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... See more...

Aliases for CLTRN Gene

Aliases for CLTRN Gene

  • Collectrin, Amino Acid Transport Regulator 2 3 5
  • Transmembrane Protein 27 2 3 4
  • Collectrin 2 3 4
  • TMEM27 3 4
  • NX17 2 3
  • Kidney-Specific Membrane Protein 3
  • NX-17 3
  • CLTRN 5

External Ids for CLTRN Gene

Previous HGNC Symbols for CLTRN Gene

  • TMEM27

Summaries for CLTRN Gene

Entrez Gene Summary for CLTRN Gene

  • 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]

GeneCards Summary for CLTRN Gene

CLTRN (Collectrin, Amino Acid Transport Regulator) is a Protein Coding gene. Diseases associated with CLTRN include Aminoaciduria and Hartnup Disorder. Among its related pathways are Metabolism of proteins and Peptide hormone metabolism. An important paralog of this gene is ENSG00000285602.

UniProtKB/Swiss-Prot Summary for CLTRN Gene

  • Plays an important role in amino acid transport by acting as binding partner of amino acid transporters SLC6A18 and SLC6A19, regulating their trafficking on the cell surface and their amino acid transporter activity (By similarity). May also play a role in trafficking of amino acid transporters SLC3A1 and SLC7A9 to the renal cortical cell membrane (By similarity). Regulator of SNARE complex function (PubMed:16330323). Stimulator of beta cell replication (PubMed:16330323).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CLTRN Gene

Genomics for CLTRN Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CLTRN Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ015673 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 633.8 -0.2 -214 3.9 SP1 CREB1 PRDM10 ZNF629 POLR2A ZNF692 TARDBP ZHX2 PRDM1 ZNF143 CLTRN CA5BP1 CA5BP1-CA5B ENSG00000285602 CA5B ENSG00000200620 PIR AP1S2 PIGA ZRSR2
GH0XJ015663 Promoter/Enhancer 0.9 EPDnew Ensembl ENCODE dbSUPER 632.6 +11.0 11048 2.4 ZNF652 CLTRN ENSG00000285602 PTMAP14 CA5BP1 CA5BP1-CA5B ACE2
GH0XJ015596 Promoter/Enhancer 1.2 EPDnew Ensembl ENCODE 27.9 +75.9 75913 7 GATAD2A RXRB CEBPA MNT SOX13 TCF7 CEBPB FOXA2 JUN MAFF ACE2 CLTRN PIR CA5BP1 CA5B GS1-594A7.3 lnc-ACE2-1 HNRNPDLP5 ENSG00000285602
GH0XJ015604 Enhancer 0.7 Ensembl ENCODE 40 +69.4 69365 4.5 ZNF316 MAFF MAFK HIC1 ZNF48 EMSY PKNOX1 CLTRN ACE2 GS1-594A7.3 piR-31534-708 ENSG00000285602
GH0XJ015737 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 13.4 -62.9 -62865 2.6 SP1 CREB1 TEAD4 PRDM10 IKZF1 ZNF692 PRDM1 ZNF143 PATZ1 POLR2A CA5B CLTRN CA5BP1 ENSG00000200620 VEGFD piR-32214-707 lnc-CLTRN-2 ZRSR2 CA5BP1-CA5B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLTRN on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CLTRN

Genomic Locations for CLTRN Gene

Genomic Locations for CLTRN Gene
chrX:15,627,318-15,675,624
(GRCh38/hg38)
Size:
48,307 bases
Orientation:
Minus strand
chrX:15,645,441-15,683,154
(GRCh37/hg19)
Size:
37,714 bases
Orientation:
Minus strand

Genomic View for CLTRN Gene

Genes around CLTRN on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLTRN Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLTRN Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLTRN Gene

Proteins for CLTRN Gene

  • Protein details for CLTRN Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HBJ8-CLTRN_HUMAN
    Recommended name:
    Collectrin
    Protein Accession:
    Q9HBJ8
    Secondary Accessions:
    • B2R9M1
    • Q6UW07

    Protein attributes for CLTRN Gene

    Size:
    222 amino acids
    Molecular mass:
    25235 Da
    Quaternary structure:
    • Monomer (PubMed:22628310). Homodimer; dimerization prevents CLTRN cleavage by BACE2 (PubMed:22628310). Interacts with SLC6A18; this interaction regulates the trafficking of SLC6A18 to the cell membrane and its amino acid transporter activity (By similarity). Interacts with SLC6A19; this interaction regulates the trafficking of SLC6A19 to the cell membrane and its amino acid transporter activity (By similarity). Interacts with SNAPIN (PubMed:16330323).
    SequenceCaution:
    • Sequence=AAQ89419.1; Type=Frameshift; Evidence={ECO:0000305};

neXtProt entry for CLTRN Gene

Post-translational modifications for CLTRN Gene

  • Glycosylated. Glycosylation is required for plasma membrane localization and for its cleavage by BACE2.
  • Proteolytically processed in pancreatic beta cells by BACE2 leading to the generation and extracellular release of soluble CLTRN, and a corresponding cell-associated C-terminal fragment which is later cleaved by gamma-secretase. This shedding process inactivates CLTRN (By similarity). Three cleavage sites have been identified for BACE2, two clustered sites after Phe-116 and Leu-118 and a more membrane proximal site at Phe-125; the preferred BACE2 cleavage site seems to be between Phe-125 and Leu-126, Phe-116 and Leu-118 act as alternative sites (PubMed:21907142, PubMed:22628310).
  • Glycosylation at Asn76 and Asn93
  • Modification sites at PhosphoSitePlus

Other Protein References for CLTRN Gene

No data available for DME Specific Peptides for CLTRN Gene

Domains & Families for CLTRN Gene

Gene Families for CLTRN Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Transporters

Protein Domains for CLTRN Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CLTRN Gene

GenScript: Design optimal peptide antigens:
  • Transmembrane protein 27 (TMM27_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9HBJ8

UniProtKB/Swiss-Prot:

CLTRN_HUMAN :
  • The cleavage site containing the double Phe-Phe motif acts as negative regulator of shedding by BACE2.
  • Belongs to the CLTRN family.
Domain:
  • The cleavage site containing the double Phe-Phe motif acts as negative regulator of shedding by BACE2.
Family:
  • Belongs to the CLTRN family.
genes like me logo Genes that share domains with CLTRN: view

Function for CLTRN Gene

Molecular function for CLTRN Gene

UniProtKB/Swiss-Prot Function:
Plays an important role in amino acid transport by acting as binding partner of amino acid transporters SLC6A18 and SLC6A19, regulating their trafficking on the cell surface and their amino acid transporter activity (By similarity). May also play a role in trafficking of amino acid transporters SLC3A1 and SLC7A9 to the renal cortical cell membrane (By similarity). Regulator of SNARE complex function (PubMed:16330323). Stimulator of beta cell replication (PubMed:16330323).

Gene Ontology (GO) - Molecular Function for CLTRN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16330323
GO:0042803 protein homodimerization activity IDA 22628310
genes like me logo Genes that share ontologies with CLTRN: view
genes like me logo Genes that share phenotypes with CLTRN: view

Animal Models for CLTRN Gene

MGI Knock Outs for CLTRN:

Animal Model Products

  • Taconic Biosciences Mouse Models for CLTRN

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for CLTRN Gene

Localization for CLTRN Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLTRN Gene

Cell membrane. Single-pass type I membrane protein. Note=Localizes to the brush border membranes of cells in the proximal tubules of kidney (By similarity). Colocalizes with SLC6A19 in the early proximal S1 tubule (By similarity). {ECO:0000250 UniProtKB:Q9ESG4}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLTRN gene
Compartment Confidence
plasma membrane 5
extracellular 4
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CLTRN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA 16330323
GO:0005886 plasma membrane IEA,IDA 21907142
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0070062 extracellular exosome HDA 19056867
genes like me logo Genes that share ontologies with CLTRN: view

Pathways & Interactions for CLTRN Gene

PathCards logo

SuperPathways for CLTRN Gene

genes like me logo Genes that share pathways with CLTRN: view

Pathways by source for CLTRN Gene

Gene Ontology (GO) - Biological Process for CLTRN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0035543 positive regulation of SNARE complex assembly IDA 16330323
GO:0035774 positive regulation of insulin secretion involved in cellular response to glucose stimulus IDA 16330323
GO:0045956 positive regulation of calcium ion-dependent exocytosis IDA 16330323
GO:0051957 positive regulation of amino acid transport IBA 21873635
genes like me logo Genes that share ontologies with CLTRN: view

No data available for SIGNOR curated interactions for CLTRN Gene

Drugs & Compounds for CLTRN Gene

No Compound Related Data Available

Transcripts for CLTRN Gene

mRNA/cDNA for CLTRN Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Alternative Splicing Database (ASD) splice patterns (SP) for CLTRN Gene

No ASD Table

Relevant External Links for CLTRN Gene

GeneLoc Exon Structure for
CLTRN

Expression for CLTRN Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLTRN

mRNA Expression by UniProt/SwissProt for CLTRN Gene:

Q9HBJ8-CLTRN_HUMAN
Tissue specificity: Kidney; collecting ducts. Pancreas; beta cells of islets.

Evidence on tissue expression from TISSUES for CLTRN Gene

  • Kidney(4.8)
  • Intestine(4.3)
  • Bone marrow(4)
  • Liver(2.4)
  • Pancreas(2.2)
genes like me logo Genes that share expression patterns with CLTRN: view

Primer Products

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLTRN Gene

Orthologs for CLTRN Gene

This gene was present in the common ancestor of animals.

Orthologs for CLTRN Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TMEM27 31
  • 100 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia TMEM27 30 31
  • 90.09 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia TMEM27 30 31
  • 88.74 (n)
OneToMany
-- 31
  • 84 (a)
OneToMany
Mouse
(Mus musculus)
Mammalia Tmem27 30 31
  • 86.64 (n)
OneToOne
Cltrn 17
Rat
(Rattus norvegicus)
Mammalia Tmem27 30
  • 86.34 (n)
Oppossum
(Monodelphis domestica)
Mammalia TMEM27 31
  • 70 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia TMEM27 31
  • 61 (a)
OneToOne
Chicken
(Gallus gallus)
Aves TMEM27 30 31
  • 67.12 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia TMEM27 31
  • 60 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia tmem27 30
  • 55.05 (n)
African clawed frog
(Xenopus laevis)
Amphibia MGC68634 30
Zebrafish
(Danio rerio)
Actinopterygii si:dkey-194e6.1 30
  • 53 (n)
TMEM27 31
  • 40 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Ance-2 31
  • 1 (a)
OneToMany
Ance-4 31
  • 1 (a)
OneToMany
Ance-5 31
  • 1 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea acn-1 31
  • 3 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 15 (a)
ManyToMany
Species where no ortholog for CLTRN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for CLTRN Gene

ENSEMBL:
Gene Tree for CLTRN (if available)
TreeFam:
Gene Tree for CLTRN (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLTRN: view image

Paralogs for CLTRN Gene

Paralogs for CLTRN Gene

genes like me logo Genes that share paralogs with CLTRN: view

Variants for CLTRN Gene

Additional dbSNP identifiers (rs#s) for CLTRN Gene

Structural Variations from Database of Genomic Variants (DGV) for CLTRN Gene

Variant ID Type Subtype PubMed ID
esv2758862 CNV loss 17122850

Variation tolerance for CLTRN Gene

Residual Variation Intolerance Score: 21.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.43; 9.38% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLTRN Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLTRN

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLTRN Gene

Disorders for CLTRN Gene

MalaCards: The human disease database

(7) MalaCards diseases for CLTRN Gene - From: ClinVar, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search CLTRN in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with CLTRN: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLTRN Gene

Publications for CLTRN Gene

  1. Collectrin, a collecting duct-specific transmembrane glycoprotein, is a novel homolog of ACE2 and is developmentally regulated in embryonic kidneys. (PMID: 11278314) Zhang H … Makino H (The Journal of biological chemistry 2001) 2 3 4 23
  2. Tmem27 dimerization, deglycosylation, plasma membrane depletion, and the extracellular Phe-Phe motif are negative regulators of cleavage by Bace2. (PMID: 22628310) Esterházy D … Stoffel M (Biological chemistry 2012) 3 4
  3. Bace2 is a β cell-enriched protease that regulates pancreatic β cell function and mass. (PMID: 21907142) Esterházy D … Stoffel M (Cell metabolism 2011) 3 4
  4. Not just angiotensinases: new roles for the angiotensin-converting enzymes. (PMID: 19763395) Lambert DW … Turner AJ (Cellular and molecular life sciences : CMLS 2010) 3 23
  5. The role of transmembrane protein 27 (TMEM27) in islet physiology and its potential use as a beta cell mass biomarker. (PMID: 20386877) Altirriba J … Gomis R (Diabetologia 2010) 3 23

Products for CLTRN Gene

Sources for CLTRN Gene