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

    Gene ID: 8884, updated on 17-Jun-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SLC5A6 in Genome Data Viewer
    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    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

    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)

    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_021095.4NP_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:24550
      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_047446243.1XP_047302199.1  sodium-dependent multivitamin transporter isoform X1

      UniProtKB/Swiss-Prot
      B2RB85, D6W549, Q969Y5, Q9Y289
    2. XM_024453206.2XP_024308974.1  sodium-dependent multivitamin transporter isoform X2

      Conserved Domains (1) summary
      cl00456
      Location:24517
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    3. XM_024453207.2XP_024308975.1  sodium-dependent multivitamin transporter isoform X3

      Conserved Domains (1) summary
      cl00456
      Location:24515
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    4. XM_006712129.2XP_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:24550
      SLC5sbd_SMVT; Na(+)/multivitamin cotransporter SMVT and related proteins; solute-binding domain
    5. XM_047446244.1XP_047302200.1  sodium-dependent multivitamin transporter isoform X3

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

    7. XM_006712130.2XP_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:24550
      SLC5sbd_SMVT; Na(+)/multivitamin cotransporter SMVT and related proteins; solute-binding domain
    8. XM_047446246.1XP_047302202.1  sodium-dependent multivitamin transporter isoform X3

    9. XM_006712128.3XP_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:24550
      SLC5sbd_SMVT; Na(+)/multivitamin cotransporter SMVT and related proteins; solute-binding domain
    10. XM_047446248.1XP_047302204.1  sodium-dependent multivitamin transporter isoform X5

      UniProtKB/TrEMBL
      B4DDE5
    11. XM_047446247.1XP_047302203.1  sodium-dependent multivitamin transporter isoform X4

      UniProtKB/TrEMBL
      B4DDE5
    12. XM_047446249.1XP_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_054344405.1XP_054200380.1  sodium-dependent multivitamin transporter isoform X1

      UniProtKB/Swiss-Prot
      B2RB85, D6W549, Q969Y5, Q9Y289
    2. XM_054344406.1XP_054200381.1  sodium-dependent multivitamin transporter isoform X2

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

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

      UniProtKB/Swiss-Prot
      B2RB85, D6W549, Q969Y5, Q9Y289
    5. XM_054344409.1XP_054200384.1  sodium-dependent multivitamin transporter isoform X3

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

      UniProtKB/Swiss-Prot
      B2RB85, D6W549, Q969Y5, Q9Y289
    7. XM_054344408.1XP_054200383.1  sodium-dependent multivitamin transporter isoform X3

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

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

      UniProtKB/Swiss-Prot
      B2RB85, D6W549, Q969Y5, Q9Y289
    10. XM_054344412.1XP_054200387.1  sodium-dependent multivitamin transporter isoform X5

      UniProtKB/TrEMBL
      B4DDE5
    11. XM_054344411.1XP_054200386.1  sodium-dependent multivitamin transporter isoform X4

      UniProtKB/TrEMBL
      B4DDE5
    12. XM_054344413.1XP_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