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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
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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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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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