SLC46A3 solute carrier family 46 member 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC46A3provided by HGNC
Official Full Name: solute carrier family 46 member 3provided by HGNC
Primary source: HGNC:HGNC:27501
See related: Ensembl:ENSG00000139508 MIM:616764; AllianceGenome:HGNC:27501
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: FKSG16
Summary: The protein encoded by this gene is a member of a transmembrane protein family that transports small molecules across membranes. The encoded protein has been found in lysosomal membranes, where it can transport catabolites from the lysosomes to the cytoplasm. This protein has been shown to be an effective transporter of the cytotoxic drug maytansine, which is used in antibody-based targeting of cancer cells. [provided by RefSeq, Dec 2016]
Expression: Broad expression in small intestine (RPKM 41.0), duodenum (RPKM 24.5) and 21 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q12.3

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (28700080..28718970, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (27923367..27942251, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (29274217..29293107, complement)

Chromosome 13 - NC_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

our results establish SLC46A3 as a direct transporter of maytansine-based catabolites from the lysosome to the cytoplasm
Title: SLC46A3 Is Required to Transport Catabolites of Noncleavable Antibody Maytansine Conjugates from the Lysosome to the Cytoplasm.

Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH93198 (e-PCR)
- UniSTS:87041

D8S2279 (e-PCR)
- UniSTS:473907

SHGC-145990 (e-PCR)
- UniSTS:174922

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables copper ion transmembrane transporter activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables symporter activity	IEA Inferred from Electronic Annotation more info
enables transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables transmembrane transporter activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in cellular response to 2,3,7,8-tetrachlorodibenzodioxine	IEA Inferred from Electronic Annotation more info
involved_in copper ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in vacuolar transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in vacuolar transmembrane transport	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular exosome	HDA more info	PubMed
is_active_in lysosomal membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in lysosomal membrane	IMP Inferred from Mutant Phenotype more info	PubMed

General protein information

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Preferred Names: lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3

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.

Genomic

NG_053189.2 RefSeqGene

Range

5000..23890

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001135919.2 → NP_001129391.1 lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3 isoform b precursor

See identical proteins and their annotated locations for NP_001129391.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks a segment in the 3' coding region, which results in a frameshift, compared to variant 1. The resulting protein has a distinct and longer C-terminus when it is compared to isoform a.

Source sequence(s)

AL359454

Consensus CDS

CCDS45021.1

UniProtKB/TrEMBL

B3KSM7

Related

ENSP00000370192.4, ENST00000380814.4

Conserved Domains (1) summary

pfam07690
Location:81 → 399

MFS_1; Major Facilitator Superfamily
NM_001347960.2 → NP_001334889.1 lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3 isoform a precursor

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 and 3 both encode the same isoform (a).

Source sequence(s)

AL359454

Consensus CDS

CCDS9332.1

UniProtKB/Swiss-Prot

Q3ZCV8, Q6NUK5, Q6P9B3, Q6ZVG5, Q7Z3Q1, Q96QA1

UniProtKB/TrEMBL

B3KSM7
NM_181785.4 → NP_861450.1 lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3 isoform a precursor

See identical proteins and their annotated locations for NP_861450.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript yet it encodes the shorter isoform (a). Variants 1 and 3 both encode the same isoform (a).

Source sequence(s)

AL359454

Consensus CDS

CCDS9332.1

UniProtKB/Swiss-Prot

Q3ZCV8, Q6NUK5, Q6P9B3, Q6ZVG5, Q7Z3Q1, Q96QA1

UniProtKB/TrEMBL

B3KSM7

Related

ENSP00000266943.7, ENST00000266943.11

Conserved Domains (2) summary

cd06174
Location:81 → 409

MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...

pfam07690
Location:81 → 399

MFS_1; Major Facilitator Superfamily

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_000013.11 Reference GRCh38.p14 Primary Assembly

Range

28700080..28718970 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005266361.3 → XP_005266418.1 lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3 isoform X1

See identical proteins and their annotated locations for XP_005266418.1

UniProtKB/TrEMBL

B3KSM7

Conserved Domains (1) summary

pfam07690
Location:81 → 399

MFS_1; Major Facilitator Superfamily