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CAPS calcyphosine [ Homo sapiens (human) ]

Gene ID: 828, updated on 10-Oct-2023

Summary

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Official Symbol
CAPSprovided by HGNC
Official Full Name
calcyphosineprovided by HGNC
Primary source
HGNC:HGNC:1487
See related
Ensembl:ENSG00000105519 MIM:114212; AllianceGenome:HGNC:1487
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CAPS1
Summary
This gene encodes a calcium-binding protein, which may play a role in the regulation of ion transport. A similar protein was first described as a potentially important regulatory protein in the dog thyroid and was termed as R2D5 antigen in rabbit. Alternative splicing of this gene generates two transcript variants. [provided by RefSeq, Jul 2008]
Expression
Broad expression in lung (RPKM 22.4), endometrium (RPKM 13.8) and 21 other tissues See more
Orthologs
all
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Genomic context

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See CAPS in Genome Data Viewer
Location:
19p13.3
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (5914254..5916211)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (5901694..5903651)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (5914265..5916222)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5892267-5893073 Neighboring gene MPRA-validated peak3300 silencer Neighboring gene Sharpr-MPRA regulatory region 9916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9938 Neighboring gene NADH:ubiquinone oxidoreductase subunit A11 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13818 Neighboring gene vimentin type intermediate filament associated coiled-coil protein Neighboring gene RAN binding protein 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:5939785-5939965 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5944489-5945129 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5952179-5952738 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:5953075-5954274 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5957025-5957534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5958162-5958810 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5959460-5960108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5960757-5961406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13819 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9939 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5962704-5963351 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5963485-5964036 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5964037-5964587 Neighboring gene Sharpr-MPRA regulatory region 310 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9941 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9942 Neighboring gene RANBP3 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6015021-6015520 Neighboring gene regulatory factor X2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6018397-6018898 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9943 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:6065893-6066394 Neighboring gene ribosomal protein L32 pseudogene

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. Calcyphosine promotes the proliferation of glioma cells and serves as a potential therapeutic target. Zhu Z, et al. J Pathol, 2021 Dec. PMID 34370292, Free PMC Article
  2. CAPS Mutations Are Potentially Associated with Unexplained Recurrent Pregnancy Loss. Pan H, et al. Am J Pathol, 2019 Jan. PMID 30339840
  3. Crystallization and preliminary crystallographic analysis of recombinant human calcyphosine. Dong H, et al. Protein Pept Lett, 2009. PMID 19275752
  4. Crystal-structure and biochemical characterization of recombinant human calcyphosine delineates a novel EF-hand-containing protein family. Dong H, et al. J Mol Biol, 2008 Nov 14. PMID 18775726
  5. Identification of brain cell death associated proteins in human post-mortem cerebrospinal fluid. Burgess JA, et al. J Proteome Res, 2006 Jul. PMID 16823975

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Calcyphosine promotes the proliferation of glioma cells and serves as a potential therapeutic target.
    Title: Calcyphosine promotes the proliferation of glioma cells and serves as a potential therapeutic target.
  2. The results indicated that the autosomal recessive homozygous mutation, p.Leu127Trpfs, in CAPS might be a maternal effect causative mutation of RPL pathogenesis.
    Title: CAPS Mutations Are Potentially Associated with Unexplained Recurrent Pregnancy Loss.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: Association study of 182 candidate genes in anorexia nervosa.
  4. The calcyphosine crystal diffracted to 2.8 A and belonged to space group P2(1)2(1)2, with the unit cell parameters a=70.39 A, b=132.02 A, c=46.20 A.
    Title: Crystallization and preliminary crystallographic analysis of recombinant human calcyphosine.
  5. These results describe the crystal structure of Ca(2+)-loaded calcyphosine up to 2.65 A resolution and reveal a protein containing two pairs of Ca(2+)-binding EF-hand motifs.
    Title: Crystal-structure and biochemical characterization of recombinant human calcyphosine delineates a novel EF-hand-containing protein family.
  6. Results demonstrated the ubiquitous overexpressions of E-FABP and CAPS in EC and the correlations to the clinicopathologic parameters. CAPS might be a potential prognostic factor for survival in patients with EC
    Title: Prognostic evaluation of epidermal fatty acid-binding protein and calcyphosine, two proteins implicated in endometrial cancer using a proteomic approach.
Submit: New GeneRIF Correction

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

Clone Names

  • MGC126562

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in intracellular signal transduction TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  
located_in vesicle HDA PubMed 

General protein information

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Preferred Names
calcyphosin
Names
calcyphosine 1
epididymis secretory sperm binding protein
thyroid protein p24

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_004058.5 → NP_004049.3  calcyphosin isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AK226026, AW510425, BC011961, BU689238
    Consensus CDS
    CCDS12156.3
    UniProtKB/TrEMBL
    A0A384NYV7, Q96ET4
    Related
    ENSP00000465883.2, ENST00000588776.8
    Conserved Domains (3) summary
    cd00051
    Location:26 → 87
    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 ...
    cd15898
    Location:26 → 54
    EFh_PI-PLC; EF-hand motif [structural motif]
    cl28895
    Location:26 → 165
    EFh_PI-PLC; EF-hand motif found in eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) isozymes

  2. NM_080590.4 → NP_542157.3  calcyphosin isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. It encodes isoform b, which is shorter than isoform a.
    Source sequence(s)
    AW510425, BC019065, BU689238
    Consensus CDS
    CCDS45934.3
    UniProtKB/TrEMBL
    A0A499FJ41, K7ES72
    Related
    ENSP00000403263.3, ENST00000452990.8
    Conserved Domains (2) summary
    cd00051
    Location:26 → 87
    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 ...
    cl25352
    Location:23 → 158
    EFh_PEF; The penta-EF hand (PEF) family

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    5914254..5916211
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791810.1 Reference GRCh38.p14 PATCHES

    Range
    87823..89211
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    5901694..5903651
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13938.2 GenPept UniProtKB/Swiss-Prot:Q13938

Gene LinkOut

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