U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

CLGN calmegin [ Homo sapiens (human) ]

Gene ID: 1047, updated on 7-Apr-2024

Summary

Go to the top of the page Help
Official Symbol
CLGNprovided by HGNC
Official Full Name
calmeginprovided by HGNC
Primary source
HGNC:HGNC:2060
See related
Ensembl:ENSG00000153132 MIM:601858; AllianceGenome:HGNC:2060
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
Calmegin is a testis-specific endoplasmic reticulum chaperone protein. CLGN may play a role in spermatogeneisis and infertility. [provided by RefSeq, Jul 2008]
Expression
Biased expression in testis (RPKM 66.0), heart (RPKM 22.6) and 2 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
4q31.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (140388453..140427648, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (143708226..143747412, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (141309607..141348802, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene short coiled-coil protein Neighboring gene SCOC antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:141237061-141237740 Neighboring gene NADH:ubiquinone oxidoreductase subunit B4 pseudogene 9 Neighboring gene OCT4 hESC enhancer GRCh37_chr4:141294483-141294984 Neighboring gene ribosomal protein L14 pseudogene 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:141334799-141335364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21935 Neighboring gene MGAT4 family member D Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:141418967-141419468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:141419469-141419968 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15711 Neighboring gene ELMO domain containing 2

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Glycan specificity of a testis-specific lectin chaperone calmegin and effects of hydrophobic interactions. Sakono M, et al. Biochim Biophys Acta, 2014 Sep. PMID 24769397
  2. Coordinated transcriptional regulation of calmegin,a testis-specific molecular chaperon, by histone deacetylase and CpG methyltransferase. Kim DH, et al. Exp Mol Med, 2005 Oct 31. PMID 16264275
  3. Cloning and characterization of the human Calmegin gene encoding putative testis-specific chaperone. Tanaka H, et al. Gene, 1997 Dec 19. PMID 9434179
  4. Molecular chaperone calmegin localization to the endoplasmic reticulum of meiotic and post-meiotic germ cells in the mouse testis. Yoshinaga K, et al. Arch Histol Cytol, 1999 Aug. PMID 10495883
  5. The putative chaperone calmegin is required for sperm fertility. Ikawa M, et al. Nature, 1997 Jun 5. PMID 9177349

See all (61) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. In gene-based analysis CLGN1 represented one of a cluster of genes, which interacted with sodium to influence Blood Pressure.
    Title: Genome-Wide Gene-Sodium Interaction Analyses on Blood Pressure: The Genetic Epidemiology Network of Salt-Sensitivity Study.
  2. Although their similarity in carbohydrate binding specificities is high, there seems to be some differences in the mode of substrate recognition between calmegin and calnexin.
    Title: Glycan specificity of a testis-specific lectin chaperone calmegin and effects of hydrophobic interactions.
  3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  4. calmegin expression is regulated by histone deacetylase and CpG methyltransferase in a coordinative way
    Title: Coordinated transcriptional regulation of calmegin,a testis-specific molecular chaperon, by histone deacetylase and CpG methyltransferase.
Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

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 with select biomarker traits in the Framingham Heart Study.
EBI GWAS Catalog

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

Go to the top of the page Help

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 is identified to have a physical interaction with calmegin (CLGN) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 interacts with CLGN; predicted interaction to be within the endoplasmic reticulum PubMed
env HIV-1 gp160 is identified to have a physical interaction with calmegin (CLGN) 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

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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 protein folding chaperone IEA
Inferred from Electronic Annotation
more info
  
enables unfolded protein binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in ERAD pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in binding of sperm to zona pellucida IEA
Inferred from Electronic Annotation
more info
  
involved_in protein folding IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein-containing complex assembly IEA
Inferred from Electronic Annotation
more info
  
involved_in single fertilization TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
  
is_active_in endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

Go to the top of the page Help
Preferred Names
calmegin
Names
testis tissue sperm-binding protein Li 79P

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001130675.2 → NP_001124147.1  calmegin precursor

    See identical proteins and their annotated locations for NP_001124147.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an extra exon in the 5' UTR, compared to variant 1.
    Source sequence(s)
    AL045602, BC028357, D86322, DC396076
    Consensus CDS
    CCDS3751.1
    UniProtKB/Swiss-Prot
    B3KS90, B4DXV8, D3DNY8, O14967
    UniProtKB/TrEMBL
    A0A140VKG2, A8K454
    Related
    ENSP00000392782.1, ENST00000414773.5
    Conserved Domains (1) summary
    pfam00262
    Location:62 → 429
    Calreticulin; Calreticulin family

  2. NM_004362.3 → NP_004353.1  calmegin precursor

    See identical proteins and their annotated locations for NP_004353.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) is the shorter transcript. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    BC028357, D86322, DC396076
    Consensus CDS
    CCDS3751.1
    UniProtKB/Swiss-Prot
    B3KS90, B4DXV8, D3DNY8, O14967
    UniProtKB/TrEMBL
    A0A140VKG2, A8K454
    Related
    ENSP00000326699.5, ENST00000325617.10
    Conserved Domains (1) summary
    pfam00262
    Location:62 → 429
    Calreticulin; Calreticulin 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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    140388453..140427648 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    143708226..143747412 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O14967.1 GenPept UniProtKB/Swiss-Prot:O14967

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous