SLC38A2 solute carrier family 38 member 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC38A2provided by HGNC
Official Full Name: solute carrier family 38 member 2provided by HGNC
Primary source: HGNC:HGNC:13448
See related: Ensembl:ENSG00000134294 MIM:605180; AllianceGenome:HGNC:13448
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: ATA2; SAT2; SNAT2; PRO1068
Summary: Enables neutral amino acid:sodium symporter activity. Involved in several processes, including amino acid transport; cellular response to arsenite(3-); and positive regulation of RNA splicing. Located in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in skin (RPKM 105.3), liver (RPKM 101.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q13.11

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (46358188..46372773, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (46317747..46332332, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (46751971..46766556, complement)

Chromosome 12 - NC_000012.12 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?

CHOP upregulation and dysregulation of the mature form of the SNAT2 amino acid transporter in the placentas from small for gestational age newborns.
Title: CHOP upregulation and dysregulation of the mature form of the SNAT2 amino acid transporter in the placentas from small for gestational age newborns.
Hsa_circRNA_001859 regulates pancreatic cancer progression and epithelial-mesenchymal transition through the miR-21-5p/SLC38A2 pathway.
Title: Hsa_circRNA_001859 regulates pancreatic cancer progression and epithelial-mesenchymal transition through the miR-21-5p/SLC38A2 pathway.
Single-cell RNA sequencing reveals XBP1-SLC38A2 axis as a metabolic regulator in cytotoxic T lymphocytes in multiple myeloma.
Title: Single-cell RNA sequencing reveals XBP1-SLC38A2 axis as a metabolic regulator in cytotoxic T lymphocytes in multiple myeloma.
Comprehensive analysis of the biological function and immune infiltration of SLC38A2 in gastric cancer.
Title: Comprehensive analysis of the biological function and immune infiltration of SLC38A2 in gastric cancer.
SNAT2/SLC38A2 Confers the Stemness of Gastric Cancer Cells via Regulating Glutamine Level.
Title: SNAT2/SLC38A2 Confers the Stemness of Gastric Cancer Cells via Regulating Glutamine Level.
LAT1 and SNAT2 Protein Expression and Membrane Localization of LAT1 Are Not Acutely Altered by Dietary Amino Acids or Resistance Exercise Nor Positively Associated with Leucine or Phenylalanine Incorporation in Human Skeletal Muscle.
Title: LAT1 and SNAT2 Protein Expression and Membrane Localization of LAT1 Are Not Acutely Altered by Dietary Amino Acids or Resistance Exercise Nor Positively Associated with Leucine or Phenylalanine Incorporation in Human Skeletal Muscle.
SLC38A2 Overexpression Induces a Cancer-like Metabolic Profile and Cooperates with SLC1A5 in Pan-cancer Prognosis.
Title: SLC38A2 Overexpression Induces a Cancer-like Metabolic Profile and Cooperates with SLC1A5 in Pan-cancer Prognosis.
Increased expression of glutamine transporter SNAT2/SLC38A2 promotes glutamine dependence and oxidative stress resistance, and is associated with worse prognosis in triple-negative breast cancer.
Title: Increased expression of glutamine transporter SNAT2/SLC38A2 promotes glutamine dependence and oxidative stress resistance, and is associated with worse prognosis in triple-negative breast cancer.
Functional Consequences of Low Activity of Transport System A for Neutral Amino Acids in Human Bone Marrow Mesenchymal Stem Cells.
Title: Functional Consequences of Low Activity of Transport System A for Neutral Amino Acids in Human Bone Marrow Mesenchymal Stem Cells.
We describe how Slc38a2 senses amino acid availability and passes this onto intracellular signaling pathways and how it regulates protein synthesis, cellular proliferation and apoptosis through the mechanistic (mammalian) target of rapamycin (mTOR) and general control nonderepressible 2 (GCN2) pathways--{REVIEW}
Title: Multifaceted regulation of the system A transporter Slc38a2 suggests nanoscale regulation of amino acid metabolism and cellular signaling.

Submit: New GeneRIF Correction See all GeneRIFs (37)

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)

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 SLC38A2	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

D12S2010 (e-PCR)
- UniSTS:772

WI-11919 (e-PCR)
- UniSTS:3397

RH17405 (e-PCR)
- UniSTS:51325

RH67932 (e-PCR)
- UniSTS:15533

RH11173 (e-PCR)
- UniSTS:76002

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables L-glutamine transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables L-glutamine transmembrane transporter activity	ISS Inferred from Sequence or Structural Similarity more info
enables L-serine transmembrane transporter activity	ISS Inferred from Sequence or Structural Similarity more info
enables acidic amino acid transmembrane transporter activity	ISS Inferred from Sequence or Structural Similarity more info
enables alanine:sodium symporter activity	ISS Inferred from Sequence or Structural Similarity more info
enables amino acid transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables amino acid transmembrane transporter activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables amino acid transmembrane transporter activity	TAS Traceable Author Statement more info
enables amino acid:sodium symporter activity	IDA Inferred from Direct Assay more info	PubMed
enables neutral L-amino acid:sodium symporter activity	IDA Inferred from Direct Assay more info	PubMed
enables proline:sodium symporter activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in L-glutamine import across plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
involved_in L-proline import across plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
involved_in L-serine import across plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
involved_in L-serine transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in acidic amino acid transport	IEA Inferred from Electronic Annotation more info
involved_in alanine transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in amino acid import	ISS Inferred from Sequence or Structural Similarity more info
involved_in amino acid transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in amino acid transmembrane transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in amino acid transport	IDA Inferred from Direct Assay more info	PubMed
involved_in amino acid transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in amino acid transport	TAS Traceable Author Statement more info
involved_in cellular response to amino acid starvation	IEA Inferred from Electronic Annotation more info
involved_in cellular response to arsenite(3-)	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to mechanical stimulus	IEA Inferred from Electronic Annotation more info
involved_in cerebral cortex development	IEA Inferred from Electronic Annotation more info
involved_in female pregnancy	IEA Inferred from Electronic Annotation more info
involved_in glutamine transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in glutamine transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in glycine betaine transport	IEA Inferred from Electronic Annotation more info
involved_in neurotransmitter transport	TAS Traceable Author Statement more info
involved_in neutral amino acid transport	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of RNA splicing	IPI Inferred from Physical Interaction more info	PubMed
involved_in positive regulation of gene expression	IPI Inferred from Physical Interaction more info	PubMed
involved_in proline transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cellular response to stress	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of glutamate secretion, neurotransmission	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to muscle activity	IEA Inferred from Electronic Annotation more info
involved_in sodium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in transport across blood-brain barrier	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in axon	IEA Inferred from Electronic Annotation more info
located_in brush border	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in dendrite	IEA Inferred from Electronic Annotation more info
located_in neuronal cell body	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in sarcolemma	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: sodium-coupled neutral amino acid symporter 2

Names: amino acid transporter 2; amino acid transporter A2; protein 40-9-1; sodium-coupled neutral amino acid transporter 2; system A amino acid transporter 2; system A transporter 1; system N amino acid transporter 2

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_001307936.2 → NP_001294865.1 sodium-coupled neutral amino acid symporter 2 isoform 2

See identical proteins and their annotated locations for NP_001294865.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an exon in its 5' coding region compared to variant 1. This variant represents translation initiation at an alternate start codon compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the alternate start codon to encode an isoform (2) that has a distinct and shorter N-terminus, compared to isoform 1.

Source sequence(s)

AK001700, BC029379, BC040342, DA725217

Consensus CDS

CCDS76551.1

UniProtKB/Swiss-Prot

Q96QD8

UniProtKB/TrEMBL

Q8NHT5

Conserved Domains (1) summary

cl00456
Location:5 → 395

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
NM_018976.5 → NP_061849.2 sodium-coupled neutral amino acid symporter 2 isoform 1

See identical proteins and their annotated locations for NP_061849.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC025031, BC040342, DA725217

Consensus CDS

CCDS8749.1

UniProtKB/Swiss-Prot

Q6IA88, Q6ZMG2, Q96QD8, Q9HAV3, Q9NVA8, Q9P2G5

UniProtKB/TrEMBL

A8K6H9

Related

ENSP00000256689.5, ENST00000256689.10

Conserved Domains (1) summary

cl00456
Location:69 → 495

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

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

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

46358188..46372773 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047429019.1 → XP_047284975.1 sodium-coupled neutral amino acid symporter 2 isoform X1

Related

ENSP00000482873.1, ENST00000612232.1
XM_047429020.1 → XP_047284976.1 sodium-coupled neutral amino acid symporter 2 isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

46317747..46332332 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054372315.1 → XP_054228290.1 sodium-coupled neutral amino acid symporter 2 isoform X1
XM_054372316.1 → XP_054228291.1 sodium-coupled neutral amino acid symporter 2 isoform X2