The protein encoded by this gene is a member of the calcium-binding protein superfamily that includes calmodulin and troponin C. Originally described as a 27 kDa protein, it is now known to be a 28 kDa protein. It contains four active calcium-binding domains, and has two modified domains that are thought to have lost their calcium binding capability. This protein is thought to ... See more...

Aliases for CALB1 Gene

Aliases for CALB1 Gene

  • Calbindin 1 2 3 5
  • Vitamin D-Dependent Calcium-Binding Protein, Avian-Type 3 4
  • Calbindin 1, 28kDa 2 3
  • Calbindin D28 3 4
  • Calbindin 3 4
  • D-28K 3 4
  • Calbindin 1, (28kD) 3
  • RTVL-H Protein 3
  • Calbindin 27 3
  • CALB1 5
  • CAB27 4
  • CALB 3

External Ids for CALB1 Gene

Previous HGNC Symbols for CALB1 Gene

  • CALB

Previous GeneCards Identifiers for CALB1 Gene

  • GC08M089502
  • GC08M090803
  • GC08M091027
  • GC08M091140
  • GC08M091070
  • GC08M086281

Summaries for CALB1 Gene

Entrez Gene Summary for CALB1 Gene

  • The protein encoded by this gene is a member of the calcium-binding protein superfamily that includes calmodulin and troponin C. Originally described as a 27 kDa protein, it is now known to be a 28 kDa protein. It contains four active calcium-binding domains, and has two modified domains that are thought to have lost their calcium binding capability. This protein is thought to buffer entry of calcium upon stimulation of glutamate receptors. Depletion of this protein was noted in patients with Huntington disease. [provided by RefSeq, Jan 2015]

GeneCards Summary for CALB1 Gene

CALB1 (Calbindin 1) is a Protein Coding gene. Diseases associated with CALB1 include Cerebellar Disease and Huntington Disease. Among its related pathways are Neuroscience and Ca, cAMP and Lipid Signaling. Gene Ontology (GO) annotations related to this gene include calcium ion binding and vitamin D binding. An important paralog of this gene is CALB2.

UniProtKB/Swiss-Prot Summary for CALB1 Gene

  • Buffers cytosolic calcium. May stimulate a membrane Ca(2+)-ATPase and a 3',5'-cyclic nucleotide phosphodiesterase.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CALB1 Gene

Genomics for CALB1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CALB1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH08J090083 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 600.4 +13.2 13174 1.8 CTCF PRDM10 REST TFE3 IKZF1 TARDBP JUND ZNF24 POLR2A HDAC1 CALB1 NBN DECR1 piR-32559-436 lnc-NBN-3 lnc-CALB1-1
GH08J090091 Promoter 0.3 Ensembl 600.7 +1.9 1874 4 CALB1 MG598800-035 piR-32559-437 piR-36770-105 lnc-NBN-3 piR-37432-121 piR-48950-204 NBN DECR1
GH08J089789 Enhancer 0.6 Ensembl ENCODE dbSUPER 4.6 +305.0 304974 1.4 MYNN ENSG00000251136 CALB1 piR-38352-546 NONHSAG050701.2 RIPK2 lnc-NBN-5 OSGIN2
GH08J090329 Enhancer 0.5 Ensembl 4.5 -234.0 -234026 0.2 NFE2 ZNF316 MAFG KLF9 ZNF592 NR4A1 CBFA2T3 EMSY CALB1 piR-44253-021 lnc-CALB1-5 piR-39341-401 LINC00534 ENSG00000254180 TMEM64
GH08J090284 Enhancer 0.2 Ensembl 4.5 -189.4 -189426 0.2 CALB1 piR-39341-401 piR-44253-021 LINC00534 ENSG00000254180 TMEM64
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CALB1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CALB1

Top Transcription factor binding sites by QIAGEN in the CALB1 gene promoter:
  • C/EBPalpha
  • CHOP-10
  • Nkx6-1
  • NRSF form 1
  • NRSF form 2
  • POU2F1a
  • POU2F1b
  • POU2F1c

Genomic Locations for CALB1 Gene

Genomic Locations for CALB1 Gene
chr8:90,058,608-90,095,475
(GRCh38/hg38)
Size:
36,868 bases
Orientation:
Minus strand
chr8:91,070,836-91,107,703
(GRCh37/hg19)
Size:
36,868 bases
Orientation:
Minus strand

Genomic View for CALB1 Gene

Genes around CALB1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CALB1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CALB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CALB1 Gene

Proteins for CALB1 Gene

  • Protein details for CALB1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P05937-CALB1_HUMAN
    Recommended name:
    Calbindin
    Protein Accession:
    P05937
    Secondary Accessions:
    • B2R696
    • B7Z9J4

    Protein attributes for CALB1 Gene

    Size:
    261 amino acids
    Molecular mass:
    30025 Da
    Quaternary structure:
    • Interacts with RANBP9.

    Three dimensional structures from OCA and Proteopedia for CALB1 Gene

    Alternative splice isoforms for CALB1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CALB1 Gene

Post-translational modifications for CALB1 Gene

  • Glycosylation at Asn230
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • CALB1_HUMAN (1056)

Other Protein References for CALB1 Gene

No data available for DME Specific Peptides for CALB1 Gene

Domains & Families for CALB1 Gene

Gene Families for CALB1 Gene

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

Protein Domains for CALB1 Gene

Suggested Antigen Peptide Sequences for CALB1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ92852, Homo sapiens calbindin 1, 28kDa (CALB1), mRNA (B2R696_HUMAN)
  • cDNA, FLJ78858, highly similar to Calbindin (B7Z9J4_HUMAN)
  • Vitamin D-dependent calcium-binding protein, avian-type (CALB1_HUMAN)
  • Vitamin D-dependent calcium binding protein calbindin (O75552_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P05937

UniProtKB/Swiss-Prot:

CALB1_HUMAN :
  • This protein has four functional calcium-binding sites; potential sites II and VI have lost affinity for calcium.
  • Belongs to the calbindin family.
Domain:
  • This protein has four functional calcium-binding sites; potential sites II and VI have lost affinity for calcium.
Family:
  • Belongs to the calbindin family.
genes like me logo Genes that share domains with CALB1: view

Function for CALB1 Gene

Molecular function for CALB1 Gene

UniProtKB/Swiss-Prot Function:
Buffers cytosolic calcium. May stimulate a membrane Ca(2+)-ATPase and a 3',5'-cyclic nucleotide phosphodiesterase.
GENATLAS Biochemistry:
calbindin (28kDa),vitamin D dependent calcium binding protein 1,from the intestine

Phenotypes From GWAS Catalog for CALB1 Gene

Gene Ontology (GO) - Molecular Function for CALB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005499 vitamin D binding IEA --
GO:0005509 calcium ion binding IEA,IMP 18359862
GO:0005515 protein binding IPI 16763551
GO:0008270 zinc ion binding IMP 18359862
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with CALB1: view
genes like me logo Genes that share phenotypes with CALB1: view

Animal Models for CALB1 Gene

MGI Knock Outs for CALB1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CALB1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for CALB1 Gene

Localization for CALB1 Gene

Subcellular locations from

COMPARTMENTS
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 CALB1 gene
Compartment Confidence
nucleus 5
extracellular 4
cytoskeleton 4
cytosol 4
mitochondrion 3
plasma membrane 2
endoplasmic reticulum 2
lysosome 2
peroxisome 1
endosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CALB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005623 cell IEA --
GO:0005634 nucleus IBA,IDA 16928804
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0030424 axon ISS --
genes like me logo Genes that share ontologies with CALB1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for CALB1 Gene

Pathways & Interactions for CALB1 Gene

genes like me logo Genes that share pathways with CALB1: view

Pathways by source for CALB1 Gene

2 Reactome pathways for CALB1 Gene
1 GeneGo (Thomson Reuters) pathway for CALB1 Gene
  • Transcription_Role of VDR in regulation of genes involved in osteoporosis
2 Cell Signaling Technology pathways for CALB1 Gene

Gene Ontology (GO) - Biological Process for CALB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007611 learning or memory IEA --
GO:0007614 short-term memory IMP 22796338
GO:0007616 long-term memory IMP 22796338
GO:0007626 locomotory behavior IEA --
GO:0010842 retina layer formation IEA --
genes like me logo Genes that share ontologies with CALB1: view

No data available for SIGNOR curated interactions for CALB1 Gene

Drugs & Compounds for CALB1 Gene

(32) Drugs for CALB1 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium citrate Approved, Investigational Pharma Carrier, substrate 0
Calcium Phosphate Approved Pharma Carrier, substrate 0
Calcium phosphate dihydrate Approved Pharma Carrier 0
Calcium Nutra 6556

(13) Additional Compounds for CALB1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CALB1: view

Transcripts for CALB1 Gene

mRNA/cDNA for CALB1 Gene

2 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CALB1

Alternative Splicing Database (ASD) splice patterns (SP) for CALB1 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b
SP1: - - - - -
SP2: - - -
SP3: -
SP4:
SP5:

Relevant External Links for CALB1 Gene

GeneLoc Exon Structure for
CALB1

Expression for CALB1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CALB1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CALB1 Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x9.9), Brain - Caudate (basal ganglia) (x8.5), Kidney - Cortex (x6.5), Brain - Cerebellum (x6.3), and Brain - Putamen (basal ganglia) (x6.1).

Protein differential expression in normal tissues from HIPED for CALB1 Gene

This gene is overexpressed in Kidney (39.5) and Retina (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CALB1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CALB1

SOURCE GeneReport for Unigene cluster for CALB1 Gene:

Hs.65425

Evidence on tissue expression from TISSUES for CALB1 Gene

  • Nervous system(5)
  • Kidney(4.8)
  • Lung(4.4)
  • Eye(3.3)
  • Skin(2.6)
  • Intestine(2.6)
  • Muscle(2.2)
  • Blood(2.1)
  • Adrenal gland(2)
genes like me logo Genes that share expression patterns with CALB1: view

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CALB1 Gene

Orthologs for CALB1 Gene

This gene was present in the common ancestor of animals.

Orthologs for CALB1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CALB1 30 31
  • 99.87 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia CALB1 31
  • 95 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia CALB1 30 31
  • 93.87 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CALB1 30 31
  • 93.87 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Calb1 30 17 31
  • 92.46 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia CALB1 31
  • 92 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Calb1 30
  • 91.32 (n)
Chicken
(Gallus gallus)
Aves CALB1 30 31
  • 78.85 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CALB1 31
  • 75 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia calb1 30
  • 75.77 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.459 30
Zebrafish
(Danio rerio)
Actinopterygii calb1 30 31
  • 69.78 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Cbp53E 31 32
  • 38 (a)
OneToMany
Species where no ortholog for CALB1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for CALB1 Gene

ENSEMBL:
Gene Tree for CALB1 (if available)
TreeFam:
Gene Tree for CALB1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CALB1: view image

Paralogs for CALB1 Gene

Paralogs for CALB1 Gene

(2) SIMAP similar genes for CALB1 Gene using alignment to 5 proteins:

  • CALB1_HUMAN
  • B7Z9J4_HUMAN
  • E5RG14_HUMAN
  • E5RIZ8_HUMAN
  • O75552_HUMAN
genes like me logo Genes that share paralogs with CALB1: view

Variants for CALB1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CALB1 Gene

SNP ID Clinical significance and condition Chr 08 pos Variation AA Info Type
736493 Likely Benign: not provided 90,069,022(-) G/A SYNONYMOUS_VARIANT
739023 Benign: not provided 90,060,698(-) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for CALB1 Gene

Structural Variations from Database of Genomic Variants (DGV) for CALB1 Gene

Variant ID Type Subtype PubMed ID
esv2759628 CNV gain+loss 17122850

Variation tolerance for CALB1 Gene

Residual Variation Intolerance Score: 24.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.33; 7.41% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CALB1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CALB1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CALB1 Gene

Disorders for CALB1 Gene

MalaCards: The human disease database

(31) MalaCards diseases for CALB1 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
cerebellar disease
  • cerebellar dysfunction
huntington disease
  • hd
temporal lobe epilepsy
  • epilepsy, temporal lobe
status epilepticus
  • grand mal status
breast fibrosarcoma
  • fibrosarcoma of the breast
- elite association - COSMIC cancer census association via MalaCards
Search CALB1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CALB1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with CALB1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CALB1 Gene

Publications for CALB1 Gene

  1. Calbindin-1 association and Parkinson's disease. (PMID: 19674066) Soto-Ortolaza AI … Ross OA (European journal of neurology 2010) 3 23 41
  2. Calbindin 1, fibroblast growth factor 20, and alpha-synuclein in sporadic Parkinson's disease. (PMID: 18568448) Mizuta I … Toda T (Human genetics 2008) 3 23 41
  3. The X-ray structure of human calbindin-D28K: an improved model. (PMID: 30289411) Noble JW … Atack JR (Acta crystallographica. Section D, Structural biology 2018) 3 4
  4. Calbindin positive Purkinje cells in the pathology of human cerebellum occurring at the time of its development. (PMID: 20054781) Laure-Kamionowska M … Maślińska D (Folia neuropathologica 2009) 3 23
  5. Zn2+ binding to human calbindin D(28k) and the role of histidine residues. (PMID: 18359862) Bauer MC … Linse S (Protein science : a publication of the Protein Society 2008) 3 23

Products for CALB1 Gene

Sources for CALB1 Gene