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
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

Location:: 2p23.3

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (27199587..27212787, complement)
110	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (27241206..27253903, complement)
105.20220307	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:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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).
This study shows for the first time the functional and molecular presence of SMVT in immortalized human corneal epithelial (HCEC) and retinal pigment epithelial (D407) cells
Title: Functional and molecular aspects of biotin uptake via SMVT in human corneal epithelial (HCEC) and retinal pigment epithelial (D407) cells.
PCR analysis had confirmed the existence of FR-alpha, SMVT, and B ((0, +)) in Y-79 and ARPE-19 cells.
Title: Differential expression of folate receptor-alpha, sodium-dependent multivitamin transporter, and amino acid transporter (B (0, +)) in human retinoblastoma (Y-79) and retinal pigment epithelial (ARPE-19) cell lines.
This study for the first time confirms the molecular expression of SMVT and demonstrates that SMVT, responsible for biotin uptake, is functionally active in PC-3 prostate cancer cells
Title: Molecular expression and functional activity of sodium dependent multivitamin transporter in human prostate cancer cells.

Submit: New GeneRIF Correction See all GeneRIFs (23)

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 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

Homology

Homologs of the SLC5A6 gene: The SLC5A6 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, zebrafish, and frog.
Orthologs from Annotation Pipeline: 419 organisms have orthologs with human gene SLC5A6
Orthologs

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 pantothenate transmembrane transporter activity	IMP Inferred from Mutant Phenotype more info	PubMed
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	PubMed
enables vitamin transmembrane transporter activity	IDA Inferred from Direct Assay 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 transport	IBA Inferred from Biological aspect of Ancestor 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	PubMed
involved_in pantothenate transmembrane transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sodium ion transport	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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	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
located_in vesicle membrane	IEA Inferred from Electronic Annotation 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

Q969Y5, Q9Y289

UniProtKB/TrEMBL

Q9HD19

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: Homo sapiens Annotation Release 110 details...

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

Q969Y5
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

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

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

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
XM_047446247.1 → XP_047302203.1 sodium-dependent multivitamin transporter isoform X4
XM_047446249.1 → XP_047302205.1 sodium-dependent multivitamin transporter isoform X6