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

Gene ID: 6561, updated on 2-Nov-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 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)

Genotypes

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 sulfate transmembrane transport 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 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

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