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

Gene ID: 57393, updated on 5-Mar-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_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (15627318..15675644, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (15210303..15247770, complement)
105.20220307 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
  • 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. 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
  5. Multimodal imaging of pancreatic beta cells in vivo by targeting transmembrane protein 27 (TMEM27). Vats D, et al. Diabetologia, 2012 Sep. PMID 22790173, Free PMC Article

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_2023_10

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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