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

Summary

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

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_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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

NG_017008.2 RefSeqGene

Range

5001..10655

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

137229730..137236555

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

A2BFA1, Q8N130
XM_047422786.1 → XP_047278742.1 sodium-dependent phosphate transport protein 2C isoform X1
XM_047422788.1 → XP_047278744.1 sodium-dependent phosphate transport protein 2C isoform X1
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
XM_047422789.1 → XP_047278745.1 sodium-dependent phosphate transport protein 2C isoform X1
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
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
XM_047422790.1 → XP_047278746.1 sodium-dependent phosphate transport protein 2C isoform X1
XM_047422787.1 → XP_047278743.1 sodium-dependent phosphate transport protein 2C isoform X1
XM_047422791.1 → XP_047278747.1 sodium-dependent phosphate transport protein 2C isoform X2
XM_047422792.1 → XP_047278748.1 sodium-dependent phosphate transport protein 2C isoform X3
XM_047422785.1 → XP_047278741.1 sodium-dependent phosphate transport protein 2C isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060933.1 Alternate T2T-CHM13v2.0

Range

149468426..149474224

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054361994.1 → XP_054217969.1 sodium-dependent phosphate transport protein 2C isoform X1
XM_054361995.1 → XP_054217970.1 sodium-dependent phosphate transport protein 2C isoform X1
XM_054361999.1 → XP_054217974.1 sodium-dependent phosphate transport protein 2C isoform X4
XM_054361996.1 → XP_054217971.1 sodium-dependent phosphate transport protein 2C isoform X1
XM_054362000.1 → XP_054217975.1 sodium-dependent phosphate transport protein 2C isoform X4
XM_054361997.1 → XP_054217972.1 sodium-dependent phosphate transport protein 2C isoform X2
XM_054361998.1 → XP_054217973.1 sodium-dependent phosphate transport protein 2C isoform X3