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    SLC13A1 solute carrier family 13 member 1 [ Homo sapiens (human) ]

    Gene ID: 6561, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SLC13A1provided by HGNC
    Official Full Name
    solute carrier family 13 member 1provided by HGNC
    Primary source
    HGNC:HGNC:10916
    See related
    Ensembl:ENSG00000081800 MIM:606193; AllianceGenome:HGNC:10916
    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
    NAS1; NaSi-1
    Summary
    The protein encoded by this gene is an apical membrane Na(+)-sulfate cotransporter involved in sulfate homeostasis in the kidney. Defects in this gene lead to many pathophysiologic problems. [provided by RefSeq, May 2016]
    Expression
    Biased expression in kidney (RPKM 26.2), small intestine (RPKM 5.7) and 1 other tissue See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC13A1 in Genome Data Viewer
    Location:
    7q31.32
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (123113531..123199971, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (124430320..124518597, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (122753585..122840025, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:122572022-122572522 Neighboring gene NANOG hESC enhancer GRCh37_chr7:122627466-122627971 Neighboring gene taste 2 receptor member 16 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26566 Neighboring gene LYPLA1 pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:122925059-122925682 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:122925683-122926306 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18583 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:123079020-123079892 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:123079893-123080763 Neighboring gene RNA, U6 small nuclear 296, pseudogene Neighboring gene IQ motif and ubiquitin domain containing

    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. Rare variant analyses in large-scale cohorts identified SLC13A1 associated with chronic pain. Ao X, et al. Pain, 2023 Aug 1. PMID 36943258, Free PMC Article
    2. Serum sulfate level and Slc13a1 mRNA expression remain unaltered in a mouse model of moderate vitamin D deficiency. Atcheson RJ, et al. Mol Cell Biochem, 2023 Aug. PMID 36566486
    3. Biallelic variants in the SLC13A1 sulfate transporter gene cause hyposulfatemia with a mild spondylo-epi-metaphyseal dysplasia. van de Kamp JM, et al. Clin Genet, 2023 Jan. PMID 36175384, Free PMC Article
    4. Rare SLC13A1 variants associate with intervertebral disc disorder highlighting role of sulfate in disc pathology. Bjornsdottir G, et al. Nat Commun, 2022 Feb 2. PMID 35110524, Free PMC Article
    5. Serines 260 and 288 are involved in sulfate transport by hNaSi-1. Li H, et al. J Biol Chem, 2003 Sep 26. PMID 12857732

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Cryo-EM structures of the human NaS1 and NaDC1 transporters revealed the elevator transport and allosteric regulation mechanism.
      Title: Cryo-EM structures of the human NaS1 and NaDC1 transporters revealed the elevator transport and allosteric regulation mechanism.
    2. Rare variant analyses in large-scale cohorts identified SLC13A1 associated with chronic pain.
      Title: Rare variant analyses in large-scale cohorts identified SLC13A1 associated with chronic pain.
    3. Serum sulfate level and Slc13a1 mRNA expression remain unaltered in a mouse model of moderate vitamin D deficiency.
      Title: Serum sulfate level and Slc13a1 mRNA expression remain unaltered in a mouse model of moderate vitamin D deficiency.
    4. Biallelic variants in the SLC13A1 sulfate transporter gene cause hyposulfatemia with a mild spondylo-epi-metaphyseal dysplasia.
      Title: Biallelic variants in the SLC13A1 sulfate transporter gene cause hyposulfatemia with a mild spondylo-epi-metaphyseal dysplasia.
    5. Rare SLC13A1 variants associate with intervertebral disc disorder highlighting role of sulfate in disc pathology.
      Title: Rare SLC13A1 variants associate with intervertebral disc disorder highlighting role of sulfate in disc pathology.
    6. Consistent with sulfate's role in xenobiotic detoxification and protection against acetaminophen-induced hepatotoxicity, SLC13A1 nonsense SNV carriers had higher aminotransferase levels compared to noncarriers.
      Title: From Genotype to Phenotype: Nonsense Variants in SLC13A1 Are Associated with Decreased Serum Sulfate and Increased Serum Aminotransferases.
    7. Observational study and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Association of genetic polymorphisms with hepatotoxicity in patients with childhood acute lymphoblastic leukemia or lymphoma.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: High-density SNP association study and copy number variation analysis of the AUTS1 and AUTS5 loci implicate the IMMP2L-DOCK4 gene region in autism susceptibility.
    9. Serines 260 and 288 are involved in sulfate transport by hNaSi-1.
      Title: Serines 260 and 288 are involved in sulfate transport by hNaSi-1.
    10. Amino acid residue Asn591, located in the carboxyl (COOH) terminus of NaSi-1, is used as the glycosylation site and is critical for transport activity in NaSi-1.
      Title: Mutagenesis of the N-glycosylation site of hNaSi-1 reduces transport activity.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables monoatomic anion:sodium symporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables sodium:sulfate symporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables sodium:sulfate symporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables sodium:sulfate symporter activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in monoatomic anion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in sodium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in sodium ion transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in sulfate transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in apical plasma membrane 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 TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    solute carrier family 13 member 1
    Names
    Na(+)/sulfate cotransporter
    renal sodium/sulfate cotransporter
    solute carrier family 13 (sodium/sulfate symporters), member 1
    solute carrier family 13 (sodium/sulphate symporters), member 1

    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

    1. NG_050641.2 RefSeqGene

      Range
      5002..91440
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001324400.1 → NP_001311329.1  solute carrier family 13 member 1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AC073054, AC091319, AF260824, AK026413, BC111775
      UniProtKB/Swiss-Prot
      Q9BZW2
      UniProtKB/TrEMBL
      Q2NKK0
      Conserved Domains (1) summary
      cl21473
      Location:118 → 453
      ArsB_NhaD_permease; Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices ...

    2. NM_022444.4 → NP_071889.2  solute carrier family 13 member 1 isoform 1

      See identical proteins and their annotated locations for NP_071889.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC073054, AC091319
      Consensus CDS
      CCDS5786.1
      UniProtKB/Swiss-Prot
      Q9BZW2, Q9H5Z0
      UniProtKB/TrEMBL
      A4D0X1
      Related
      ENSP00000194130.2, ENST00000194130.7
      Conserved Domains (2) summary
      COG0471
      Location:48 → 577
      CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]
      cd01115
      Location:41 → 569
      SLC13_permease; Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is ...

    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

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      123113531..123199971 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047420754.1 → XP_047276710.1  solute carrier family 13 member 1 isoform X3

    2. XM_011516516.4 → XP_011514818.1  solute carrier family 13 member 1 isoform X2

      Conserved Domains (2) summary
      COG0471
      Location:48 → 599
      CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]
      cd01115
      Location:41 → 591
      SLC13_permease; Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is ...

    3. XM_011516515.4 → XP_011514817.1  solute carrier family 13 member 1 isoform X1

      Conserved Domains (2) summary
      COG0471
      Location:48 → 633
      CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]
      cd01115
      Location:41 → 625
      SLC13_permease; Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is ...

    4. XM_011516517.3 → XP_011514819.1  solute carrier family 13 member 1 isoform X4

      Conserved Domains (2) summary
      COG0471
      Location:7 → 569
      CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]
      cl21473
      Location:1 → 561
      ArsB_NhaD_permease; Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices ...

    5. XM_024446885.2 → XP_024302653.1  solute carrier family 13 member 1 isoform X8

      Conserved Domains (1) summary
      cl21473
      Location:118 → 453
      ArsB_NhaD_permease; Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices ...

    6. XM_011516518.4 → XP_011514820.1  solute carrier family 13 member 1 isoform X6

      Conserved Domains (2) summary
      COG0471
      Location:40 → 158
      CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]
      cl21473
      Location:41 → 154
      ArsB_NhaD_permease; Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices ...

    7. XM_017012555.2 → XP_016868044.1  solute carrier family 13 member 1 isoform X5

    8. XM_011516519.4 → XP_011514821.1  solute carrier family 13 member 1 isoform X7

      Conserved Domains (2) summary
      COG0471
      Location:40 → 158
      CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]
      cl21473
      Location:41 → 154
      ArsB_NhaD_permease; Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      124430320..124518597 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358852.1 → XP_054214827.1  solute carrier family 13 member 1 isoform X3

    2. XM_054358851.1 → XP_054214826.1  solute carrier family 13 member 1 isoform X2

    3. XM_054358850.1 → XP_054214825.1  solute carrier family 13 member 1 isoform X1

    4. XM_054358853.1 → XP_054214828.1  solute carrier family 13 member 1 isoform X9

      UniProtKB/Swiss-Prot
      Q9BZW2, Q9H5Z0
      UniProtKB/TrEMBL
      A4D0X1

    5. XM_054358854.1 → XP_054214829.1  solute carrier family 13 member 1 isoform X4

    6. XM_054358858.1 → XP_054214833.1  solute carrier family 13 member 1 isoform X8

    7. XM_054358856.1 → XP_054214831.1  solute carrier family 13 member 1 isoform X6

    8. XM_054358855.1 → XP_054214830.1  solute carrier family 13 member 1 isoform X5

    9. XM_054358857.1 → XP_054214832.1  solute carrier family 13 member 1 isoform X7

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BZW2.1 GenPept UniProtKB/Swiss-Prot:Q9BZW2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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