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SLC38A6 solute carrier family 38 member 6 [ Homo sapiens (human) ]

Gene ID: 145389, updated on 11-Apr-2024

Summary

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Official Symbol
SLC38A6provided by HGNC
Official Full Name
solute carrier family 38 member 6provided by HGNC
Primary source
HGNC:HGNC:19863
See related
Ensembl:ENSG00000139974 MIM:616518; AllianceGenome:HGNC:19863
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
NAT-1; SNAT6
Summary
Predicted to enable L-glutamine transmembrane transporter activity. Predicted to be involved in amino acid transmembrane transport and glutamine transport. Predicted to be located in plasma membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 2.1), gall bladder (RPKM 1.9) and 24 other tissues See more
Orthologs
mouse all
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Genomic context

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See SLC38A6 in Genome Data Viewer
Location:
14q23.1
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (60981245..61083733)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (55187785..55290408)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (61447963..61550451)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene MNAT1 component of CDK activating kinase Neighboring gene Sharpr-MPRA regulatory region 12651 Neighboring gene Sharpr-MPRA regulatory region 14697 Neighboring gene Sharpr-MPRA regulatory region 5996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8484 Neighboring gene SRM pseudogene 2 Neighboring gene RNA, U6 small nuclear 398, pseudogene Neighboring gene uncharacterized LOC101927756 Neighboring gene tRNA methyltransferase 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:61555743-61556244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8485 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:61567888-61568804 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:61570068-61571267 Neighboring gene Sharpr-MPRA regulatory region 14232 Neighboring gene NANOG hESC enhancer GRCh37_chr14:61641010-61641511 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:61644371-61644872 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:61644987-61646186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8486 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:61721487-61722686 Neighboring gene protein kinase C eta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61736629-61737128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:61746518-61747481 Neighboring gene Sharpr-MPRA regulatory region 13098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5818 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61788641-61789185 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61789186-61789729 Neighboring gene PRKCH antisense RNA 1 Neighboring gene transmembrane protein 30B

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. SLC38A6, regulated by EP300-mediated modifications of H3K27ac, promotes cell proliferation, glutamine metabolism and mitochondrial respiration in hepatocellular carcinoma. Huang L, et al. Carcinogenesis, 2022 Oct 22. PMID 35901507
  2. New Transcriptomic Biomarkers of 5-Fluorouracil Resistance. Fekete JT, et al. Int J Mol Sci, 2023 Jan 12. PMID 36675023, Free PMC Article
  3. Histological analysis of SLC38A6 (SNAT6) expression in mouse brain shows selective expression in excitatory neurons with high expression in the synapses. Bagchi S, et al. PLoS One, 2014. PMID 24752331, Free PMC Article
  4. Evolutionary origin of amino acid transporter families SLC32, SLC36 and SLC38 and physiological, pathological and therapeutic aspects. Schiöth HB, et al. Mol Aspects Med, 2013 Apr-Jun. PMID 23506890
  5. USP7 targets XIAP for cancer progression: Establishment of a p53-independent therapeutic avenue for glioma. Saha G, et al. Oncogene, 2022 Nov. PMID 36243803

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. New Transcriptomic Biomarkers of 5-Fluorouracil Resistance.
    Title: New Transcriptomic Biomarkers of 5-Fluorouracil Resistance.
  2. SLC38A6, regulated by EP300-mediated modifications of H3K27ac, promotes cell proliferation, glutamine metabolism and mitochondrial respiration in hepatocellular carcinoma.
    Title: SLC38A6, regulated by EP300-mediated modifications of H3K27ac, promotes cell proliferation, glutamine metabolism and mitochondrial respiration in hepatocellular carcinoma.
  3. SLC38A6 is primarily expressed in excitatory neurons and is not expressed in the astrocytes.
    Title: Histological analysis of SLC38A6 (SNAT6) expression in mouse brain shows selective expression in excitatory neurons with high expression in the synapses.
Submit: New GeneRIF Correction

Phenotypes

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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)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of solute carrier family 38, member 6 (SLC38A6) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells 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

Homology

Clone Names

  • MGC102697

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables L-glutamate transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
  
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 protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in L-glutamate transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in amino acid transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in glutamine transport IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in synapse IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
solute carrier family 38 member 6; probable sodium-coupled neutral amino acid transporter 6
Names
N system amino acid transporter NAT-1
N-system amino acid transporter 1
Na(+)-coupled neutral amino acid transporter 6
Sodium-coupled neutral amino acid transporter 6
amino acid transporter SLC38A6

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)

  1. NM_001172702.2 → NP_001166173.1  solute carrier family 38 member 6 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest coding transcript and encodes the longer isoform (1).
    Source sequence(s)
    BC050349, BX248072, DR002669
    Consensus CDS
    CCDS53900.1
    UniProtKB/TrEMBL
    A0A0C4DG39
    Related
    ENSP00000395851.1, ENST00000451406.5
    Conserved Domains (2) summary
    COG0814
    Location:50 → 434
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    cl00456
    Location:46 → 429
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

  2. NM_153811.3 → NP_722518.2  solute carrier family 38 member 6 isoform 2

    See identical proteins and their annotated locations for NP_722518.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses a distinct splice pattern in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AL160234, BC110378, BX648332
    Consensus CDS
    CCDS9751.1
    UniProtKB/Swiss-Prot
    C9JWA6, Q86SY5, Q8IZM9
    UniProtKB/TrEMBL
    A0A0C4DG39
    Related
    ENSP00000267488.4, ENST00000267488.9
    Conserved Domains (2) summary
    COG0814
    Location:50 → 451
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    cl00456
    Location:46 → 451
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

RNA

  1. NR_033344.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' region, and uses an alternate splice acceptor site at the terminal exon. 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)
    AK303839, AL160236, BC050349, BP352279, BX248072, DC394244
    Related
    ENST00000529345.6

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

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    60981245..61083733
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017021022.2 → XP_016876511.1  probable sodium-coupled neutral amino acid transporter 6 isoform X4

    UniProtKB/TrEMBL
    B4E1H1

  2. XM_047431002.1 → XP_047286958.1  probable sodium-coupled neutral amino acid transporter 6 isoform X1

  3. XM_017021020.2 → XP_016876509.1  probable sodium-coupled neutral amino acid transporter 6 isoform X1

    UniProtKB/TrEMBL
    A0A0C4DG39

  4. XM_047431001.1 → XP_047286957.1  probable sodium-coupled neutral amino acid transporter 6 isoform X1

  5. XM_017021021.2 → XP_016876510.1  probable sodium-coupled neutral amino acid transporter 6 isoform X2

  6. XM_047431003.1 → XP_047286959.1  probable sodium-coupled neutral amino acid transporter 6 isoform X2

  7. XM_017021023.2 → XP_016876512.1  probable sodium-coupled neutral amino acid transporter 6 isoform X5

    UniProtKB/TrEMBL
    A0A0C4DG39

  8. XM_047431005.1 → XP_047286961.1  probable sodium-coupled neutral amino acid transporter 6 isoform X6

  9. XM_047431006.1 → XP_047286962.1  probable sodium-coupled neutral amino acid transporter 6 isoform X7

  10. XM_047431004.1 → XP_047286960.1  probable sodium-coupled neutral amino acid transporter 6 isoform X3

  11. XM_047431008.1 → XP_047286964.1  probable sodium-coupled neutral amino acid transporter 6 isoform X11

  12. XM_047431009.1 → XP_047286965.1  probable sodium-coupled neutral amino acid transporter 6 isoform X12

  13. XM_047431010.1 → XP_047286966.1  probable sodium-coupled neutral amino acid transporter 6 isoform X13

    Related
    ENSP00000515189.1, ENST00000703134.1

  14. XM_011536469.3 → XP_011534771.1  probable sodium-coupled neutral amino acid transporter 6 isoform X9

    UniProtKB/TrEMBL
    A0A8V8TRG7
    Conserved Domains (1) summary
    cl00456
    Location:46 → 309
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

  15. XM_017021025.2 → XP_016876514.1  probable sodium-coupled neutral amino acid transporter 6 isoform X8

  16. XM_047431007.1 → XP_047286963.1  probable sodium-coupled neutral amino acid transporter 6 isoform X10

  17. XM_024449496.2 → XP_024305264.1  probable sodium-coupled neutral amino acid transporter 6 isoform X14

    Conserved Domains (1) summary
    cl00456
    Location:3 → 228
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

RNA

  1. XR_007063987.1 RNA Sequence

  2. XR_007063988.1 RNA Sequence

  3. XR_001750164.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    55187785..55290408
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054375442.1 → XP_054231417.1  probable sodium-coupled neutral amino acid transporter 6 isoform X1

  2. XM_054375440.1 → XP_054231415.1  probable sodium-coupled neutral amino acid transporter 6 isoform X1

  3. XM_054375441.1 → XP_054231416.1  probable sodium-coupled neutral amino acid transporter 6 isoform X1

  4. XM_054375443.1 → XP_054231418.1  probable sodium-coupled neutral amino acid transporter 6 isoform X2

  5. XM_054375444.1 → XP_054231419.1  probable sodium-coupled neutral amino acid transporter 6 isoform X2

  6. XM_054375447.1 → XP_054231422.1  probable sodium-coupled neutral amino acid transporter 6 isoform X5

  7. XM_054375445.1 → XP_054231420.1  probable sodium-coupled neutral amino acid transporter 6 isoform X3

  8. XM_054375457.1 → XP_054231432.1  probable sodium-coupled neutral amino acid transporter 6 isoform X11

  9. XM_054375458.1 → XP_054231433.1  probable sodium-coupled neutral amino acid transporter 6 isoform X12

  10. XM_054375459.1 → XP_054231434.1  probable sodium-coupled neutral amino acid transporter 6 isoform X13

  11. XM_054375455.1 → XP_054231430.1  probable sodium-coupled neutral amino acid transporter 6 isoform X9

  12. XM_054375446.1 → XP_054231421.1  probable sodium-coupled neutral amino acid transporter 6 isoform X4

  13. XM_054375448.1 → XP_054231423.1  probable sodium-coupled neutral amino acid transporter 6 isoform X6

  14. XM_054375451.1 → XP_054231426.1  probable sodium-coupled neutral amino acid transporter 6 isoform X8

  15. XM_054375449.1 → XP_054231424.1  probable sodium-coupled neutral amino acid transporter 6 isoform X7

  16. XM_054375453.1 → XP_054231428.1  probable sodium-coupled neutral amino acid transporter 6 isoform X16

  17. XM_054375450.1 → XP_054231425.1  probable sodium-coupled neutral amino acid transporter 6 isoform X8

  18. XM_054375452.1 → XP_054231427.1  probable sodium-coupled neutral amino acid transporter 6 isoform X15

  19. XM_054375454.1 → XP_054231429.1  probable sodium-coupled neutral amino acid transporter 6 isoform X17

  20. XM_054375456.1 → XP_054231431.1  probable sodium-coupled neutral amino acid transporter 6 isoform X10

  21. XM_054375460.1 → XP_054231435.1  probable sodium-coupled neutral amino acid transporter 6 isoform X14

RNA

  1. XR_008488823.1 RNA Sequence

  2. XR_008488824.1 RNA Sequence

  3. XR_008488825.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IZM9.2 GenPept UniProtKB/Swiss-Prot:Q8IZM9

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