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

Gene ID: 142680, updated on 5-Mar-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
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Genomic context

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Location:
9q34.3
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (137229730..137236555)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (149468426..149474224)
105.20220307 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

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. 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. Novel heterozygous GATA3 and SLC34A3 variants in a 6-year-old boy with Barakat syndrome and hypercalciuria. Yu S, et al. Mol Genet Genomic Med, 2020 May. PMID 32155322, Free PMC Article
  3. SLC34A3 Intronic Deletion in an Iranian Kindred with Hereditary Hypophosphatemic Rickets with Hypercalciuria. Hasani-Ranjbar S, et al. J Clin Res Pediatr Endocrinol, 2018 Nov 29. PMID 29809158, Free PMC Article
  4. Association between compound heterozygous mutations of SLC34A3 and hypercalciuria. Abe Y, et al. Horm Res Paediatr, 2014. PMID 24924704
  5. Mutations in SLC34A3/NPT2c are associated with kidney stones and nephrocalcinosis. Dasgupta D, et al. J Am Soc Nephrol, 2014 Oct. PMID 24700880, Free PMC Article

See all (27) 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
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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

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_2023_10

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

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