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Aliases for HPCAL4 Gene

Aliases for HPCAL4 Gene

  • Hippocalcin Like 4 2 3 5
  • HLP4 3 4
  • Hippocalcin-Like Protein 4 3

External Ids for HPCAL4 Gene

Previous GeneCards Identifiers for HPCAL4 Gene

  • GC01M040174
  • GC01M039148
  • GC01M039608
  • GC01M039557
  • GC01M039813
  • GC01M039916
  • GC01M038263

Summaries for HPCAL4 Gene

Entrez Gene Summary for HPCAL4 Gene

  • The protein encoded by this gene is highly similar to human hippocalcin protein and hippocalcin like-1 protein. It also has similarity to rat neural visinin-like Ca2+-binding protein-type 1 and 2 proteins. This encoded protein may be involved in the calcium-dependent regulation of rhodopsin phosphorylation. The transcript of this gene has multiple polyadenylation sites. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]

GeneCards Summary for HPCAL4 Gene

HPCAL4 (Hippocalcin Like 4) is a Protein Coding gene. Diseases associated with HPCAL4 include Holoprosencephaly 3. Among its related pathways are Visual Cycle in Retinal Rods. Gene Ontology (GO) annotations related to this gene include calcium ion binding and protein C-terminus binding. An important paralog of this gene is VSNL1.

UniProtKB/Swiss-Prot for HPCAL4 Gene

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

Gene Wiki entry for HPCAL4 Gene

Additional gene information for HPCAL4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HPCAL4 Gene

Genomics for HPCAL4 Gene

GeneHancer (GH) Regulatory Elements for HPCAL4 Gene

Promoters and enhancers for HPCAL4 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
GH01J039690 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 669.4 0.0 -42 1.8 PKNOX1 ZSCAN4 INSM2 KLF17 SIN3A BMI1 ZNF2 ZNF335 FOS SP3 HPCAL4 PPIE EXO5 MYCBP RLF TRIT1
GH01J039645 Enhancer 1.1 Ensembl ENCODE dbSUPER 24.3 +44.8 44802 3.4 BCOR TAF9B MAX SIN3A ZMYM3 TCF12 ZFHX2 POLR2A EGR1 ADNP HPCAL4 NT5C1A PPIE PABPC4 HEYL OXCT2
GH01J039638 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 10.7 +52.0 52042 2.5 ATF1 SIN3A ZNF2 YY1 ZNF121 GLIS2 ZNF213 ZNF143 ATF7 SP3 HEYL EXO5 PPIE HPCAL4 PPIEL OXCT2P1 ENSG00000225903 OXCT2
GH01J039652 Enhancer 0.9 ENCODE dbSUPER 24 +38.9 38876 1.4 CTCF RB1 ZNF384 ZNF2 RAD21 ZEB1 ZNF664 CC2D1A ZFHX2 CTBP1 HPCAL4 PPIE EXO5 PABPC4 PPIEL TRIT1 HEYL NT5C1A
GH01J039670 Promoter/Enhancer 1.2 EPDnew ENCODE 13.1 +19.9 19924 2 CTCF ZBTB6 RB1 ZBTB21 SUZ12 TEAD4 RAD21 ZNF335 ZFHX2 PATZ1 NT5C1A HPCAL4 OXCT2 HEYL
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HPCAL4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HPCAL4 gene promoter:
  • Max1
  • POU2F2C
  • Sp1
  • Oct-B1
  • oct-B2
  • oct-B3
  • POU2F1
  • POU2F1a
  • POU2F2
  • POU2F2B

Genomic Locations for HPCAL4 Gene

Genomic Locations for HPCAL4 Gene
13,063 bases
Minus strand
13,042 bases
Minus strand

Genomic View for HPCAL4 Gene

Genes around HPCAL4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HPCAL4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HPCAL4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HPCAL4 Gene

Proteins for HPCAL4 Gene

  • Protein details for HPCAL4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Hippocalcin-like protein 4
    Protein Accession:
    Secondary Accessions:
    • B2R5U2
    • D3DPU1
    • Q5TG97
    • Q8N611

    Protein attributes for HPCAL4 Gene

    191 amino acids
    Molecular mass:
    22202 Da
    Quaternary structure:
    No Data Available
    • Probably binds two or three calcium ions.

neXtProt entry for HPCAL4 Gene

Post-translational modifications for HPCAL4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HPCAL4 Gene

No data available for DME Specific Peptides for HPCAL4 Gene

Domains & Families for HPCAL4 Gene

Gene Families for HPCAL4 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for HPCAL4 Gene

Suggested Antigen Peptide Sequences for HPCAL4 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 HPCAL4: view

Function for HPCAL4 Gene

Molecular function for HPCAL4 Gene

UniProtKB/Swiss-Prot Function:
May be involved in the calcium-dependent regulation of rhodopsin phosphorylation.

Phenotypes From GWAS Catalog for HPCAL4 Gene

Gene Ontology (GO) - Molecular Function for HPCAL4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005246 calcium channel regulator activity IEA --
GO:0005509 calcium ion binding TAS,IEA --
GO:0005515 protein binding IPI 16189514
GO:0008022 protein C-terminus binding IEA --
GO:0019904 protein domain specific binding IEA --
genes like me logo Genes that share ontologies with HPCAL4: view
genes like me logo Genes that share phenotypes with HPCAL4: view

Animal Models for HPCAL4 Gene

MGI Knock Outs for HPCAL4:
  • Hpcal4 Hpcal4<tm1.1(KOMP)Vlcg>

Animal Model Products

miRNA for HPCAL4 Gene

miRTarBase miRNAs that target HPCAL4

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HPCAL4 Gene

Localization for HPCAL4 Gene

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 HPCAL4 gene
Compartment Confidence
cytosol 3
peroxisome 2
extracellular 1
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HPCAL4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IDA --
genes like me logo Genes that share ontologies with HPCAL4: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for HPCAL4 Gene

Pathways & Interactions for HPCAL4 Gene

SuperPathways for HPCAL4 Gene

SuperPathway Contained pathways
1 Visual Cycle in Retinal Rods
genes like me logo Genes that share pathways with HPCAL4: view

Pathways by source for HPCAL4 Gene

1 Qiagen pathway for HPCAL4 Gene

Gene Ontology (GO) - Biological Process for HPCAL4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction IEA --
GO:0007417 central nervous system development TAS 10520747
GO:0065009 regulation of molecular function IEA --
genes like me logo Genes that share ontologies with HPCAL4: view

No data available for SIGNOR curated interactions for HPCAL4 Gene

Drugs & Compounds for HPCAL4 Gene

(1) Drugs for HPCAL4 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
genes like me logo Genes that share compounds with HPCAL4: view

Transcripts for HPCAL4 Gene

mRNA/cDNA for HPCAL4 Gene

Unigene Clusters for HPCAL4 Gene

Hippocalcin like 4:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HPCAL4 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4a · 4b · 4c ^ 5a · 5b
SP1: - -
SP2: -
SP3: - - -
SP4: -

Relevant External Links for HPCAL4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HPCAL4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HPCAL4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HPCAL4 Gene

This gene is overexpressed in Brain - Anterior cingulate cortex (BA24) (x6.4), Brain - Cortex (x6.2), Brain - Amygdala (x5.8), Brain - Frontal Cortex (BA9) (x5.3), Brain - Nucleus accumbens (basal ganglia) (x5.1), Brain - Hippocampus (x4.5), Brain - Cerebellum (x4.2), and Brain - Cerebellar Hemisphere (x4.1).

Protein differential expression in normal tissues from HIPED for HPCAL4 Gene

This gene is overexpressed in Brain (34.6) and Frontal cortex (11.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HPCAL4 Gene

Protein tissue co-expression partners for HPCAL4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HPCAL4 Gene:


SOURCE GeneReport for Unigene cluster for HPCAL4 Gene:


Evidence on tissue expression from TISSUES for HPCAL4 Gene

  • Nervous system(5)
genes like me logo Genes that share expression patterns with HPCAL4: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HPCAL4 Gene

Orthologs for HPCAL4 Gene

This gene was present in the common ancestor of animals.

Orthologs for HPCAL4 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HPCAL4 34 33
  • 100 (n)
(Canis familiaris)
Mammalia HPCAL4 34 33
  • 95.46 (n)
(Bos Taurus)
Mammalia HPCAL4 34 33
  • 94.59 (n)
(Mus musculus)
Mammalia Hpcal4 16 34 33
  • 93.37 (n)
(Rattus norvegicus)
Mammalia Hpcal4 33
  • 92.5 (n)
(Monodelphis domestica)
Mammalia HPCAL4 34
  • 89 (a)
(Gallus gallus)
Aves HPCAL4 34 33
  • 87.09 (n)
(Anolis carolinensis)
Reptilia HPCAL4 34
  • 94 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hpcal4 33
  • 78.53 (n)
(Danio rerio)
Actinopterygii hpcal4 34 33
  • 79.41 (n)
fruit fly
(Drosophila melanogaster)
Insecta Nca 34 35
  • 71 (a)
CG7646 35
  • 43 (a)
(Caenorhabditis elegans)
Secernentea ncs-2 35
  • 46 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 64 (a)
Species where no ortholog for HPCAL4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • 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 HPCAL4 Gene

Gene Tree for HPCAL4 (if available)
Gene Tree for HPCAL4 (if available)
Evolutionary constrained regions (ECRs) for HPCAL4: view image

Paralogs for HPCAL4 Gene

(18) SIMAP similar genes for HPCAL4 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with HPCAL4: view

Variants for HPCAL4 Gene

Sequence variations from dbSNP and Humsavar for HPCAL4 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000025305 -- 39,680,422(-) T/C 3_prime_UTR_variant
rs1000070459 -- 39,688,016(-) G/A intron_variant
rs1000215259 -- 39,686,613(-) G/A intron_variant
rs1000218072 -- 39,692,663(-) C/T upstream_transcript_variant
rs1000270321 -- 39,692,982(-) G/A upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for HPCAL4 Gene

Variant ID Type Subtype PubMed ID
nsv1116447 OTHER inversion 24896259
nsv546062 CNV gain 21841781
nsv7177 OTHER inversion 18451855

Variation tolerance for HPCAL4 Gene

Residual Variation Intolerance Score: 36.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.19; 4.35% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HPCAL4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HPCAL4 Gene

Disorders for HPCAL4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for HPCAL4 Gene - From: DISEASES

Disorder Aliases PubMed IDs
holoprosencephaly 3
  • hpe3
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for HPCAL4

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HPCAL4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HPCAL4 Gene

Publications for HPCAL4 Gene

  1. Isolation of two human cDNAs, HLP3 and HLP4, homologous to the neuron-specific calcium-binding protein genes. (PMID: 10520747) Kobayashi M … Takamatsu K (DNA sequence : the journal of DNA sequencing and mapping 1998) 2 3 4 22 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  4. 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
  5. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 3 4 58

Products for HPCAL4 Gene

Sources for HPCAL4 Gene

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