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    HS1BP3 HCLS1 binding protein 3 [ Homo sapiens (human) ]

    Gene ID: 64342, updated on 5-Mar-2024

    Summary

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    Official Symbol
    HS1BP3provided by HGNC
    Official Full Name
    HCLS1 binding protein 3provided by HGNC
    Primary source
    HGNC:HGNC:24979
    See related
    Ensembl:ENSG00000118960 MIM:609359; AllianceGenome:HGNC:24979
    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
    ETM2; HS1-BP3
    Summary
    The protein encoded by this gene shares similarity with mouse Hs1bp3, an Hcls1/Hs1-interacting protein that may be involved in lymphocyte activation. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in kidney (RPKM 5.9), adrenal (RPKM 5.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HS1BP3 in Genome Data Viewer
    Location:
    2p24.1
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (20553861..20651098, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (20587197..20684403, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (20817578..20850858, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985856 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20687149-20687946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11209 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11210 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11208 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15392 Neighboring gene uncharacterized LOC102724948 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20732136-20733133 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20734131-20735128 Neighboring gene NDUFAF2 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20741509-20742494 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20742495-20743479 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11211 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20760853-20761375 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20763577-20764533 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20771337-20771837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20774924-20775424 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15393 Neighboring gene VISTA enhancer hs2384 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20780177-20780738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20780739-20781299 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20784034-20784599 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20784600-20785164 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20785731-20786294 Neighboring gene HS1BP3 intronic transcript 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20798625-20799569 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20808925-20809424 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20814716-20815668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20816583-20817474 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15396 Neighboring gene ribosomal protein S25 pseudogene 3 Neighboring gene uncharacterized LOC124907740 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15397 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20840103-20840604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15399 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20850539-20851276 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15400 Neighboring gene uncharacterized LOC105373466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20865647-20866477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11213 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11214 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11215 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15401 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20869955-20870900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15402 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15404 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15405 Neighboring gene growth differentiation factor 7

    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. Extended study of A265G variant of HS1BP3 in essential tremor and Parkinson disease. Deng H, et al. Neurology, 2005 Aug 23. PMID 16116142
    2. A variant in the HS1-BP3 gene is associated with familial essential tremor. Higgins JJ, et al. Neurology, 2005 Feb 8. PMID 15699368, Free PMC Article
    3. DRD3 Ser9Gly and HS1BP3 Ala265Gly are not associated with Parkinson disease. Keeling BH, et al. Neurosci Lett, 2009 Sep 18. PMID 19524641, Free PMC Article
    4. HS1BP3 negatively regulates autophagy by modulation of phosphatidic acid levels. Holland P, et al. Nat Commun, 2016 Dec 22. PMID 28004827, Free PMC Article
    5. Human HS1BP3 induces cell apoptosis and activates AP-1. Shi T, et al. BMB Rep, 2011 Jun. PMID 21699750

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. HS1BP3 is localized to ATG16L1- and ATG9-positive autophagosome precursors and we show that HS1BP3 binds phosphatidic acid (PA) through its PX domain. Furthermore, we find the total PA content of cells to be significantly upregulated in the absence of HS1BP3.
      Title: HS1BP3 negatively regulates autophagy by modulation of phosphatidic acid levels.
    2. Results suggest that HS1BP3 regulates apoptosis via HS1 and stimulates AP-1-mediated transcription.
      Title: Human HS1BP3 induces cell apoptosis and activates AP-1.
    3. Results do not support a role for these DRD3 and HS1BP3 variants in PD.
      Title: DRD3 Ser9Gly and HS1BP3 Ala265Gly are not associated with Parkinson disease.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: DRD3 Ser9Gly and HS1BP3 Ala265Gly are not associated with Parkinson disease.
    5. HS1PB3 protein is mutated in essential tremor combined with Parkinson disease.
      Title: Extended study of A265G variant of HS1BP3 in essential tremor and Parkinson disease.
    6. The 828C-->G mutation causes a substitution of a glycine for an alanine residue in the HS1-BP3 protein. It was found in 2 unrelated patients with familial essential tremor.
      Title: A variant in the HS1-BP3 gene is associated with familial essential tremor.
    Submit: New GeneRIF Correction

    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

    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

    Clone Names

    • FLJ14249

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidylinositol binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    HCLS1-binding protein 3
    Names
    HS1-binding protein 3
    HSP1BP-3

    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.

    mRNA and Protein(s)

    1. NM_022460.4 → NP_071905.3  HCLS1-binding protein 3

      See identical proteins and their annotated locations for NP_071905.3

      Status: REVIEWED

      Source sequence(s)
      AC012065, AK024311, BC027947, BC050636, BX354596, N62141
      Consensus CDS
      CCDS1700.1
      UniProtKB/Swiss-Prot
      B2RAW2, D6W529, Q53T59, Q86VC2, Q8N367
      Related
      ENSP00000305193.3, ENST00000304031.8
      Conserved Domains (1) summary
      cd06868
      Location:19 → 138
      PX_HS1BP3; The phosphoinositide binding Phox Homology domain of HS1BP3

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      20553861..20651098 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017004698.2 → XP_016860187.1  HCLS1-binding protein 3 isoform X3

    2. XM_017004696.3 → XP_016860185.1  HCLS1-binding protein 3 isoform X1

    3. XM_017004697.3 → XP_016860186.1  HCLS1-binding protein 3 isoform X2

    4. XM_017004701.2 → XP_016860190.1  HCLS1-binding protein 3 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      20587197..20684403 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054343369.1 → XP_054199344.1  HCLS1-binding protein 3 isoform X3

    2. XM_054343367.1 → XP_054199342.1  HCLS1-binding protein 3 isoform X1

    3. XM_054343368.1 → XP_054199343.1  HCLS1-binding protein 3 isoform X2

    4. XM_054343370.1 → XP_054199345.1  HCLS1-binding protein 3 isoform X4

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_106552.1: Suppressed sequence

      Description
      NM_106552.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q53T59.1 GenPept UniProtKB/Swiss-Prot:Q53T59

    Gene LinkOut

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