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CALU calumenin [ Homo sapiens (human) ]

Gene ID: 813, updated on 5-Mar-2024

Summary

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Official Symbol
CALUprovided by HGNC
Official Full Name
calumeninprovided by HGNC
Primary source
HGNC:HGNC:1458
See related
Ensembl:ENSG00000128595 MIM:603420; AllianceGenome:HGNC:1458
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
Summary
The product of this gene is a calcium-binding protein localized in the endoplasmic reticulum (ER) and it is involved in such ER functions as protein folding and sorting. This protein belongs to a family of multiple EF-hand proteins (CERC) that include reticulocalbin, ERC-55, and Cab45 and the product of this gene. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Oct 2008]
Expression
Ubiquitous expression in heart (RPKM 44.6), placenta (RPKM 44.1) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
7q32.1
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (128739359..128773400)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (130051503..130085553)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (128379413..128413454)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene golgi associated RAB2 interactor 1A Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:128341516-128342715 Neighboring gene RNA, 5S ribosomal pseudogene 243 Neighboring gene uncharacterized LOC124901825 Neighboring gene golgi associated RAB2 interactor 1B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18612 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26603 Neighboring gene RNA, 7SL, cytoplasmic 81, pseudogene Neighboring gene blue cone (S) opsin upstream regulatory region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18614 Neighboring gene opsin 1, short wave sensitive Neighboring gene tRNA-Pro (anticodon AGG) 2-3 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:128431137-128431405 Neighboring gene coiled-coil domain containing 136

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. Calumenin contributes to ER-Ca(2+) homeostasis in bronchial epithelial cells expressing WT and F508del mutated CFTR and to F508del-CFTR retention. Philippe R, et al. Cell Calcium, 2017 Mar. PMID 28189267
  2. CALU polymorphism A29809G affects calumenin availability involving vascular calcification. Jover E, et al. J Mol Cell Cardiol, 2015 May. PMID 25823396
  3. CALU A29809G polymorphism in coronary atherothrombosis: Implications for coronary calcification and prognosis. Hernández-Romero D, et al. Ann Med, 2010 Sep. PMID 20673165
  4. A polymorphism in the VKORC1 regulator calumenin predicts higher warfarin dose requirements in African Americans. Voora D, et al. Clin Pharmacol Ther, 2010 Apr. PMID 20200517, Free PMC Article
  5. Human calumenin localizes to the secretory pathway and is secreted to the medium. Vorum H, et al. Exp Cell Res, 1999 May 1. PMID 10222138

See all (157) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Establishment of a CALU, AURKA, and MCM2 gene panel for discrimination of metastasis from primary colon and lung cancers.
    Title: Establishment of a CALU, AURKA, and MCM2 gene panel for discrimination of metastasis from primary colon and lung cancers.
  2. Replacing Leu with Gly (L150G) in Calu1 enables the protein to adopt a structural fold even in the Ca(2+) free form. The fourth (of seven) EF-hand of HsCalu1 nucleates the structural fold of the protein depending on the switch residue (Gly or Leu).
    Title: The Differential Response to Ca(2+) from Vertebrate and Invertebrate Calumenin Is Governed by a Single Amino Acid Residue.
  3. The Calumenin modulates Sarco/Endoplasmic reticulumCa2+ATPase (SERCA) pump activity without drastically affecting ER-Ca(2+) concentration.
    Title: Calumenin contributes to ER-Ca(2+) homeostasis in bronchial epithelial cells expressing WT and F508del mutated CFTR and to F508del-CFTR retention.
  4. irradiated tumor cells were observed to significantly up-regulate the expression of calcium-binding proteins CALM1, CALU, and RCN1, suggesting important roles for these mediators in promoting irradiated tumor cell survival during hypoxia
    Title: Irradiation of Epithelial Carcinoma Cells Upregulates Calcium-Binding Proteins That Promote Survival under Hypoxic Conditions.
  5. Calu-15, a novel isoform of Calu with phosphorylation-dependent nuclear localization, has a critical role in promoting filopodia formation and cell migration by upregulating the GDF-15 transcription.
    Title: Calumenin-15 facilitates filopodia formation by promoting TGF-β superfamily cytokine GDF-15 transcription.
  6. Results provide direct evidence for the involvement of CALU and LGALS3BP as potential negative regulators in the virus-triggered induction of the typeI interferons.
    Title: Quantitative Proteomics Reveals the Roles of Peroxisome-associated Proteins in Antiviral Innate Immune Responses.
  7. Results show that OSBPL5 and CALU were expressed at higher levels in the lung tissues of metastasis-positive cases than that in the metastasis-negative cases suggesting they can promote invasiveness of lung cancer cells.
    Title: Identification and evaluation of metastasis-related proteins, oxysterol binding protein-like 5 and calumenin, in lung tumors.
  8. CALU polymorphism A29809G affects calumenin availability involving vascular calcification
    Title: CALU polymorphism A29809G affects calumenin availability involving vascular calcification.
  9. Calumenin is characterized as a charged protein exhibiting close similarity with intrinsically disordered proteins and is hypothesized to regulate F508del-CFTR folding by electrostatic effects.
    Title: Biophysical characterisation of calumenin as a charged F508del-CFTR folding modulator.
  10. Calumenin is a new CFTR chaperone.
    Title: Proteomic identification of calumenin as a G551D-CFTR associated protein.
Submit: New GeneRIF Correction See all GeneRIFs (19)

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

EBI GWAS Catalog

Description
Genome-wide association study of primary tooth eruption identifies pleiotropic loci associated with height and craniofacial distances.
EBI GWAS Catalog

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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 is identified to have a physical interaction with calumenin (CALU) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ90608

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 IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
  
located_in endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in melanosome IEA
Inferred from Electronic Annotation
more info
  
located_in membrane HDA PubMed 
located_in sarcoplasmic reticulum lumen IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
calumenin
Names
IEF SSP 9302
crocalbin-like protein
multiple EF-hand protein

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

  1. NG_033110.1 RefSeqGene

    Range
    5068..39109
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001130674.3 → NP_001124146.1  calumenin isoform b precursor

    See identical proteins and their annotated locations for NP_001124146.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate in-frame exon, compared to variant 1. The resulting isoform (b) is of the same length but has a different internal segment, compared to isoform a.
    Source sequence(s)
    AC024952, AF345637, BF438624, HM002611
    Consensus CDS
    CCDS47703.1
    UniProtKB/TrEMBL
    B3KNG6
    Related
    ENSP00000408838.2, ENST00000449187.7
    Conserved Domains (1) summary
    cd16228
    Location:37 → 299
    EFh_CREC_Calumenin; EF-hand, calcium binding motif, found in calumenin

  2. NM_001199671.2 → NP_001186600.1  calumenin isoform c precursor

    See identical proteins and their annotated locations for NP_001186600.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has an additional exon in the 5' region, introducing an in-frame upstream AUG start codon, compared to variant 1. The resulting isoform (c) has a longer N-terminus, compared to isoform a.
    Source sequence(s)
    AC024952, AK056338, BF438624, HM002604
    Consensus CDS
    CCDS56506.1
    UniProtKB/TrEMBL
    B3KQF5
    Related
    ENSP00000420381.1, ENST00000479257.5
    Conserved Domains (1) summary
    cd16228
    Location:45 → 307
    EFh_CREC_Calumenin; EF-hand, calcium binding motif, found in calumenin

  3. NM_001199672.2 → NP_001186601.1  calumenin isoform d precursor

    See identical proteins and their annotated locations for NP_001186601.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has an additional exon in the 5' region, introducing an in-frame upstream AUG start codon, and has an alternate in-frame coding exon, compared to variant 1. The resulting isoform (d) has a longer N-terminus and a different internal segment, compared to isoform a.
    Source sequence(s)
    AC024952, AK056338, BF438624, HM002605, HM002606
    Consensus CDS
    CCDS56507.1
    UniProtKB/TrEMBL
    B3KNG6
    Related
    ENSP00000438248.1, ENST00000542996.7
    Conserved Domains (1) summary
    cd16228
    Location:45 → 307
    EFh_CREC_Calumenin; EF-hand, calcium binding motif, found in calumenin

  4. NM_001199673.2 → NP_001186602.1  calumenin isoform e precursor

    See identical proteins and their annotated locations for NP_001186602.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks a coding exon in the 3' region, resulting in frame-shift, compared to variant 1. The resulting isoform (e) has a shorter and different C-terminus, compared to isoform a.
    Source sequence(s)
    AC024952, BC013383, BF438624, HM002611
    Consensus CDS
    CCDS56508.1
    UniProtKB/Swiss-Prot
    O43852
    Related
    ENSP00000442110.1, ENST00000535011.6
    Conserved Domains (2) summary
    cd15899
    Location:37 → 65
    EFh_CREC; EF-hand motif [structural motif]
    cl25354
    Location:37 → 223
    EFh_CREC; EF-hand, calcium binding motif, found in CREC-EF hand family

  5. NM_001219.5 → NP_001210.1  calumenin isoform a precursor

    See identical proteins and their annotated locations for NP_001210.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the predominant isoform (a).
    Source sequence(s)
    AC024952, AK074862, BF438624, HM002604
    Consensus CDS
    CCDS5805.1
    UniProtKB/Swiss-Prot
    B3KPG9, D6QS48, D6QS49, D6QS50, D6QS51, D6QS52, D6QS53, D6QS54, D6QS55, D6QS56, D6QS57, D6QS58, D6QS59, F5H1Q9, F5H879, O43852, O60456, Q6FHB9, Q96RL3, Q9NR43
    UniProtKB/TrEMBL
    B3KQF5, Q6IAW5
    Related
    ENSP00000249364.4, ENST00000249364.9
    Conserved Domains (1) summary
    cd16228
    Location:37 → 299
    EFh_CREC_Calumenin; EF-hand, calcium binding motif, found in calumenin

RNA

  1. NR_074086.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks two consecutive exons in the 5' region, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the primary ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC024952, BC013383, BF438624, HM002616

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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    128739359..128773400
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    130051503..130085553
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001199674.1: Suppressed sequence

    Description
    NM_001199674.1: This RefSeq was permanently suppressed because it is now thought that this transcript does not encode a protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43852.2 GenPept UniProtKB/Swiss-Prot:O43852

Gene LinkOut

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