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    SLC22A5 solute carrier family 22 member 5 [ Homo sapiens (human) ]

    Gene ID: 6584, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SLC22A5provided by HGNC
    Official Full Name
    solute carrier family 22 member 5provided by HGNC
    Primary source
    HGNC:HGNC:10969
    See related
    Ensembl:ENSG00000197375 MIM:603377; AllianceGenome:HGNC:10969
    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
    CDSP; OCTN2
    Summary
    Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. The encoded protein is a plasma integral membrane protein which functions both as an organic cation transporter and as a sodium-dependent high affinity carnitine transporter. The encoded protein is involved in the active cellular uptake of carnitine. Mutations in this gene are the cause of systemic primary carnitine deficiency (CDSP), an autosomal recessive disorder manifested early in life by hypoketotic hypoglycemia and acute metabolic decompensation, and later in life by skeletal myopathy or cardiomyopathy. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2015]
    Expression
    Broad expression in kidney (RPKM 17.3), small intestine (RPKM 11.3) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC22A5 in Genome Data Viewer
    Location:
    5q31.1
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (132369710..132395612)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (132889604..132915514)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (131705402..131731304)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16316 Neighboring gene solute carrier family 22 member 4 Neighboring gene MIR3936 host gene Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:131656893-131657393 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131657550-131658068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131658069-131658587 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:131681529-131681701 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:131690402-131691014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23067 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16317 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131712295-131712796 Neighboring gene microRNA 3936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23070 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23071 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16318 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16319 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:131751322-131751510 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23075 Neighboring gene long intergenic non-protein coding RNA 2863 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131763030-131763616 Neighboring gene colitis associated IRF1 antisense regulator of intestinal homeostasis Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131763617-131764201 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:131780806-131781485 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:131786393-131787031 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:131791634-131791826 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131792105-131792775 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131792776-131793445 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131799668-131800632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131800633-131801597 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131801783-131802284 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16323 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23079 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23080 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:131821689-131822888 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16324 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131825338-131825985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16326 Neighboring gene interferon regulatory factor 1

    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. Abnormal Newborn Screening in a Healthy Infant of a Mother with Undiagnosed Medium-Chain Acyl-CoA Dehydrogenase Deficiency. Aksglaede L, et al. JIMD Rep, 2015. PMID 25763512, Free PMC Article
    2. Systemic Primary Carnitine Deficiency. Adam MP, et al. , 1993. PMID 22420015
    3. Primary carnitine deficiency: novel mutations and insights into the cardiac phenotype. Shibbani K, et al. Clin Genet, 2014 Feb. PMID 23379544
    4. Validation of dye-binding/high-resolution thermal denaturation for the identification of mutations in the SLC22A5 gene. Dobrowolski SF, et al. Hum Mutat, 2005 Mar. PMID 15714519
    5. Functional expression of organic cation/carnitine transporter 2 (OCTN2/SLC22A5) in human brain capillary endothelial cell line hCMEC/D3, a human blood-brain barrier model. Okura T, et al. Drug Metab Pharmacokinet, 2014. PMID 23877104

    See all (196) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The activity and surface presence of organic cation/carnitine transporter OCTN2 (SLC22A5) in breast cancer cells depends on AKT kinase.
      Title: The activity and surface presence of organic cation/carnitine transporter OCTN2 (SLC22A5) in breast cancer cells depends on AKT kinase.
    2. Evaluation of the gene encoding carnitine transporter (OCTN2/SLC22A5) expression in human breast cancer and its association with clinicopathological characteristics.
      Title: Evaluation of the gene encoding carnitine transporter (OCTN2/SLC22A5) expression in human breast cancer and its association with clinicopathological characteristics.
    3. Functional genomics of OCTN2 variants informs protein-specific variant effect predictor for Carnitine Transporter Deficiency.
      Title: Functional genomics of OCTN2 variants informs protein-specific variant effect predictor for Carnitine Transporter Deficiency.
    4. [Analysis of metabolic profile and genetic variants for newborns with primary carnitine deficiency from Guangxi].
      Title: [Analysis of metabolic profile and genetic variants for newborns with primary carnitine deficiency from Guangxi].
    5. Screening and follow-up results of fatty acid oxidative metabolism disorders in 608 818 newborns in Jining, Shandong province.
      Title: Screening and follow-up results of fatty acid oxidative metabolism disorders in 608 818 newborns in Jining, Shandong province.
    6. Cholesterol stimulates the cellular uptake of L-carnitine by the carnitine/organic cation transporter novel 2 (OCTN2).
      Title: Cholesterol stimulates the cellular uptake of L-carnitine by the carnitine/organic cation transporter novel 2 (OCTN2).
    7. LPS-induced inflammation delays the transportation of ASP(+) due to down-regulation of OCTN1/2 in alveolar epithelial cells.
      Title: LPS-induced inflammation delays the transportation of ASP(+) due to down-regulation of OCTN1/2 in alveolar epithelial cells.
    8. Glioma cells survival depends both on fatty acid oxidation and on functional carnitine transport by SLC22A5.
      Title: Glioma cells survival depends both on fatty acid oxidation and on functional carnitine transport by SLC22A5.
    9. Tooth loss and adiposity: possible role of carnitine transporter (OCTN1/2) polymorphisms in women but not in men.
      Title: Tooth loss and adiposity: possible role of carnitine transporter (OCTN1/2) polymorphisms in women but not in men.
    10. Biochemical and genetic characteristics of 40 neonates with carnitine deficiency.", trans "40.
      Title: Biochemical and genetic characteristics of 40 neonates with carnitine deficiency.
    Submit: New GeneRIF Correction See all GeneRIFs (116)

    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

    Associated conditions

    Description Tests
    Renal carnitine transport defect
    MedGen: C0342788 OMIM: 212140 GeneReviews: Systemic Primary Carnitine Deficiency
    		Compare labs

    EBI GWAS Catalog

    Description
    A large-scale, consortium-based genomewide association study of asthma.
    EBI GWAS Catalog
    An atlas of genetic influences on human blood metabolites.
    EBI GWAS Catalog
    Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
    EBI GWAS Catalog
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog
    Novel loci, including those related to Crohn disease, psoriasis, and inflammation, identified in a genome-wide association study of fibrinogen in 17 686 women: the Women's Genome Health Study.
    EBI GWAS Catalog

    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

    Clone Names

    • FLJ46769

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NOT enables (R)-carnitine transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables (R)-carnitine transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables (R)-carnitine transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables (R)-carnitine transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables PDZ domain binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables amino-acid betaine transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables carnitine transmembrane transporter activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables carnitine transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables carnitine transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables carnitine transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables quaternary ammonium group transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables quaternary ammonium group transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables quaternary ammonium group transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables symporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables xenobiotic transmembrane transporter activity IC
    Inferred by Curator
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in (R)-carnitine transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in (R)-carnitine transmembrane transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in (R)-carnitine transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    NOT involved_in (R)-carnitine transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in (R)-carnitine transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in carnitine transmembrane transport TAS
    Traceable Author Statement
    more info
    		  
    involved_in carnitine transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in carnitine transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of intestinal epithelial structure maintenance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in quaternary ammonium group transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in quaternary ammonium group transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in quaternary ammonium group transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to symbiotic bacterium IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to tumor necrosis factor IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to type II interferon IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in sodium ion transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in sodium-dependent organic cation transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in transport across blood-brain barrier ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in transport across blood-brain barrier NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in xenobiotic detoxification by transmembrane export across the plasma membrane IC
    Inferred by Curator
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in apical plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in basal plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in brush border membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in brush border membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in plasma membrane IC
    Inferred by Curator
    more info
    		 PubMed 
    NOT located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    organic cation/carnitine transporter 2
    Names
    high-affinity sodium dependent carnitine cotransporter
    systemic carnitine deficiency

    NCBI Reference Sequences (RefSeq)

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    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.

    Genomic

    1. NG_008982.2 RefSeqGene

      Range
      5007..30909
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001308122.2 → NP_001295051.1  organic cation/carnitine transporter 2 isoform a

      See identical proteins and their annotated locations for NP_001295051.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, also known as OCTN2VT) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AB291606, AK128610, DA567722
      Consensus CDS
      CCDS78058.1
      UniProtKB/TrEMBL
      A0A8I5KTN6
      Related
      ENSP00000402760.2, ENST00000435065.7
      Conserved Domains (2) summary
      cd06174
      Location:162 → 534
      MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
      TIGR00898
      Location:12 → 544
      2A0119; cation transport protein

    2. NM_003060.4 → NP_003051.1  organic cation/carnitine transporter 2 isoform b

      See identical proteins and their annotated locations for NP_003051.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
      Source sequence(s)
      AF057164, AK128610, BC012325, DA186237, DA567722
      Consensus CDS
      CCDS4154.1
      UniProtKB/Swiss-Prot
      A2Q0V1, B2R844, D3DQ87, O76082, Q6ZQZ8, Q96EH6
      UniProtKB/TrEMBL
      A0A8I5KTN6
      Related
      ENSP00000245407.3, ENST00000245407.8
      Conserved Domains (2) summary
      cd06174
      Location:123 → 510
      MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
      TIGR00898
      Location:12 → 520
      2A0119; cation transport protein

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      132369710..132395612
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017009778.3 → XP_016865267.1  organic cation/carnitine transporter 2 isoform X1

      UniProtKB/TrEMBL
      Q59FH6

    2. XM_047417595.1 → XP_047273551.1  organic cation/carnitine transporter 2 isoform X2

      Related
      ENSP00000401860.2, ENST00000448810.6

    3. XM_047417597.1 → XP_047273553.1  organic cation/carnitine transporter 2 isoform X5

      Related
      ENSP00000510721.1, ENST00000686757.1

    4. XM_047417598.1 → XP_047273554.1  organic cation/carnitine transporter 2 isoform X6

    5. XM_047417596.1 → XP_047273552.1  organic cation/carnitine transporter 2 isoform X3

    6. XM_011543590.3 → XP_011541892.1  organic cation/carnitine transporter 2 isoform X4

      Conserved Domains (1) summary
      cd06174
      Location:132 → 304
      MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      132889604..132915514
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353250.1 → XP_054209225.1  organic cation/carnitine transporter 2 isoform X1

    2. XM_054353251.1 → XP_054209226.1  organic cation/carnitine transporter 2 isoform X2

    3. XM_054353254.1 → XP_054209229.1  organic cation/carnitine transporter 2 isoform X5

    4. XM_054353255.1 → XP_054209230.1  organic cation/carnitine transporter 2 isoform X6

    5. XM_054353252.1 → XP_054209227.1  organic cation/carnitine transporter 2 isoform X3

    6. XM_054353253.1 → XP_054209228.1  organic cation/carnitine transporter 2 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O76082.1 GenPept UniProtKB/Swiss-Prot:O76082

    Gene LinkOut

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