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Aliases for HPCAL1 Gene

Aliases for HPCAL1 Gene

  • Hippocalcin Like 1 2 3 5
  • Calcium-Binding Protein BDR-1 2 3 4
  • Visinin-Like Protein 3 2 3 4
  • VILIP-3 3 4
  • BDR1 3 4
  • HLP2 3 4
  • Hippocalcin-Like Protein 1 3

External Ids for HPCAL1 Gene

Previous GeneCards Identifiers for HPCAL1 Gene

  • GC02P010228
  • GC02P010494
  • GC02P010464
  • GC02P010443

Summaries for HPCAL1 Gene

Entrez Gene Summary for HPCAL1 Gene

  • The protein encoded by this gene is a member of neuron-specific calcium-binding proteins family found in the retina and brain. It is highly similar to human hippocalcin protein and nearly identical to the rat and mouse hippocalcin like-1 proteins. It may be involved in the calcium-dependent regulation of rhodopsin phosphorylation and may be of relevance for neuronal signalling in the central nervous system. Several alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Apr 2012]

GeneCards Summary for HPCAL1 Gene

HPCAL1 (Hippocalcin Like 1) is a Protein Coding gene. Among its related pathways are Visual Cycle in Retinal Rods. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is HPCA.

UniProtKB/Swiss-Prot for HPCAL1 Gene

  • May be involved in the calcium-dependent regulation of rhodopsin phosphorylation.

Gene Wiki entry for HPCAL1 Gene

Additional gene information for HPCAL1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HPCAL1 Gene

Genomics for HPCAL1 Gene

GeneHancer (GH) Regulatory Elements for HPCAL1 Gene

Promoters and enhancers for HPCAL1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J010300 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 650.7 +0.5 537 5.8 HDGF PKNOX1 FOXA2 SMAD1 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 HPCAL1 LOC101929691 KLF11 LOC101929882 PIR41580
GH02J010355 Promoter/Enhancer 1.2 EPDnew ENCODE dbSUPER 662.1 +53.3 53286 1.2 NFIC POLR2A NFIB SMARCC2 CEBPB HPCAL1 SNORA80B PIR41580
GH02J010403 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 56.9 +105.1 105136 8.3 HDGF PKNOX1 ARNT ARID4B NEUROD1 SIN3A YBX1 DMAP1 ZNF2 IRF4 HPCAL1 LOC101929882 LOC101929691 SNORA80B PIR41580
GH02J010327 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 46.1 +27.8 27820 6.1 HDGF PKNOX1 SMAD1 ARNT ZFP64 DMAP1 ZNF121 ZNF766 ATF7 ZNF263 HPCAL1 TAF1B LOC101929691 LOC101929882 SNORA80B PIR41580
GH02J010399 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 25.2 +98.6 98560 3.6 FOXA2 MLX ARID4B DMAP1 ZNF48 YY1 FOS RUNX3 RXRA SP5 HPCAL1 LOC101929691 SNORA80B KLF11 PIR41580
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HPCAL1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HPCAL1 gene promoter:
  • Meis-1b
  • Meis-1a
  • Meis-1
  • AP-2beta
  • HNF-4alpha2
  • HNF-4alpha1

Genomic Locations for HPCAL1 Gene

Genomic Locations for HPCAL1 Gene
124,729 bases
Plus strand
124,729 bases
Plus strand

Genomic View for HPCAL1 Gene

Genes around HPCAL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HPCAL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HPCAL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HPCAL1 Gene

Proteins for HPCAL1 Gene

  • Protein details for HPCAL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Hippocalcin-like protein 1
    Protein Accession:
    Secondary Accessions:
    • Q969S5

    Protein attributes for HPCAL1 Gene

    193 amino acids
    Molecular mass:
    22313 Da
    Quaternary structure:
    No Data Available
    • Probably binds two or three calcium ions.

    Three dimensional structures from OCA and Proteopedia for HPCAL1 Gene

neXtProt entry for HPCAL1 Gene

Post-translational modifications for HPCAL1 Gene

  • Ubiquitination at Lys7
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for HPCAL1 Gene

Domains & Families for HPCAL1 Gene

Gene Families for HPCAL1 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for HPCAL1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the recoverin family.
  • Belongs to the recoverin family.
genes like me logo Genes that share domains with HPCAL1: view

Function for HPCAL1 Gene

Molecular function for HPCAL1 Gene

UniProtKB/Swiss-Prot Function:
May be involved in the calcium-dependent regulation of rhodopsin phosphorylation.
GENATLAS Biochemistry:
calcium binding protein,hippocalcin-like,expressed in brain

Phenotypes From GWAS Catalog for HPCAL1 Gene

Gene Ontology (GO) - Molecular Function for HPCAL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI 16189514
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with HPCAL1: view
genes like me logo Genes that share phenotypes with HPCAL1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for HPCAL1

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HPCAL1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HPCAL1 Gene

Localization for HPCAL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HPCAL1 Gene

Membrane; Lipid-anchor.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HPCAL1 gene
Compartment Confidence
extracellular 5
cytosol 3
nucleus 2

Gene Ontology (GO) - Cellular Components for HPCAL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0070062 extracellular exosome HDA --
genes like me logo Genes that share ontologies with HPCAL1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HPCAL1 Gene

Pathways & Interactions for HPCAL1 Gene

SuperPathways for HPCAL1 Gene

SuperPathway Contained pathways
1 Visual Cycle in Retinal Rods
genes like me logo Genes that share pathways with HPCAL1: view

Pathways by source for HPCAL1 Gene

1 Qiagen pathway for HPCAL1 Gene

Gene Ontology (GO) - Biological Process for HPCAL1 Gene


No data available for SIGNOR curated interactions for HPCAL1 Gene

Drugs & Compounds for HPCAL1 Gene

(1) Drugs for HPCAL1 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
genes like me logo Genes that share compounds with HPCAL1: view

Transcripts for HPCAL1 Gene

Unigene Clusters for HPCAL1 Gene

Hippocalcin-like 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HPCAL1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HPCAL1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13a · 13b · 13c · 13d
SP1: - - - - - - - -
SP2: - - - - - - - - -
SP3: - - - - -
SP5: - - - - - -
SP6: - - - -
SP8: - - -
SP9: - -

Relevant External Links for HPCAL1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HPCAL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HPCAL1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HPCAL1 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x5.0) and Brain - Cerebellum (x4.4).

Protein differential expression in normal tissues from HIPED for HPCAL1 Gene

This gene is overexpressed in Bone (21.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HPCAL1 Gene

Protein tissue co-expression partners for HPCAL1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HPCAL1 Gene:


SOURCE GeneReport for Unigene cluster for HPCAL1 Gene:


Evidence on tissue expression from TISSUES for HPCAL1 Gene

  • Nervous system(4.7)
  • Liver(4.2)
  • Pancreas(4.2)
genes like me logo Genes that share expression patterns with HPCAL1: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HPCAL1 Gene

Orthologs for HPCAL1 Gene

This gene was present in the common ancestor of animals.

Orthologs for HPCAL1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HPCAL1 34 33
  • 99.31 (n)
(Monodelphis domestica)
Mammalia HPCAL1 34
  • 99 (a)
(Canis familiaris)
Mammalia HPCAL1 34 33
  • 94.13 (n)
(Bos Taurus)
Mammalia HPCAL1 34 33
  • 93.78 (n)
(Rattus norvegicus)
Mammalia Hpcal1 33
  • 92.4 (n)
(Mus musculus)
Mammalia Hpcal1 16 34 33
  • 92.06 (n)
(Ornithorhynchus anatinus)
Mammalia HPCAL1 34
  • 90 (a)
(Gallus gallus)
Aves HPCAL1 34 33
  • 87.74 (n)
(Anolis carolinensis)
Reptilia HPCAL1 34
  • 99 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hpcal1 33
  • 82.9 (n)
(Danio rerio)
Actinopterygii HPCAL1 34
  • 91 (a)
zgc:63695 33
  • 83.42 (n)
zgc73126 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007247 33
  • 76.72 (n)
fruit fly
(Drosophila melanogaster)
Insecta Nca 35 33
  • 70.37 (n)
CG5744 35
  • 59 (a)
Frq 35
  • 58 (a)
CG7646 35
  • 47 (a)
(Caenorhabditis elegans)
Secernentea ncs-3 35
  • 55 (a)
ncs-2 35
  • 51 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 80 (a)
Species where no ortholog for HPCAL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for HPCAL1 Gene

Gene Tree for HPCAL1 (if available)
Gene Tree for HPCAL1 (if available)
Evolutionary constrained regions (ECRs) for HPCAL1: view image

Paralogs for HPCAL1 Gene

(24) SIMAP similar genes for HPCAL1 Gene using alignment to 5 proteins:

  • C9JW46_HUMAN
  • E9PC71_HUMAN
genes like me logo Genes that share paralogs with HPCAL1: view

Variants for HPCAL1 Gene

Sequence variations from dbSNP and Humsavar for HPCAL1 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000024924 -- 10,419,555(+) AGAG/AG intron_variant
rs1000047474 -- 10,410,921(+) C/G intron_variant
rs1000048108 -- 10,338,826(+) G/T genic_upstream_transcript_variant, intron_variant
rs1000075751 -- 10,300,967(+) C/T upstream_transcript_variant
rs1000086534 -- 10,353,608(+) C/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for HPCAL1 Gene

Variant ID Type Subtype PubMed ID
dgv587e201 CNV deletion 23290073
dgv679e199 CNV deletion 23128226
esv1007136 CNV insertion 20482838
esv2719644 CNV deletion 23290073
esv2719646 CNV deletion 23290073
esv2719648 CNV deletion 23290073
esv2719650 CNV deletion 23290073
esv27364 CNV loss 19812545
esv3395574 CNV duplication 20981092
esv3446200 CNV insertion 20981092
esv3589797 CNV loss 21293372
esv3589798 CNV loss 21293372
nsv1007185 CNV gain 25217958
nsv1071973 CNV deletion 25765185
nsv1077349 CNV duplication 25765185
nsv2605 CNV insertion 18451855
nsv508827 CNV insertion 20534489

Variation tolerance for HPCAL1 Gene

Residual Variation Intolerance Score: 32.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.36; 7.94% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HPCAL1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HPCAL1 Gene

Disorders for HPCAL1 Gene

Additional Disease Information for HPCAL1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for HPCAL1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HPCAL1 Gene

Publications for HPCAL1 Gene

  1. Hypertension susceptibility genes on chromosome 2p24-p25 in a general Japanese population. (PMID: 15834280) Kamide K … Miyata T (Journal of hypertension 2005) 3 22 44 58
  2. Molecular cloning of a novel calcium-binding protein structurally related to hippocalcin from human brain and chromosomal mapping of its gene. (PMID: 8038222) Kobayashi M … Noguchi T (Biochimica et biophysica acta 1994) 2 3 4 58
  3. Functional contribution of Ca2+ and Mg2+ to the intermolecular interaction of visinin-like proteins. (PMID: 16703469) Jheng FF … Chang LS (The protein journal 2006) 3 22 58
  4. Neuronal calcium sensor protein visinin-like protein-3 interacts with microsomal cytochrome b5 in a Ca2+-dependent manner. (PMID: 14739275) Oikawa K … Tateno M (The Journal of biological chemistry 2004) 2 3 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for HPCAL1 Gene

Sources for HPCAL1 Gene

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