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

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; iodide transmembrane transporter activity; and pantothenate transmembrane transporter activity. Involved in iodide transmembrane transport; transport across blood-brain barrier; and vitamin transmembrane transport. Located in apical plasma membrane. [provided by Alliance of Genome Resources, Dec 2024]
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

Location:: 2p23.3

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (27199587..27212787, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (27241206..27254815, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (27422455..27435136, complement)

Chromosome 2 - NC_000002.12 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
Novel biallelic variants expand the SLC5A6-related phenotypic spectrum.
Title: Novel biallelic variants expand the SLC5A6-related phenotypic spectrum.
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.
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.
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.
SMVT-mediated transport is highly specific for R-(+)-alpha-lipoic acid.
Title: Interaction of α-Lipoic Acid with the Human Na+/Multivitamin Transporter (hSMVT).
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.
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	not available
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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-19577 (e-PCR)
- UniSTS:33556

RH102984 (e-PCR)
- UniSTS:97318

G62043 (e-PCR)
- UniSTS:139137

G59682 (e-PCR)
- UniSTS:136836

RH45418 (e-PCR)
- UniSTS:16518

G19673 (e-PCR)
- UniSTS:45261

A001U43 (e-PCR)
- UniSTS:45262

RH45117 (e-PCR)
- UniSTS:46287

PMC166200P4 (e-PCR)
- UniSTS:271576

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)

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

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_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

27199587..27212787 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

B2RB85, D6W549, Q969Y5, Q9Y289
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
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
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
XM_047446244.1 → XP_047302200.1 sodium-dependent multivitamin transporter isoform X3
XM_047446245.1 → XP_047302201.1 sodium-dependent multivitamin transporter isoform X3
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
XM_047446246.1 → XP_047302202.1 sodium-dependent multivitamin transporter isoform X3
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
XM_047446248.1 → XP_047302204.1 sodium-dependent multivitamin transporter isoform X5

UniProtKB/TrEMBL

B4DDE5
XM_047446247.1 → XP_047302203.1 sodium-dependent multivitamin transporter isoform X4

UniProtKB/TrEMBL

B4DDE5
XM_047446249.1 → XP_047302205.1 sodium-dependent multivitamin transporter isoform X6

RNA

XR_007084322.1 RNA Sequence
XR_002959357.2 RNA Sequence
XR_002959358.2 RNA Sequence
XR_002959356.2 RNA Sequence
XR_001739022.2 RNA Sequence
XR_001739023.2 RNA Sequence
XR_001739024.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

27241206..27254815 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

B2RB85, D6W549, Q969Y5, Q9Y289
XM_054344406.1 → XP_054200381.1 sodium-dependent multivitamin transporter isoform X2
XM_054344407.1 → XP_054200382.1 sodium-dependent multivitamin transporter isoform X3
XM_054344403.1 → XP_054200378.1 sodium-dependent multivitamin transporter isoform X1

UniProtKB/Swiss-Prot

B2RB85, D6W549, Q969Y5, Q9Y289
XM_054344409.1 → XP_054200384.1 sodium-dependent multivitamin transporter isoform X3
XM_054344404.1 → XP_054200379.1 sodium-dependent multivitamin transporter isoform X1

UniProtKB/Swiss-Prot

B2RB85, D6W549, Q969Y5, Q9Y289
XM_054344408.1 → XP_054200383.1 sodium-dependent multivitamin transporter isoform X3
XM_054344410.1 → XP_054200385.1 sodium-dependent multivitamin transporter isoform X3
XM_054344402.1 → XP_054200377.1 sodium-dependent multivitamin transporter isoform X1

UniProtKB/Swiss-Prot

B2RB85, D6W549, Q969Y5, Q9Y289
XM_054344412.1 → XP_054200387.1 sodium-dependent multivitamin transporter isoform X5

UniProtKB/TrEMBL

B4DDE5
XM_054344411.1 → XP_054200386.1 sodium-dependent multivitamin transporter isoform X4

UniProtKB/TrEMBL

B4DDE5
XM_054344413.1 → XP_054200388.1 sodium-dependent multivitamin transporter isoform X6