HPCA hippocalcin [Homo sapiens (human)] - Gene

Summary

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

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
HPCA mutations lead to recessively inherited dystonia
Title: HPCA confirmed as a genetic cause of DYT2-like dystonia phenotype.
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].
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?
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.
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.
Mutations in HPCA cause autosomal-recessive primary isolated dystonia.
Title: Mutations in HPCA cause autosomal-recessive primary isolated dystonia.
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.
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.
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

RH15950 (e-PCR)
- UniSTS:7774

G29323 (e-PCR)
- UniSTS:78517

D1S285E (e-PCR)
- UniSTS:147426

G34862 (e-PCR)
- UniSTS:50679

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

NG_042176.1 RefSeqGene

Range

5405..13560

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

32885996..32894646

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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]
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

NC_060925.1 Alternate T2T-CHM13v2.0

Range

32745769..32754441

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

B2R9T3, D3DPQ7, P32076, P41211, P70510, P84074
XM_054336226.1 → XP_054192201.1 neuron-specific calcium-binding protein hippocalcin isoform X1

UniProtKB/Swiss-Prot

B2R9T3, D3DPQ7, P32076, P41211, P70510, P84074