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    SLC5A6 solute carrier family 5 member 6 [ Homo sapiens (human) ]

    Gene ID: 8884, updated on 3-Apr-2024

    Summary

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    Official Symbol
    SLC5A6provided by HGNC
    Official Full Name
    solute carrier family 5 member 6provided by HGNC
    Primary source
    HGNC:HGNC:11041
    See related
    Ensembl:ENSG00000138074 MIM:604024; AllianceGenome:HGNC:11041
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SMVT; COMNB; NERIB; SMVTD; hSMVT
    Summary
    Enables biotin transmembrane transporter activity and pantothenate transmembrane transporter activity. Involved in anion transmembrane transport and transport across blood-brain barrier. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in placenta (RPKM 17.5), testis (RPKM 16.1) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    2p23.3
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (27199587..27212787, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (27241206..27254815, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (27422455..27435136, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene proline rich 30 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15492 Neighboring gene transcription factor 23 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15493 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11288 Neighboring gene Sharpr-MPRA regulatory region 2640 Neighboring gene MPRA-validated peak3631 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:27432993-27433790 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11289 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11290 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11291 Neighboring gene all-trans retinoic acid induced differentiation factor Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:27454350-27455549 Neighboring gene carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:27465505-27466704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:27472326-27473120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:27473121-27473914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11292 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11293 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11294 Neighboring gene solute carrier family 30 member 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11295 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11296 Neighboring gene DnaJ heat shock protein family (Hsp40) member C5 gamma

    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. Novel biallelic variants expand the SLC5A6-related phenotypic spectrum. Holling T, et al. Eur J Hum Genet, 2022 Apr. PMID 35013551, Free PMC Article
    2. Identification and targeted management of a neurodegenerative disorder caused by biallelic mutations in SLC5A6. Byrne AB, et al. NPJ Genom Med, 2019. PMID 31754459, Free PMC Article
    3. Mutations in SLC5A6 associated with brain, immune, bone, and intestinal dysfunction in a young child. Subramanian VS, et al. Hum Genet, 2017 Feb. PMID 27904971, Free PMC Article
    4. Interaction of α-Lipoic Acid with the Human Na+/Multivitamin Transporter (hSMVT). Zehnpfennig B, et al. J Biol Chem, 2015 Jun 26. PMID 25971966, Free PMC Article
    5. Biotin uptake by T47D breast cancer cells: functional and molecular evidence of sodium-dependent multivitamin transporter (SMVT). Vadlapudi AD, et al. Int J Pharm, 2013 Jan 30. PMID 23142496

    See all (57) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel missense variants cause intermediate phenotypes in the phenotypic spectrum of SLC5A6-related disorders.
      Title: Novel missense variants cause intermediate phenotypes in the phenotypic spectrum of SLC5A6-related disorders.
    2. Novel SLC5A6 mutations lead to B lymphocyte maturation defects with metabolic abnormality rescuable by biotin replenishment.
      Title: Novel SLC5A6 mutations lead to B lymphocyte maturation defects with metabolic abnormality rescuable by biotin replenishment.
    3. A novel SLC5A6 homozygous variant in a family with multivitamin-dependent neurometabolic disorder: Phenotype expansion and long-term follow-up.
      Title: A novel SLC5A6 homozygous variant in a family with multivitamin-dependent neurometabolic disorder: Phenotype expansion and long-term follow-up.
    4. Novel biallelic variants expand the SLC5A6-related phenotypic spectrum.
      Title: Novel biallelic variants expand the SLC5A6-related phenotypic spectrum.
    5. Integrated profiling identifies SLC5A6 and MFAP2 as novel diagnostic and prognostic biomarkers in gastric cancer patients.
      Title: Integrated profiling identifies SLC5A6 and MFAP2 as novel diagnostic and prognostic biomarkers in gastric cancer patients.
    6. This study shows for the first time that LPS inhibits colonic biotin uptake via decreasing membrane expression of its transporter and that these effects likely involve a CK2-mediated pathway.
      Title: Lipopolysaccharide inhibits colonic biotin uptake via interference with membrane expression of its transporter: a role for a casein kinase 2-mediated pathway.
    7. S. typhimurium infection inhibits intestinal biotin uptake by SLC5A6, and that the inhibition is mediated via the action of proinflammatory cytokines.
      Title: Salmonella infection inhibits intestinal biotin transport: cellular and molecular mechanisms.
    8. SMVT-mediated transport is highly specific for R-(+)-alpha-lipoic acid.
      Title: Interaction of α-Lipoic Acid with the Human Na+/Multivitamin Transporter (hSMVT).
    9. SLC5A6 is responsible for the supplies of biotin and pantothenic acid into the brain across the blood brain barrier.
      Title: Major involvement of Na(+) -dependent multivitamin transporter (SLC5A6/SMVT) in uptake of biotin and pantothenic acid by human brain capillary endothelial cells.
    10. these studies demonstrated for the first time the functional and molecular expression of sodium dependent multivitamin transporter (SMVT) in human derived breast cancer (T47D) cells
      Title: Biotin uptake by T47D breast cancer cells: functional and molecular evidence of sodium-dependent multivitamin transporter (SMVT).
    Submit: New GeneRIF Correction See all GeneRIFs (26)

    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
    Neurodegeneration, infantile-onset, biotin-responsive
    MedGen: C5436520 OMIM: 618973 GeneReviews: Not available
    		Compare labs
    Peripheral motor neuropathy, childhood-onset, biotin-responsive
    MedGen: C5676997 OMIM: 619903 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    An atlas of genetic influences on human blood metabolites.
    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of SLC5A6 PubMed

    Go to the HIV-1, Human Interaction Database

    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 biotin transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables biotin transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables iodide transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables monocarboxylate:sodium symporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables pantothenate transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables pantothenate transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables pantothenate:sodium symporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sodium-dependent multivitamin transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables vitamin transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables vitamin transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in biotin import across plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in biotin import across plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in biotin metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in biotin transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in biotin transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in biotin transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in iodide transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in pantothenate transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in pantothenate transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in pantothenate transmembrane transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in sodium ion import across plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in sodium ion transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transport across blood-brain barrier IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in transport across blood-brain barrier NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in apical plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in apical plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in basal plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in basolateral plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in brush border membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    sodium-dependent multivitamin transporter
    Names
    Na(+)-dependent multivitamin transporter
    Na+-dependent multivitamin transporter
    solute carrier family 5 (sodium-dependent vitamin transporter), member 6
    solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6

    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.

    mRNA and Protein(s)

    1. NM_021095.4 → NP_066918.2  sodium-dependent multivitamin transporter

      See identical proteins and their annotated locations for NP_066918.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the functional protein.
      Source sequence(s)
      AC013403
      Consensus CDS
      CCDS1740.1
      UniProtKB/Swiss-Prot
      B2RB85, D6W549, Q969Y5, Q9Y289
      Related
      ENSP00000310208.3, ENST00000310574.8
      Conserved Domains (1) summary
      cd11504
      Location:24 → 550
      SLC5sbd_SMVT; Na(+)/multivitamin cotransporter SMVT and related proteins; solute-binding domain

    RNA

    1. NR_028323.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has two differences in the presence and absence of alternate segments, compared to variant 1. This variant is represented as non-coding because the use of the 5' most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC013403
      Related
      ENST00000488743.6

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      27199587..27212787 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047446243.1 → XP_047302199.1  sodium-dependent multivitamin transporter isoform X1

      UniProtKB/Swiss-Prot
      B2RB85, D6W549, Q969Y5, Q9Y289

    2. XM_024453206.2 → XP_024308974.1  sodium-dependent multivitamin transporter isoform X2

      Conserved Domains (1) summary
      cl00456
      Location:24 → 517
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

    3. XM_024453207.2 → XP_024308975.1  sodium-dependent multivitamin transporter isoform X3

      Conserved Domains (1) summary
      cl00456
      Location:24 → 515
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

    4. XM_006712129.2 → XP_006712192.1  sodium-dependent multivitamin transporter isoform X1

      See identical proteins and their annotated locations for XP_006712192.1

      UniProtKB/Swiss-Prot
      B2RB85, D6W549, Q969Y5, Q9Y289
      Conserved Domains (1) summary
      cd11504
      Location:24 → 550
      SLC5sbd_SMVT; Na(+)/multivitamin cotransporter SMVT and related proteins; solute-binding domain

    5. XM_047446244.1 → XP_047302200.1  sodium-dependent multivitamin transporter isoform X3

    6. XM_047446245.1 → XP_047302201.1  sodium-dependent multivitamin transporter isoform X3

    7. XM_006712130.2 → XP_006712193.1  sodium-dependent multivitamin transporter isoform X1

      See identical proteins and their annotated locations for XP_006712193.1

      UniProtKB/Swiss-Prot
      B2RB85, D6W549, Q969Y5, Q9Y289
      Conserved Domains (1) summary
      cd11504
      Location:24 → 550
      SLC5sbd_SMVT; Na(+)/multivitamin cotransporter SMVT and related proteins; solute-binding domain

    8. XM_047446246.1 → XP_047302202.1  sodium-dependent multivitamin transporter isoform X3

    9. XM_006712128.3 → XP_006712191.1  sodium-dependent multivitamin transporter isoform X1

      See identical proteins and their annotated locations for XP_006712191.1

      UniProtKB/Swiss-Prot
      B2RB85, D6W549, Q969Y5, Q9Y289
      Related
      ENSP00000384853.1, ENST00000408041.5
      Conserved Domains (1) summary
      cd11504
      Location:24 → 550
      SLC5sbd_SMVT; Na(+)/multivitamin cotransporter SMVT and related proteins; solute-binding domain

    10. XM_047446248.1 → XP_047302204.1  sodium-dependent multivitamin transporter isoform X5

    11. XM_047446247.1 → XP_047302203.1  sodium-dependent multivitamin transporter isoform X4

    12. XM_047446249.1 → XP_047302205.1  sodium-dependent multivitamin transporter isoform X6

    RNA

    1. XR_007084322.1 RNA Sequence

    2. XR_002959357.2 RNA Sequence

    3. XR_002959358.2 RNA Sequence

    4. XR_002959356.2 RNA Sequence

    5. XR_001739022.2 RNA Sequence

    6. XR_001739023.2 RNA Sequence

    7. XR_001739024.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      27241206..27254815 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054344405.1 → XP_054200380.1  sodium-dependent multivitamin transporter isoform X1

      UniProtKB/Swiss-Prot
      B2RB85, D6W549, Q969Y5, Q9Y289

    2. XM_054344406.1 → XP_054200381.1  sodium-dependent multivitamin transporter isoform X2

    3. XM_054344407.1 → XP_054200382.1  sodium-dependent multivitamin transporter isoform X3

    4. XM_054344403.1 → XP_054200378.1  sodium-dependent multivitamin transporter isoform X1

      UniProtKB/Swiss-Prot
      B2RB85, D6W549, Q969Y5, Q9Y289

    5. XM_054344409.1 → XP_054200384.1  sodium-dependent multivitamin transporter isoform X3

    6. XM_054344404.1 → XP_054200379.1  sodium-dependent multivitamin transporter isoform X1

      UniProtKB/Swiss-Prot
      B2RB85, D6W549, Q969Y5, Q9Y289

    7. XM_054344408.1 → XP_054200383.1  sodium-dependent multivitamin transporter isoform X3

    8. XM_054344410.1 → XP_054200385.1  sodium-dependent multivitamin transporter isoform X3

    9. XM_054344402.1 → XP_054200377.1  sodium-dependent multivitamin transporter isoform X1

      UniProtKB/Swiss-Prot
      B2RB85, D6W549, Q969Y5, Q9Y289

    10. XM_054344412.1 → XP_054200387.1  sodium-dependent multivitamin transporter isoform X5

    11. XM_054344411.1 → XP_054200386.1  sodium-dependent multivitamin transporter isoform X4

    12. XM_054344413.1 → XP_054200388.1  sodium-dependent multivitamin transporter isoform X6

    RNA

    1. XR_008486596.1 RNA Sequence

    2. XR_008486597.1 RNA Sequence

    3. XR_008486598.1 RNA Sequence

    4. XR_008486592.1 RNA Sequence

    5. XR_008486595.1 RNA Sequence

    6. XR_008486593.1 RNA Sequence

    7. XR_008486594.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y289.2 GenPept UniProtKB/Swiss-Prot:Q9Y289

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