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    HPCA hippocalcin [ Homo sapiens (human) ]

    Gene ID: 3208, updated on 10-Dec-2024

    Summary

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    Official Symbol
    HPCAprovided by HGNC
    Official Full Name
    hippocalcinprovided by HGNC
    Primary source
    HGNC:HGNC:5144
    See related
    Ensembl:ENSG00000121905 MIM:142622; AllianceGenome:HGNC:5144
    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
    BDR2; DYT2
    Summary
    The protein encoded by this gene is a member of neuron-specific calcium-binding proteins family found in the retina and brain. This protein is associated with the plasma membrane. It has similarities to proteins located in the photoreceptor cells that regulate photosignal transduction in a calcium-sensitive manner. This protein displays recoverin activity and a calcium-dependent inhibition of rhodopsin kinase. It is identical to the rat and mouse hippocalcin proteins and thought to play an important role in neurons of the central nervous system in a number of species. [provided by RefSeq, Jul 2008]
    Expression
    Restricted expression toward brain (RPKM 57.7) See more
    Orthologs
    mouse all
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    Genomic context

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    See HPCA in Genome Data Viewer
    Location:
    1p35.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (32885996..32894646)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (32745769..32754441)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (33352092..33360247)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33333351-33333852 Neighboring gene fibronectin type III domain containing 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33338281-33339137 Neighboring gene uncharacterized LOC105378631 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_6918 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 610 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_6924 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 611 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33361017-33361615 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 612 Neighboring gene uncharacterized LOC105378632 Neighboring gene transmembrane protein 54 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33390633-33391176 Neighboring gene Sharpr-MPRA regulatory region 2329 Neighboring gene ring finger protein 19B Neighboring gene NANOG hESC enhancer GRCh37_chr1:33413154-33413655 Neighboring gene metallothionein-1E-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. The genetics of idiopathic torsion dystonia. Fletcher NA. J Med Genet, 1990 Jul. PMID 2203908, Free PMC Article
    2. High-affinity interaction of the N-terminal myristoylation motif of the neuronal calcium sensor protein hippocalcin with phosphatidylinositol 4,5-bisphosphate. O'Callaghan DW, et al. Biochem J, 2005 Oct 15. PMID 16053445, Free PMC Article
    3. Dynamics and calcium sensitivity of the Ca2+/myristoyl switch protein hippocalcin in living cells. O'Callaghan DW, et al. J Cell Biol, 2003 Nov 24. PMID 14638856, Free PMC Article
    4. Mutations in HPCA cause autosomal-recessive primary isolated dystonia. Charlesworth G, et al. Am J Hum Genet, 2015 Apr 2. PMID 25799108, Free PMC Article
    5. HPCA-related dystonia: Too rare to be found? Dobričić V, et al. Mov Disord, 2016 Jul. PMID 27145302

    See all (35) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. MiR-24-3p is an important miRNA that regulates neuronal differentiation by controlling HPCA expression.
      Title: MicroRNA-24-3p regulates neuronal differentiation by controlling hippocalcin expression.
    2. HPCA mutations lead to recessively inherited dystonia
      Title: HPCA confirmed as a genetic cause of DYT2-like dystonia phenotype.
    3. Current known dystonia genes include those related to dopamine metabolism, transcription factor, cytoskeleton, transport of glucose and sodium ion, etc.
      Title: [Dystonia genes and elucidation of their roles in dystonia pathogenesis].
    4. Sequence analysis of the HPCA gene in 505 patients with dystonia did not reveal variants in the coding regions of HPCA.
      Title: HPCA-related dystonia: Too rare to be found?
    5. hippocalcin forms oligomers upon calcium binding and directly interacts with VGCCs. The dystonia-causing mutations did not affect protein stability or folding. In common for both T71N and A190T mutants was an impaired calcium-dependent oligomerisation and increased intracellular calcium influx after KCl depolarisation.
      Title: Biophysical and functional characterization of hippocalcin mutants responsible for human dystonia.
    6. None of the patients enrolled was found to carry HPCA mutations, rising suspicion that these probably represent a very rare cause of dystonia in childhood-adolescence.
      Title: DYT2 screening in early-onset isolated dystonia.
    7. Mutations in HPCA cause autosomal-recessive primary isolated dystonia.
      Title: Mutations in HPCA cause autosomal-recessive primary isolated dystonia.
    8. analysis of a novel acetylation cycle of transcription co-activator Yes-associated protein that is downstream of Hippo pathway is triggered in response to SN2 alkylating agents
      Title: A novel acetylation cycle of transcription co-activator Yes-associated protein that is downstream of Hippo pathway is triggered in response to SN2 alkylating agents.
    9. diminished hippocalcin expression does not contribute to Huntington disease-related neurodegeneration
      Title: Diminished hippocalcin expression in Huntington's disease brain does not account for increased striatal neuron vulnerability as assessed in primary neurons.
    10. Hippocalcin and MLK2 were colocalized in the halo of Lewy bodies in Parkinson disease patients, and neither protein was detected in normal pigmented neurons.
      Title: Mixed lineage kinase 2 and hippocalcin are localized in Lewy bodies of Parkinson's disease.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    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
    Torsion dystonia 2
    MedGen: C1857093 OMIM: 224500 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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 actin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables calcium ion binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables identical protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables kinase 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 calcium-mediated signaling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular response to L-glutamate IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular response to calcium ion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cellular response to electrical stimulus IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in inner ear development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of protein targeting to membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of postsynaptic neurotransmitter receptor internalization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of voltage-gated calcium channel activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to Aroclor 1254 IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to ketamine IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in retina development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in axon IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in dendrite cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in dendrite membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in dendritic spine head IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in neuronal cell body membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in perikaryon IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    neuron-specific calcium-binding protein hippocalcin
    Names
    calcium-binding protein BDR-2
    dystonia 2, torsion (autosomal recessive)

    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_042176.1 RefSeqGene

      Range
      5405..13560
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_002143.3 → NP_002134.2  neuron-specific calcium-binding protein hippocalcin

      See identical proteins and their annotated locations for NP_002134.2

      Status: REVIEWED

      Source sequence(s)
      AC114493, BC001777
      Consensus CDS
      CCDS370.1
      UniProtKB/Swiss-Prot
      B2R9T3, D3DPQ7, P32076, P41211, P70510, P84074
      UniProtKB/TrEMBL
      Q5U068
      Related
      ENSP00000362566.3, ENST00000373467.4
      Conserved Domains (1) summary
      COG5126
      Location:13 → 179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      32885996..32894646
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005270792.4 → XP_005270849.1  neuron-specific calcium-binding protein hippocalcin isoform X1

      See identical proteins and their annotated locations for XP_005270849.1

      UniProtKB/Swiss-Prot
      B2R9T3, D3DPQ7, P32076, P41211, P70510, P84074
      UniProtKB/TrEMBL
      Q5U068
      Conserved Domains (1) summary
      COG5126
      Location:13 → 179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

    2. XM_017001118.3 → XP_016856607.1  neuron-specific calcium-binding protein hippocalcin isoform X1

      UniProtKB/Swiss-Prot
      B2R9T3, D3DPQ7, P32076, P41211, P70510, P84074
      UniProtKB/TrEMBL
      Q5U068
      Conserved Domains (1) summary
      COG5126
      Location:13 → 179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      32745769..32754441
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336227.1 → XP_054192202.1  neuron-specific calcium-binding protein hippocalcin isoform X1

      UniProtKB/Swiss-Prot
      B2R9T3, D3DPQ7, P32076, P41211, P70510, P84074
      UniProtKB/TrEMBL
      Q5U068

    2. XM_054336226.1 → XP_054192201.1  neuron-specific calcium-binding protein hippocalcin isoform X1

      UniProtKB/Swiss-Prot
      B2R9T3, D3DPQ7, P32076, P41211, P70510, P84074
      UniProtKB/TrEMBL
      Q5U068
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P84074.2 GenPept UniProtKB/Swiss-Prot:P84074

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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