U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

HPCA hippocalcin [ Homo sapiens (human) ]

Gene ID: 3208, updated on 3-Apr-2024

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
1p35.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (32885996..32894646)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (32745769..32754441)
105.20220307 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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. HPCA confirmed as a genetic cause of DYT2-like dystonia phenotype. Atasu B, et al. Mov Disord, 2018 Aug. PMID 30145809
  2. DYT2 screening in early-onset isolated dystonia. Carecchio M, et al. Eur J Paediatr Neurol, 2017 Mar. PMID 27771228
  3. HPCA-related dystonia: Too rare to be found? Dobričić V, et al. Mov Disord, 2016 Jul. PMID 27145302
  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. 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

See all (33) 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

Go to the top of the page Help

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

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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 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

Go to the top of the page Help
Preferred Names
neuron-specific calcium-binding protein hippocalcin
Names
calcium-binding protein BDR-2
dystonia 2, torsion (autosomal recessive)

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_2023_10

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

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

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

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous