
    A8K9Q7
    Conserved Domains (2) summary
    cd01206
    Location:3 → 111
    EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
    cl25732
    Location:149 → 338
    SMC_N; RecF/RecN/SMC N terminal domain

  10. XM_006720776.5 → XP_006720839.1  homer protein homolog 2 isoform X3

    UniProtKB/TrEMBL
    A8K9Q7
    Conserved Domains (2) summary
    cd01206
    Location:3 → 111
    EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
    cl23720
    Location:221 → 334
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

  11. XM_047433361.1 → XP_047289317.1  homer protein homolog 2 isoform X8

  12. XM_011522233.4 → XP_011520535.1  homer protein homolog 2 isoform X2

    UniProtKB/TrEMBL
    A8K9Q7
    Conserved Domains (2) summary
    cd01206
    Location:11 → 119
    EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
    cl23720
    Location:229 → 342
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

  13. XM_047433362.1 → XP_047289318.1  homer protein homolog 2 isoform X8

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    80701241..80850554 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054379235.1 → XP_054235210.1  homer protein homolog 2 isoform X7

  2. XM_054379231.1 → XP_054235206.1  homer protein homolog 2 isoform X5

  3. XM_054379227.1 → XP_054235202.1  homer protein homolog 2 isoform X1

  4. XM_054379236.1 → XP_054235211.1  homer protein homolog 2 isoform X8

  5. XM_054379234.1 → XP_054235209.1  homer protein homolog 2 isoform X7

  6. XM_054379230.1 → XP_054235205.1  homer protein homolog 2 isoform X4

    UniProtKB/Swiss-Prot
    O95269, O95349, Q9NSB6, Q9NSB7, Q9NSB8, Q9UNT7

  7. XM_054379232.1 → XP_054235207.1  homer protein homolog 2 isoform X5

  8. XM_054379226.1 → XP_054235201.1  homer protein homolog 2 isoform X1

  9. XM_054379233.1 → XP_054235208.1  homer protein homolog 2 isoform X6

  10. XM_054379229.1 → XP_054235204.1  homer protein homolog 2 isoform X3

  11. XM_054379228.1 → XP_054235203.1  homer protein homolog 2 isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_199331.2: Suppressed sequence

    Description
    NM_199331.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

  2. NM_199332.2: Suppressed sequence

    Description
    NM_199332.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NSB8.1 GenPept UniProtKB/Swiss-Prot:Q9NSB8

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