SLC46A2 solute carrier family 46 member 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC46A2provided by HGNC
Official Full Name: solute carrier family 46 member 2provided by HGNC
Primary source: HGNC:HGNC:16055
See related: Ensembl:ENSG00000119457 MIM:608956; AllianceGenome:HGNC:16055
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: Ly110; TSCOT
Summary: Predicted to enable transmembrane transporter activity. Involved in positive regulation of nucleotide-binding activity oligomerization domain containing 1 signaling pathway. Predicted to be located in cell surface and plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in lung (RPKM 9.2), skin (RPKM 5.1) and 6 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q32

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (112878920..112890876, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (125050362..125072489, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (115641200..115653156, complement)

Chromosome 9 - NC_000009.12 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

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?

When SLC46A2 delivers cargo into keratinocytes.
Title: When SLC46A2 delivers cargo into keratinocytes.
Mammalian SLC46A2s promote tracheal cytotoxin -triggered NOD1 activation in human epithelial cell lines, indicating that SLC46As is a conserved group of peptidoglycan transporter contributing to cytosolic immune recognition
Title: SLC46 Family Transporters Facilitate Cytosolic Innate Immune Recognition of Monomeric Peptidoglycans.
Affected sib-pairs with cervical cancer susceptibility and high mean age at diagnosis show increased sharing at all microsatellite markers at 9q31.1-33.1 and linkage signals of up to maximum lod-score of 2.74 for TSCOT single nucleotide polymorphisms.
Title: Polymorphisms in 9q32 and TSCOT are linked to cervical cancer in affected sib-pairs with high mean age at diagnosis.

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cyclic-GMP-AMP transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables symporter activity	NAS Non-traceable Author Statement more info	PubMed
enables transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in T cell homeostasis	IEA Inferred from Electronic Annotation more info
involved_in cyclic-GMP-AMP transmembrane import across plasma membrane	IDA Inferred from Direct Assay more info	PubMed
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of T cell apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of T cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in thymus development	IEA Inferred from Electronic Annotation more info
involved_in transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in cell surface	IEA Inferred from Electronic Annotation more info
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: solute carrier family 46 member 2

Names: thymic stromal co-transporter; thymic stromal cotransporter homolog

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_033051.4 → NP_149040.3 solute carrier family 46 member 2

See identical proteins and their annotated locations for NP_149040.3

Status: VALIDATED

Source sequence(s)

AF242557, BC048285, DA593062

Consensus CDS

CCDS6786.1

UniProtKB/Swiss-Prot

B1ALK1, Q86VT0, Q96NE2, Q9BY10

Related

ENSP00000363345.4, ENST00000374228.5

Conserved Domains (2) summary

pfam07690
Location:84 → 421

MFS_1; Major Facilitator Superfamily

cl21472
Location:282 → 453

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 ...