SLC38A9 solute carrier family 38 member 9 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC38A9provided by HGNC
Official Full Name: solute carrier family 38 member 9provided by HGNC
Primary source: HGNC:HGNC:26907
See related: Ensembl:ENSG00000177058 MIM:616203; AllianceGenome:HGNC:26907
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: SNAT9; URLC11
Summary: Enables several functions, including L-amino acid transmembrane transporter activity; cholesterol binding activity; and guanyl-nucleotide exchange factor activity. Involved in carboxylic acid transport; cellular response to amino acid stimulus; and positive regulation of TORC1 signaling. Located in Ragulator complex; late endosome; and lysosomal membrane. Part of FNIP-folliculin RagC/D GAP. [provided by Alliance of Genome Resources, Oct 2024]
Expression: Broad expression in placenta (RPKM 15.1), testis (RPKM 7.5) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q11.2

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (55625845..55712335, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (56453712..56540626, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (54921673..55008163, complement)

Chromosome 5 - NC_000005.10 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 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?

Structural mechanism for amino acid-dependent Rag GTPase nucleotide state switching by SLC38A9.
Title: Structural mechanism for amino acid-dependent Rag GTPase nucleotide state switching by SLC38A9.
Ragulator and SLC38A9 act on the Rag GTPases to activate the mTORC1 pathway in response to nutrient sufficiency.
Title: Ragulator and SLC38A9 activate the Rag GTPases through noncanonical GEF mechanisms.
Study validates that SLC38A9 is an arginine sensor for the mTORC1 pathway, and we uncover an unexpectedly central role for SLC38A9 in amino acid homeostasis. SLC38A9 mediates the transport, in an arginine-regulated fashion, of many essential amino acids out of lysosomes, including leucine, which mTORC1 senses through the cytosolic Sestrin proteins.
Title: mTORC1 Activator SLC38A9 Is Required to Efflux Essential Amino Acids from Lysosomes and Use Protein as a Nutrient.
Data suggest that amino acid transporter SLC38A9 controls mTORC1 activity through binding to the Rag-Ragulator complex at the lysosome upon amino acid availability.
Title: Amino Acid-Dependent mTORC1 Regulation by the Lysosomal Membrane Protein SLC38A9.
SLC38A9 is a physical and functional component of the amino acid sensing machinery that controls the activation of mTOR
Title: SLC38A9 is a component of the lysosomal amino acid sensing machinery that controls mTORC1.
SLC38A9 functions upstream of the Rag GTPases and is an excellent candidate for being an arginine sensor for the mTORC1 pathway.
Title: Metabolism. Lysosomal amino acid transporter SLC38A9 signals arginine sufficiency to mTORC1.
SNPs within SLC38A9 are correlated with inflammatory bowel disease patients' 6-thioguanine nucleotide blood concentrations.
Title: New genetic biomarkers predicting azathioprine blood concentrations in combination therapy with 5-aminosalicylic acid.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Hundreds of variants clustered in genomic loci and biological pathways affect human height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. 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

D5S664 (e-PCR), detects polymorphism
- UniSTS:6712

SHGC-111499 (e-PCR)
- UniSTS:184017

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables L-amino acid transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables L-arginine transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables L-asparagine transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables L-glutamine transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables L-leucine transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables amino acid transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables amino acid transmembrane transporter activity	TAS Traceable Author Statement more info
enables arginine binding	ISS Inferred from Sequence or Structural Similarity more info
enables cholesterol binding	IDA Inferred from Direct Assay more info	PubMed
enables guanyl-nucleotide exchange factor activity	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sterol sensor activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in L-arginine transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in amino acid transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in amino acid transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in asparagine transport	IDA Inferred from Direct Assay more info	PubMed
involved_in branched-chain amino acid transport	IEA Inferred from Electronic Annotation more info
involved_in cellular response to amino acid stimulus	IDA Inferred from Direct Assay more info	PubMed
involved_in glutamine transport	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of TOR signaling	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of TORC1 signaling	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of FNIP-folliculin RagC/D GAP	IDA Inferred from Direct Assay more info	PubMed
part_of Ragulator complex	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info
is_active_in lysosomal membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in lysosomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	IMP Inferred from Mutant Phenotype more info	PubMed
located_in lysosomal membrane	TAS Traceable Author Statement more info
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: neutral amino acid transporter 9

Names: putative sodium-coupled neutral amino acid transporter 9; sodium-coupled neutral amino acid transporter 9; up-regulated in lung cancer 11

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_001258286.1 → NP_001245215.1 neutral amino acid transporter 9 isoform 2

See identical proteins and their annotated locations for NP_001245215.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1.

Source sequence(s)

AC008784, AI580489, BC036232

Consensus CDS

CCDS58947.1

UniProtKB/Swiss-Prot

Q8NBW4

Related

ENSP00000420934.1, ENST00000515629.5

Conserved Domains (2) summary

COG0814
Location:52 → 498

SdaC; Amino acid permease [Amino acid transport and metabolism]

cl00456
Location:52 → 493

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
NM_001258287.1 → NP_001245216.1 neutral amino acid transporter 9 isoform 3

See identical proteins and their annotated locations for NP_001245216.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) has multiple differences, including translation initiation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AI580489, AK127988, BC036232, BX641065

Consensus CDS

CCDS58948.1

UniProtKB/TrEMBL

D6R9Q7

Related

ENSP00000427335.1, ENST00000512595.5

Conserved Domains (2) summary

COG0814
Location:88 → 498

SdaC; Amino acid permease [Amino acid transport and metabolism]

cl00456
Location:88 → 493

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
NM_001282429.1 → NP_001269358.1 neutral amino acid transporter 9 isoform 4

See identical proteins and their annotated locations for NP_001269358.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) uses an alternate 5' exon structure and thus differs in the 5' UTR and 5' coding region compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (4) with a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AI580489, AK122957, DC371481

Consensus CDS

CCDS75243.1

UniProtKB/TrEMBL

B3KVK8

Related

ENSP00000397429.2, ENST00000416547.6

Conserved Domains (2) summary

COG0814
Location:1 → 437

SdaC; Amino acid permease [Amino acid transport and metabolism]

cl00456
Location:4 → 432

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
NM_001349382.1 → NP_001336311.1 neutral amino acid transporter 9 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (6) differs in the 5' UTR compared to variant 1. Variants 1 6, 7 and 8 encode the same isoform (1).

Source sequence(s)

AC016632, AI580489, AK075190, BC066891, DB207931, DC371481

Consensus CDS

CCDS3968.1

UniProtKB/Swiss-Prot

A0A0A8K8P2, B3KXV1, B7Z7D0, Q0P5S0, Q6MZJ8, Q8NBW4

UniProtKB/TrEMBL

D6R9Q7

Conserved Domains (1) summary

cl00456
Location:115 → 556

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
NM_001349383.1 → NP_001336312.1 neutral amino acid transporter 9 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (7) differs in the 5' UTR compared to variant 1. Variants 1 6, 7 and 8 encode the same isoform (1).

Source sequence(s)

AC016632, AI580489, AK075190, BC066891, DB158005, DB207931, DC371481

Consensus CDS

CCDS3968.1

UniProtKB/Swiss-Prot

A0A0A8K8P2, B3KXV1, B7Z7D0, Q0P5S0, Q6MZJ8, Q8NBW4

UniProtKB/TrEMBL

D6R9Q7

Conserved Domains (1) summary

cl00456
Location:115 → 556

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
NM_001349384.1 → NP_001336313.1 neutral amino acid transporter 9 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (8) differs in the 5' UTR compared to variant 1. Variants 1 6, 7 and 8 encode the same isoform (1).

Source sequence(s)

AI580489, AK075190, BC066891, DC371481, DC398501

Consensus CDS

CCDS3968.1

UniProtKB/Swiss-Prot

A0A0A8K8P2, B3KXV1, B7Z7D0, Q0P5S0, Q6MZJ8, Q8NBW4

UniProtKB/TrEMBL

D6R9Q7

Conserved Domains (1) summary

cl00456
Location:115 → 556

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
NM_001349385.1 → NP_001336314.1 neutral amino acid transporter 9 isoform 5

Status: VALIDATED

Description

Transcript Variant: This variant (9) lacks an alternate in-frame exon in the central coding region compared to variant 1. The encoded isoform (5) has the same N- and C-termiini, but is shorter than isoform 1.

Source sequence(s)

AI580489, AK075190, BC066891, DC371481

UniProtKB/TrEMBL

D6R9Q7

Related

ENSP00000423219.1, ENST00000511233.5

Conserved Domains (1) summary

cl00456
Location:115 → 491

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
NM_173514.4 → NP_775785.2 neutral amino acid transporter 9 isoform 1

See identical proteins and their annotated locations for NP_775785.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1). Variants 1 6, 7 and 8 encode the same isoform (1).

Source sequence(s)

AI580489, AK075190, BC066891, DC371481

Consensus CDS

CCDS3968.1

UniProtKB/Swiss-Prot

A0A0A8K8P2, B3KXV1, B7Z7D0, Q0P5S0, Q6MZJ8, Q8NBW4

UniProtKB/TrEMBL

D6R9Q7

Related

ENSP00000380074.2, ENST00000396865.7

Conserved Domains (1) summary

cl00456
Location:115 → 556

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

RNA

NR_047649.1 RNA Sequence

Status: VALIDATED

Description

This variant (5) uses an alternate 5' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC008784, AI580489, BC036232, BC045589, BX641065

Related

ENST00000505708.5
NR_146165.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (10) uses an alternate splice site at an internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AI580489, AK075190, BC066891, DC371481

Related

ENST00000508124.5

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_000005.10 Reference GRCh38.p14 Primary Assembly

Range

55625845..55712335 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047416799.1 → XP_047272755.1 neutral amino acid transporter 9 isoform X12
XM_047416796.1 → XP_047272752.1 neutral amino acid transporter 9 isoform X10
XM_047416789.1 → XP_047272745.1 neutral amino acid transporter 9 isoform X6
XM_017009078.3 → XP_016864567.1 neutral amino acid transporter 9 isoform X4

Conserved Domains (2) summary

COG0814
Location:115 → 504

SdaC; Amino acid permease [Amino acid transport and metabolism]

cl00456
Location:115 → 499

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_017009082.2 → XP_016864571.1 neutral amino acid transporter 9 isoform X9

UniProtKB/TrEMBL

D6R9Q7

Conserved Domains (2) summary

COG0814
Location:115 → 460

SdaC; Amino acid permease [Amino acid transport and metabolism]

cl00456
Location:115 → 455

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_017009081.2 → XP_016864570.1 neutral amino acid transporter 9 isoform X8

UniProtKB/TrEMBL

D6R9Q7
XM_024454369.2 → XP_024310137.1 neutral amino acid transporter 9 isoform X3

UniProtKB/TrEMBL

D6R9Q7

Conserved Domains (1) summary

cl00456
Location:115 → 520

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_017009077.2 → XP_016864566.1 neutral amino acid transporter 9 isoform X2

UniProtKB/TrEMBL

D6R9Q7

Conserved Domains (1) summary

cl00456
Location:115 → 526

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_047416786.1 → XP_047272742.1 neutral amino acid transporter 9 isoform X4
XM_047416783.1 → XP_047272739.1 neutral amino acid transporter 9 isoform X3
XM_006714539.4 → XP_006714602.1 neutral amino acid transporter 9 isoform X1

See identical proteins and their annotated locations for XP_006714602.1

UniProtKB/Swiss-Prot

A0A0A8K8P2, B3KXV1, B7Z7D0, Q0P5S0, Q6MZJ8, Q8NBW4

UniProtKB/TrEMBL

D6R9Q7

Conserved Domains (1) summary

cl00456
Location:115 → 556

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_047416797.1 → XP_047272753.1 neutral amino acid transporter 9 isoform X10
XM_047416791.1 → XP_047272747.1 neutral amino acid transporter 9 isoform X6
XM_047416785.1 → XP_047272741.1 neutral amino acid transporter 9 isoform X4
XM_047416794.1 → XP_047272750.1 neutral amino acid transporter 9 isoform X9
XM_017009080.2 → XP_016864569.1 neutral amino acid transporter 9 isoform X5

UniProtKB/TrEMBL

D6R9Q7

Conserved Domains (1) summary

cl00456
Location:115 → 491

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_047416782.1 → XP_047272738.1 neutral amino acid transporter 9 isoform X3
XM_047416779.1 → XP_047272735.1 neutral amino acid transporter 9 isoform X2
XM_047416790.1 → XP_047272746.1 neutral amino acid transporter 9 isoform X6
XM_047416784.1 → XP_047272740.1 neutral amino acid transporter 9 isoform X4
XM_047416795.1 → XP_047272751.1 neutral amino acid transporter 9 isoform X9
XM_047416788.1 → XP_047272744.1 neutral amino acid transporter 9 isoform X5
XM_047416781.1 → XP_047272737.1 neutral amino acid transporter 9 isoform X3
XM_047416780.1 → XP_047272736.1 neutral amino acid transporter 9 isoform X2
XM_011543183.2 → XP_011541485.1 neutral amino acid transporter 9 isoform X10

UniProtKB/TrEMBL

D6R9Q7

Conserved Domains (2) summary

COG0814
Location:115 → 439

SdaC; Amino acid permease [Amino acid transport and metabolism]

cl00456
Location:115 → 434

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_047416792.1 → XP_047272748.1 neutral amino acid transporter 9 isoform X7
XM_011543178.2 → XP_011541480.1 neutral amino acid transporter 9 isoform X4

Conserved Domains (2) summary

COG0814
Location:115 → 504

SdaC; Amino acid permease [Amino acid transport and metabolism]

cl00456
Location:115 → 499

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_011543180.2 → XP_011541482.1 neutral amino acid transporter 9 isoform X9

UniProtKB/TrEMBL

D6R9Q7

Conserved Domains (2) summary

COG0814
Location:115 → 460

SdaC; Amino acid permease [Amino acid transport and metabolism]

cl00456
Location:115 → 455

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_047416793.1 → XP_047272749.1 neutral amino acid transporter 9 isoform X8
XM_047416787.1 → XP_047272743.1 neutral amino acid transporter 9 isoform X5
XM_011543177.2 → XP_011541479.1 neutral amino acid transporter 9 isoform X3

UniProtKB/TrEMBL

D6R9Q7

Conserved Domains (1) summary

cl00456
Location:115 → 520

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_011543176.2 → XP_011541478.1 neutral amino acid transporter 9 isoform X2

UniProtKB/TrEMBL

D6R9Q7

Conserved Domains (1) summary

cl00456
Location:115 → 526

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_011543174.2 → XP_011541476.1 neutral amino acid transporter 9 isoform X1

See identical proteins and their annotated locations for XP_011541476.1

UniProtKB/Swiss-Prot

A0A0A8K8P2, B3KXV1, B7Z7D0, Q0P5S0, Q6MZJ8, Q8NBW4

UniProtKB/TrEMBL

D6R9Q7

Conserved Domains (1) summary

cl00456
Location:115 → 556

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_047416778.1 → XP_047272734.1 neutral amino acid transporter 9 isoform X1

UniProtKB/Swiss-Prot

A0A0A8K8P2, B3KXV1, B7Z7D0, Q0P5S0, Q6MZJ8, Q8NBW4
XM_047416798.1 → XP_047272754.1 neutral amino acid transporter 9 isoform X11