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    CLTRN collectrin, amino acid transport regulator [ Homo sapiens (human) ]

    Gene ID: 57393, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CLTRNprovided by HGNC
    Official Full Name
    collectrin, amino acid transport regulatorprovided by HGNC
    Primary source
    HGNC:HGNC:29437
    See related
    Ensembl:ENSG00000147003 MIM:300631; AllianceGenome:HGNC:29437
    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
    NX17; NX-17; TMEM27
    Summary
    This gene encodes a type 1 transmembrane protein that is important for trafficking amino acid transporters to the apical brush border of proximal tubules. The encoded protein binds to amino acid transporters and regulates their expression on the plasma membrane. It also plays a role in controlling insulin exocytosis by regulating formation of the SNARE (soluble N-ethylmaleimide-sensitive-factor attachment protein receptor) complex in pancreatic beta cells. The extracellular domain of the encoded protein may be cleaved and shed from the plasma membrane specifically in pancreatic beta cells. [provided by RefSeq, Jun 2013]
    Expression
    Biased expression in kidney (RPKM 116.5) and liver (RPKM 8.9) See more
    Orthologs
    mouse all
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    Genomic context

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    See CLTRN in Genome Data Viewer
    Location:
    Xp22.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (15627318..15675644, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (15210303..15247770, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (15645441..15682928, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene BMX non-receptor tyrosine kinase Neighboring gene angiotensin converting enzyme 2 Neighboring gene HNRNPDL pseudogene 5 Neighboring gene dACE2 interferon-inducible promoter region Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:15617708-15618907 Neighboring gene ACE2 promoter region Neighboring gene ACE2 divergent transcript Neighboring gene prothymosin alpha pseudogene 14 Neighboring gene nonconserved acetylation island sequence 104 enhancer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:15693246-15693864 Neighboring gene CA5BP1-CA5B readthrough Neighboring gene NANOG hESC enhancer GRCh37_chrX:15713069-15713611 Neighboring gene carbonic anhydrase 5B pseudogene 1 Neighboring gene small nucleolar RNA SNORA7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20673 Neighboring gene NANOG hESC enhancer GRCh37_chrX:15765293-15766154 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:15770987-15771772 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:15787311-15788154 Neighboring gene carbonic anhydrase 5B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29449 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29450 Neighboring gene inactivation escape 2

    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 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. TMEM27 expression and clinical characteristics and survival in clear cell renal cell carcinoma. Grewal R, et al. Acta Oncol, 2022 Dec. PMID 36369873
    2. Serum collectrin levels in patients with early- and late-onset preeclampsia. Aslan Cetin B, et al. J Matern Fetal Neonatal Med, 2018 Nov. PMID 28764560
    3. Lack of TMEM27 expression is associated with postoperative progression of clinically localized conventional renal cell carcinoma. Javorhazy A, et al. J Cancer Res Clin Oncol, 2016 Sep. PMID 27417314
    4. Collectrin gene screening in Turner syndrome patients with kidney malformation. Pasquali L, et al. J Genet, 2009 Apr. PMID 19417552
    5. Tmem27 is upregulated by vitamin D in INS-1 cells and its serum concentrations are low in patients with autoimmune diabetes. Pepaj M, et al. Scand J Clin Lab Invest, 2014 Jun. PMID 24693993

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TMEM27 expression and clinical characteristics and survival in clear cell renal cell carcinoma.
      Title: TMEM27 expression and clinical characteristics and survival in clear cell renal cell carcinoma.
    2. Collectrin (Tmem27) deficiency in proximal tubules causes hypertension in mice and a TMEM27 variant associates with blood pressure in males in a Latino cohort.
      Title: Collectrin (Tmem27) deficiency in proximal tubules causes hypertension in mice and a TMEM27 variant associates with blood pressure in males in a Latino cohort.
    3. Maternal serum collectrin levels are significantly lower in patients with preeclampsia than in the control group. There is an inverse correlation between serum collectrin levels and blood pressure.
      Title: Serum collectrin levels in patients with early- and late-onset preeclampsia.
    4. Lack of expression of the TMEM27 in conventional renal cell carcinoma defines a group of patients at high risk for cancer-related death.
      Title: Lack of TMEM27 expression is associated with postoperative progression of clinically localized conventional renal cell carcinoma.
    5. Tmem27 is present in human serum and its levels are significantly lower in subjects with autoimmune diabetes as compared to healthy individuals.
      Title: Tmem27 is upregulated by vitamin D in INS-1 cells and its serum concentrations are low in patients with autoimmune diabetes.
    6. Bace2 specifically targets Tmem27 and cleaves its extracellular domain, which is then shed from the plasma membrane of pancreatic beta cells.
      Title: Bace2 is a β cell-enriched protease that regulates pancreatic β cell function and mass.
    7. Tmem27 dimerization is a dynamic process involving Bace2
      Title: Tmem27 dimerization, deglycosylation, plasma membrane depletion, and the extracellular Phe-Phe motif are negative regulators of cleavage by Bace2.
    8. Collectrin and ACE2 in renal and intestinal amino acid transport.
      Title: Collectrin and ACE2 in renal and intestinal amino acid transport.
    9. Data support a role for TMEM27 in glucose-induced insulin secretion but not in cell proliferation. The finding that its cleavage is not specific to beta cells challenges the current support for its use as a potential beta cell mass biomarker.
      Title: The role of transmembrane protein 27 (TMEM27) in islet physiology and its potential use as a beta cell mass biomarker.
    10. No TMEM27 gene mutations were discovered among 26 patients showing a phenotype resembling Dent's disease
      Title: Locus heterogeneity of Dent's disease: OCRL1 and TMEM27 genes in patients with no CLCN5 mutations.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    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

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in SNARE complex assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_positive_effect calcium-ion regulated exocytosis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_positive_effect insulin secretion involved in cellular response to glucose stimulus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of L-proline import across plasma membrane IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in positive regulation of amino acid transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transmembrane transporter activity IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in brush border membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular exosome HDA PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    collectrin
    Names
    kidney-specific membrane protein
    transmembrane protein 27

    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_015970.1 RefSeqGene

      Range
      5227..42714
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_020665.6 → NP_065716.1  collectrin precursor

      See identical proteins and their annotated locations for NP_065716.1

      Status: REVIEWED

      Source sequence(s)
      AI470468, BC014317
      Consensus CDS
      CCDS14170.1
      UniProtKB/Swiss-Prot
      B2R9M1, Q6UW07, Q9HBJ8
      Related
      ENSP00000369699.3, ENST00000380342.4
      Conserved Domains (1) summary
      pfam16959
      Location:24 → 171
      Collectrin; Renal amino acid transporter

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      15627318..15675644 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017029680.2 → XP_016885169.1  collectrin isoform X2

      UniProtKB/TrEMBL
      A0A3B3ITM8
      Conserved Domains (1) summary
      pfam16959
      Location:1 → 119
      Collectrin; Renal amino acid transporter

    2. XM_024452411.2 → XP_024308179.1  collectrin isoform X2

      UniProtKB/TrEMBL
      A0A3B3ITM8
      Related
      ENSP00000497814.1, ENST00000650271.1
      Conserved Domains (1) summary
      pfam16959
      Location:1 → 119
      Collectrin; Renal amino acid transporter

    3. XM_017029681.2 → XP_016885170.1  collectrin isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      15210303..15247770 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054327434.1 → XP_054183409.1  collectrin isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HBJ8.1 GenPept UniProtKB/Swiss-Prot:Q9HBJ8

    Gene LinkOut

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

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