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    SLC34A3 solute carrier family 34 member 3 [ Homo sapiens (human) ]

    Gene ID: 142680, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SLC34A3provided by HGNC
    Official Full Name
    solute carrier family 34 member 3provided by HGNC
    Primary source
    HGNC:HGNC:20305
    See related
    Ensembl:ENSG00000198569 MIM:609826; AllianceGenome:HGNC:20305
    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
    HHRH; NPT2C; NPTIIc
    Summary
    This gene encodes a member of SLC34A transporter family of proteins, and is expressed primarily in the kidney. It is involved in transporting phosphate into cells via sodium cotransport in the renal brush border membrane, and contributes to the maintenance of inorganic phosphate concentration in the kidney. Mutations in this gene are associated with hereditary hypophosphatemic rickets with hypercalciuria. Alternatively spliced transcript variants varying in the 5' UTR have been found for this gene.[provided by RefSeq, Apr 2010]
    Expression
    Biased expression in kidney (RPKM 9.9) and small intestine (RPKM 2.9) See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC34A3 in Genome Data Viewer
    Location:
    9q34.3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (137229730..137236555)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (149468426..149474224)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (140125209..140131007)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene hESC enhancers GRCh37_chr9:140121623-140122123 and GRCh37_chr9:140122257-140122882 Neighboring gene cysteine rich tail 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140124150-140124650 Neighboring gene ring finger protein 224 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20596 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20597 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20598 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20599 Neighboring gene tubulin beta 4B class IVb Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140140021-140140814 Neighboring gene ciliary microtubule inner protein 2A Neighboring gene uncharacterized LOC124902316

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Relationship between clinical phenotype and in vitro analysis of 13 NPT2c/SCL34A3 mutants. Brazier F, et al. Sci Rep, 2023 Jan 3. PMID 36596813, Free PMC Article
    2. Structure-function relations of the first and fourth extracellular linkers of the type IIa Na+/Pi cotransporter: II. Substrate interaction and voltage dependency of two functionally important sites. Ehnes C, et al. J Gen Physiol, 2004 Nov. PMID 15504899, Free PMC Article
    3. Hereditary hypophosphatemic rickets with hypercalciuria: a study for the phosphate transporter gene type IIc and osteoblastic function. Yamamoto T, et al. J Bone Miner Metab, 2007. PMID 17968493
    4. A novel missense mutation in SLC34A3 that causes hereditary hypophosphatemic rickets with hypercalciuria in humans identifies threonine 137 as an important determinant of sodium-phosphate cotransport in NaPi-IIc. Jaureguiberry G, et al. Am J Physiol Renal Physiol, 2008 Aug. PMID 18480181, Free PMC Article
    5. Hypophosphatemic rickets with hypercalciuria due to mutation in SLC34A3/type IIc sodium-phosphate cotransporter: presentation as hypercalciuria and nephrolithiasis. Tencza AL, et al. J Clin Endocrinol Metab, 2009 Nov. PMID 19820004, Free PMC Article

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Rare variants in the sodium-dependent phosphate transporter gene SLC34A3 explain missing heritability of urinary stone disease.
      Title: Rare variants in the sodium-dependent phosphate transporter gene SLC34A3 explain missing heritability of urinary stone disease.
    2. Relationship between clinical phenotype and in vitro analysis of 13 NPT2c/SCL34A3 mutants.
      Title: Relationship between clinical phenotype and in vitro analysis of 13 NPT2c/SCL34A3 mutants.
    3. The genetic polymorphisms of XPR1 and SCL34A3 are associated with Fanconi syndrome in Chinese patients of tumor-induced osteomalacia.
      Title: The genetic polymorphisms of XPR1 and SCL34A3 are associated with Fanconi syndrome in Chinese patients of tumor-induced osteomalacia.
    4. Novel heterozygous GATA3 and SLC34A3 variants in a 6-year-old boy with Barakat syndrome and hypercalciuria.
      Title: Novel heterozygous GATA3 and SLC34A3 variants in a 6-year-old boy with Barakat syndrome and hypercalciuria.
    5. Digenic Heterozygous Mutations in SLC34A3 and SLC34A1 Cause Dominant Hypophosphatemic Rickets with Hypercalciuria.
      Title: Digenic Heterozygous Mutations in SLC34A3 and SLC34A1 Cause Dominant Hypophosphatemic Rickets with Hypercalciuria.
    6. Of the twelve family members three were homozygote and seven heterozygote for the same solute carrier family 34 (sodium phosphate), member 3 protein (SLC34A3) variant.
      Title: SLC34A3 Intronic Deletion in an Iranian Kindred with Hereditary Hypophosphatemic Rickets with Hypercalciuria.
    7. genetic characteristics of 15 families with hereditary hypophosphatemia: Novel Mutations in PHEX and SLC34A3
      Title: Clinical and genetic characteristics of 15 families with hereditary hypophosphatemia: Novel Mutations in PHEX and SLC34A3.
    8. This is the report of a patient with compound heterozygous mutations of SLC34A3 and normal skeletal features. Biallelic mutations in SLC34A3 can thus be associated with hypercalciuria not accompanied by rickets.
      Title: Association between compound heterozygous mutations of SLC34A3 and hypercalciuria.
    9. Individuals with mutations affecting both SLC34A3 alleles had a significantly increased risk of kidney stone formation or medullary nephrocalcinosis, namely 46% compared with 6% observed in healthy family members carrying only the wild-type allele.
      Title: Mutations in SLC34A3/NPT2c are associated with kidney stones and nephrocalcinosis.
    10. this study reports the first cases of hereditary hypophosphatemic rickets with hypercalciuria in Africa and describes a novel causal mutation within the SLC34A3 gene
      Title: Novel SLC34A3 mutation causing hereditary hypophosphataemic rickets with hypercalciuria in a Gambian family.
    Submit: New GeneRIF Correction See all GeneRIFs (21)

    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

    Associated conditions

    Description Tests
    Autosomal recessive hypophosphatemic bone disease
    MedGen: C1853271 OMIM: 241530 GeneReviews: Not available
    		Compare labs

    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

    Clone Names

    • FLJ38680

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sodium:phosphate symporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables sodium:phosphate symporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables sodium:phosphate symporter activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in intracellular phosphate ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intracellular phosphate ion homeostasis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in phosphate ion transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in sodium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in sodium ion transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in sodium-dependent phosphate transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in apical plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in apical plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    is_active_in brush border IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in brush border membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    sodium-dependent phosphate transport protein 2C
    Names
    Na(+)-dependent phosphate cotransporter 2C
    Na(+)/Pi cotransporter 2C
    naPi-2c
    sodium-phosphate transport protein 2C
    sodium/inorganic phosphate cotransporter IIC
    solute carrier family 34 (sodium phosphate), member 3
    solute carrier family 34 (type II sodium/phosphate cotransporter), member 3
    type IIc Na+/Pi cotransporter

    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_017008.2 RefSeqGene

      Range
      5001..10655
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001177316.2 → NP_001170787.2  sodium-dependent phosphate transport protein 2C

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the predominant transcript. Variants 1-3 encode the same protein.
      Source sequence(s)
      AB055000, BC029942, BX255925
      Consensus CDS
      CCDS7038.1
      UniProtKB/Swiss-Prot
      A2BFA1, Q8N130
      Related
      ENSP00000501114.1, ENST00000673835.1
      Conserved Domains (1) summary
      TIGR01013
      Location:80 → 563
      2a58; Phosphate:Na+ Symporter (PNaS) Family

    2. NM_001177317.2 → NP_001170788.2  sodium-dependent phosphate transport protein 2C

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternative acceptor splice site at the second exon resulting in a 3 nt longer 5' UTR compared to variant 1. Variants 1-3 encode the same protein.
      Source sequence(s)
      BX255925
      Consensus CDS
      CCDS7038.1
      UniProtKB/Swiss-Prot
      A2BFA1, Q8N130
      Related
      ENSP00000442397.1, ENST00000538474.5

    3. NM_080877.3 → NP_543153.2  sodium-dependent phosphate transport protein 2C

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternative 5' non-coding exon resulting in a different 5' UTR compared to variant 1. Variants 1-3 encode the same protein.
      Source sequence(s)
      BX255925
      Consensus CDS
      CCDS7038.1
      UniProtKB/Swiss-Prot
      A2BFA1, Q8N130
      Related
      ENSP00000355353.2, ENST00000361134.2

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      137229730..137236555
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047422793.1 → XP_047278749.1  sodium-dependent phosphate transport protein 2C isoform X5

      UniProtKB/Swiss-Prot
      A2BFA1, Q8N130

    2. XM_047422786.1 → XP_047278742.1  sodium-dependent phosphate transport protein 2C isoform X1

    3. XM_047422788.1 → XP_047278744.1  sodium-dependent phosphate transport protein 2C isoform X1

    4. XM_011518258.2 → XP_011516560.1  sodium-dependent phosphate transport protein 2C isoform X4

      See identical proteins and their annotated locations for XP_011516560.1

      Conserved Domains (2) summary
      TIGR01013
      Location:80 → 445
      2a58; Phosphate:Na+ Symporter (PNaS) Family
      pfam02690
      Location:85 → 176
      Na_Pi_cotrans; Na+/Pi-cotransporter

    5. XM_047422789.1 → XP_047278745.1  sodium-dependent phosphate transport protein 2C isoform X1

    6. XM_011518260.2 → XP_011516562.1  sodium-dependent phosphate transport protein 2C isoform X4

      See identical proteins and their annotated locations for XP_011516562.1

      Conserved Domains (2) summary
      TIGR01013
      Location:80 → 445
      2a58; Phosphate:Na+ Symporter (PNaS) Family
      pfam02690
      Location:85 → 176
      Na_Pi_cotrans; Na+/Pi-cotransporter

    7. XM_011518259.2 → XP_011516561.1  sodium-dependent phosphate transport protein 2C isoform X4

      See identical proteins and their annotated locations for XP_011516561.1

      Conserved Domains (2) summary
      TIGR01013
      Location:80 → 445
      2a58; Phosphate:Na+ Symporter (PNaS) Family
      pfam02690
      Location:85 → 176
      Na_Pi_cotrans; Na+/Pi-cotransporter

    8. XM_047422790.1 → XP_047278746.1  sodium-dependent phosphate transport protein 2C isoform X1

    9. XM_047422787.1 → XP_047278743.1  sodium-dependent phosphate transport protein 2C isoform X1

    10. XM_047422791.1 → XP_047278747.1  sodium-dependent phosphate transport protein 2C isoform X2

    11. XM_047422792.1 → XP_047278748.1  sodium-dependent phosphate transport protein 2C isoform X3

    12. XM_047422785.1 → XP_047278741.1  sodium-dependent phosphate transport protein 2C isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      149468426..149474224
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054361994.1 → XP_054217969.1  sodium-dependent phosphate transport protein 2C isoform X1

    2. XM_054361995.1 → XP_054217970.1  sodium-dependent phosphate transport protein 2C isoform X1

    3. XM_054361999.1 → XP_054217974.1  sodium-dependent phosphate transport protein 2C isoform X4

    4. XM_054361996.1 → XP_054217971.1  sodium-dependent phosphate transport protein 2C isoform X1

    5. XM_054362000.1 → XP_054217975.1  sodium-dependent phosphate transport protein 2C isoform X4

    6. XM_054361997.1 → XP_054217972.1  sodium-dependent phosphate transport protein 2C isoform X2

    7. XM_054361998.1 → XP_054217973.1  sodium-dependent phosphate transport protein 2C isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N130.2 GenPept UniProtKB/Swiss-Prot:Q8N130

    Gene LinkOut

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

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