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CALB2 calbindin 2 [ Homo sapiens (human) ]

Gene ID: 794, updated on 5-Mar-2024

Summary

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Official Symbol
CALB2provided by HGNC
Official Full Name
calbindin 2provided by HGNC
Primary source
HGNC:HGNC:1435
See related
Ensembl:ENSG00000172137 MIM:114051; AllianceGenome:HGNC:1435
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
CR; CAL2; CAB29
Summary
This gene encodes an intracellular calcium-binding protein belonging to the troponin C superfamily. Members of this protein family have six EF-hand domains which bind calcium. This protein plays a role in diverse cellular functions, including message targeting and intracellular calcium buffering. It also functions as a modulator of neuronal excitability, and is a diagnostic marker for some human diseases, including Hirschsprung disease and some cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2010]
Expression
Biased expression in fat (RPKM 72.8), testis (RPKM 20.4) and 4 other tissues See more
Orthologs
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Genomic context

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See CALB2 in Genome Data Viewer
Location:
16q22.2
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (71358723..71390433)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (77174637..77207658)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (71392626..71424336)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723786 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7675 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7676 Neighboring gene cap methyltransferase 2 Neighboring gene uncharacterized LOC102725168 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:71371582-71372781 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:71392357-71393322 Neighboring gene Sharpr-MPRA regulatory region 14967 Neighboring gene uncharacterized LOC105371332 Neighboring gene Sharpr-MPRA regulatory region 5468 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr16:71420497-71421047 Neighboring gene hESC enhancers GRCh37_chr16:71421048-71421598 and GRCh37_chr16:71421599-71422149 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_43990 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:71423333-71423878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:71445925-71446426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11071 Neighboring gene long intergenic non-protein coding RNA 2136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:71459785-71460285 Neighboring gene tRNA-Met (anticodon CAT) 2-1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. All-Ion Monitoring-Directed Low-Abundance Protein Quantification Reveals CALB2 as a Key Promoter in Hepatocellular Carcinoma Metastasis. Chu H, et al. Anal Chem, 2022 Apr 26. PMID 35333527
  2. Increasing Trend of Calretinin-Positive Mucosal Innervation from Aganglionic Zone toward Transition Zone in Hirschsprung's Disease. Najjar S, et al. Eur J Pediatr Surg, 2022 Apr. PMID 33513627
  3. Expression of Calretinin, Marker of Mesothelial Differentiation, in Pancreatic Ductal Adenocarcinoma: A Potential Diagnostic Pitfall. Askan G, et al. Turk Patoloji Derg, 2021. PMID 33432559, Free PMC Article
  4. Determinants of plasma calretinin in patients with malignant pleural mesothelioma. Lehnert M, et al. BMC Res Notes, 2020 Jul 29. PMID 32727552, Free PMC Article
  5. Expression of calretinin in odontogenic keratocysts and basal cell carcinomas: A study of sporadic and Gorlin-Goltz syndrome-related cases. Cesinaro AM, et al. Ann Diagn Pathol, 2020 Apr. PMID 31982676

See all (101) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. "Deciduoid" Change in Uterine Leiomyomas in Pregnancy: Aberrant Expression of Sex Cord Markers Inhibin and Calretinin.
    Title: "Deciduoid" Change in Uterine Leiomyomas in Pregnancy: Aberrant Expression of Sex Cord Markers Inhibin and Calretinin.
  2. Serum Calretinin and Genetic Variability as a Prognostic and Predictive Factor in Malignant Mesothelioma.
    Title: Serum Calretinin and Genetic Variability as a Prognostic and Predictive Factor in Malignant Mesothelioma.
  3. All-Ion Monitoring-Directed Low-Abundance Protein Quantification Reveals CALB2 as a Key Promoter in Hepatocellular Carcinoma Metastasis.
    Title: All-Ion Monitoring-Directed Low-Abundance Protein Quantification Reveals CALB2 as a Key Promoter in Hepatocellular Carcinoma Metastasis.
  4. Increasing Trend of Calretinin-Positive Mucosal Innervation from Aganglionic Zone toward Transition Zone in Hirschsprung's Disease.
    Title: Increasing Trend of Calretinin-Positive Mucosal Innervation from Aganglionic Zone toward Transition Zone in Hirschsprung's Disease.
  5. Expression of Calretinin, Marker of Mesothelial Differentiation, in Pancreatic Ductal Adenocarcinoma: A Potential Diagnostic Pitfall.", trans "Expression of Calretinin, Marker of Mesothelial Differentiation, in Pancreatic Ductal Adenocarcinoma: A Potential Diagnostic Pitfall.
    Title: Expression of Calretinin, Marker of Mesothelial Differentiation, in Pancreatic Ductal Adenocarcinoma: A Potential Diagnostic Pitfall.
  6. CLDN15 is a novel diagnostic marker for malignant pleural mesothelioma.
    Title: CLDN15 is a novel diagnostic marker for malignant pleural mesothelioma.
  7. LncRNA CALB2 sponges miR-30b-3p to promote odontoblast differentiation of human dental pulp stem cells via up-regulating RUNX2.
    Title: LncRNA CALB2 sponges miR-30b-3p to promote odontoblast differentiation of human dental pulp stem cells via up-regulating RUNX2.
  8. Determinants of plasma calretinin in patients with malignant pleural mesothelioma.
    Title: Determinants of plasma calretinin in patients with malignant pleural mesothelioma.
  9. Whole-genome sequencing of African Americans implicates differential genetic architecture in inflammatory bowel disease.
    Title: Whole-genome sequencing of African Americans implicates differential genetic architecture in inflammatory bowel disease.
  10. Expression of calretinin in odontogenic keratocysts and basal cell carcinomas: A study of sporadic and Gorlin-Goltz syndrome-related cases.
    Title: Expression of calretinin in odontogenic keratocysts and basal cell carcinomas: A study of sporadic and Gorlin-Goltz syndrome-related cases.
Submit: New GeneRIF Correction See all GeneRIFs (78)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables calcium ion binding involved in regulation of presynaptic cytosolic calcium ion concentration IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in regulation of long-term synaptic potentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of presynaptic cytosolic calcium ion concentration IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
is_active_in dendrite IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in gap junction IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in parallel fiber to Purkinje cell synapse IEA
Inferred from Electronic Annotation
more info
  
is_active_in synapse IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in terminal bouton IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
calretinin
Names
29 kDa calbindin
calbindin 2, (29kD, calretinin)
calbindin D29K
testicular secretory protein Li 8

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.

mRNA and Protein(s)

  1. NM_001740.5 → NP_001731.2  calretinin isoform 1

    See identical proteins and their annotated locations for NP_001731.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (isoform 1), which has also been designated as the full-length isoform.
    Source sequence(s)
    AK222495
    Consensus CDS
    CCDS10899.1
    UniProtKB/Swiss-Prot
    A8K4Y1, P22676, Q53HD2, Q96BK4
    UniProtKB/TrEMBL
    A0A140VK08, H3BN14
    Related
    ENSP00000307508.4, ENST00000302628.9
    Conserved Domains (2) summary
    cd00051
    Location:111 → 180
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    pfam13499
    Location:113 → 180
    EF-hand_7; EF-hand domain pair

  2. NM_007088.4 → NP_009019.1  calretinin isoform 22k

    See identical proteins and their annotated locations for NP_009019.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (CALB2c) lacks an alternate segment in the 3' coding region, which results in a frameshift and an early stop codon, compared to variant 1. The resulting protein (isoform 22k) has a shorter and distinct C-terminus, compared to isoform 1. There are no publicly available transcripts supporting this variant; it is represented based on data in PMID:7607211.
    Source sequence(s)
    AK222495
    UniProtKB/TrEMBL
    A6NER6
    Related
    ENSP00000340294.5, ENST00000349553.9
    Conserved Domains (2) summary
    cd00051
    Location:111 → 179
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    pfam13499
    Location:113 → 176
    EF-hand_7; EF-hand domain pair

RNA

  1. NR_027910.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (CALB2b) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD). This variant was described by Schwaller et al (PMID: 7607211), and proposed to encode a 20kDa isoform, but this protein has not been shown to be expressed in vivo.
    Source sequence(s)
    AK222495

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    71358723..71390433
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_013171813.1 Reference GRCh38.p14 PATCHES

    Range
    226200..257930
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    77174637..77207658
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_007087.2: Suppressed sequence

    Description
    NM_007087.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P22676.2 GenPept UniProtKB/Swiss-Prot:P22676

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