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

Summary

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

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_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
Collectrin and ACE2 in renal and intestinal amino acid transport.
Title: Collectrin and ACE2 in renal and intestinal amino acid transport.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

CHLC.GGAT16F07 (e-PCR)
- UniSTS:28307

DXS197 (e-PCR)
- UniSTS:148893

DXS197 (e-PCR)
- UniSTS:154337

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 more info	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

NG_015970.1 RefSeqGene

Range

5227..42714

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

15627318..15675644 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
XM_017029681.2 → XP_016885170.1 collectrin isoform X1