SLC34A1 solute carrier family 34 member 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC34A1provided by HGNC
Official Full Name: solute carrier family 34 member 1provided by HGNC
Primary source: HGNC:HGNC:11019
See related: Ensembl:ENSG00000131183 MIM:182309; AllianceGenome:HGNC:11019
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: NPT2; FRTS2; SLC11; HCINF2; NAPI-3; NPTIIa; NPHLOP1; SLC17A2
Summary: Enables sodium:phosphate symporter activity. Involved in several processes, including phosphate ion homeostasis; phosphate ion transport; and response to lead ion. Located in several cellular components, including apical plasma membrane; mitotic spindle; and nuclear speck. Implicated in several diseases, including Fanconi syndrome (multiple); chronic kidney disease; hereditary hypophosphatemic rickets with hypercalciuria; hypophosphatemic nephrolithiasis/osteoporosis 1; and nephrolithiasis. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Restricted expression toward kidney (RPKM 54.1) See more
Orthologs: mouse all
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Genomic context

Location:: 5q35.3

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (177384434..177398848)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (177927652..177942066)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (176811435..176825849)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Biallelic and monoallelic pathogenic variants in CYP24A1 and SLC34A1 genes cause idiopathic infantile hypercalcemia.
Title: Biallelic and monoallelic pathogenic variants in CYP24A1 and SLC34A1 genes cause idiopathic infantile hypercalcemia.
High frequency of heterozygous rare variants of the SLC34A1 and SLC9A3R1 genes in patients with atypical femur fracture.
Title: High frequency of heterozygous rare variants of the SLC34A1 and SLC9A3R1 genes in patients with atypical femur fracture.
The human pathogenic 91del7 mutation in SLC34A1 has no effect in mineral homeostasis in mice.
Title: The human pathogenic 91del7 mutation in SLC34A1 has no effect in mineral homeostasis in mice.
CYP24A1 and SLC34A1 Pathogenic Variants Are Uncommon in a Canadian Cohort of Children with Hypercalcemia or Hypercalciuria.
Title: CYP24A1 and SLC34A1 Pathogenic Variants Are Uncommon in a Canadian Cohort of Children with Hypercalcemia or Hypercalciuria.
Long-term outcome of the survivors of infantile hypercalcaemia with CYP24A1 and SLC34A1 mutations.
Title: Long-term outcome of the survivors of infantile hypercalcaemia with CYP24A1 and SLC34A1 mutations.
Idiopathic infantile hypercalcemia: mutations in SLC34A1 and CYP24A1 in two siblings and fathers.
Title: Idiopathic infantile hypercalcemia: mutations in SLC34A1 and CYP24A1 in two siblings and fathers.
Noncanonical Sequences Involving NHERF1 Interaction with NPT2A Govern Hormone-Regulated Phosphate Transport: Binding Outside the Box.
Title: Noncanonical Sequences Involving NHERF1 Interaction with NPT2A Govern Hormone-Regulated Phosphate Transport: Binding Outside the Box.
Analysis of vitamin D3 metabolites in survivors of infantile idiopathic hypercalcemia caused by CYP24A1 mutation or SLC34A1 mutation.
Title: Analysis of vitamin D(3) metabolites in survivors of infantile idiopathic hypercalcemia caused by CYP24A1 mutation or SLC34A1 mutation.
Nephrolithiasis from an Unexpected Cause: Phosphaturia.
Title: Nephrolithiasis from an Unexpected Cause: Phosphaturia.
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.

Submit: New GeneRIF Correction See all GeneRIFs (36)

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
Fanconi renotubular syndrome 2 MedGen: C3150652 OMIM: 613388 GeneReviews: Not available	Compare labs
Hypercalcemia, infantile, 2 MedGen: C4310473 OMIM: 616963 GeneReviews: Not available	Compare labs
Hypophosphatemic nephrolithiasis/osteoporosis 1 MedGen: C2676786 OMIM: 612286 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A genome-wide association study of nephrolithiasis in the Japanese population identifies novel susceptible Loci at 5q35.3, 7p14.3, and 13q14.1. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic associations for activated partial thromboplastin time and prothrombin time, their gene expression profiles, and risk of coronary artery disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies identifies six new Loci for serum calcium concentrations. EBI GWAS Catalog EBI GWAS CatalogPubMed
New loci associated with kidney function and chronic kidney disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

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 PDZ domain binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IEA Inferred from Electronic Annotation more info
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	IMP Inferred from Mutant Phenotype more info	PubMed
enables sodium:phosphate symporter activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
involved_in arsenate ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in cellular response to metal ion	IEA Inferred from Electronic Annotation more info
involved_in cellular response to parathyroid hormone stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to phosphate starvation	IEA Inferred from Electronic Annotation more info
involved_in cellular response to staurosporine	IEA Inferred from Electronic Annotation more info
involved_in dentinogenesis	IEA Inferred from Electronic Annotation more info
involved_in gentamycin metabolic process	IEA Inferred from Electronic Annotation more info
involved_in glycoprotein metabolic process	IEA Inferred from Electronic Annotation more info
involved_in indole metabolic process	IEA Inferred from Electronic Annotation more info
involved_in intracellular phosphate ion homeostasis	IBA Inferred from Biological aspect of Ancestor more info
involved_in kidney development	IEA Inferred from Electronic Annotation more info
involved_in ossification	IEA Inferred from Electronic Annotation more info
involved_in phosphate ion homeostasis	IDA Inferred from Direct Assay more info	PubMed
involved_in phosphate ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in phosphate ion transport	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of membrane potential	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of phosphate transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of sodium-dependent phosphate transport	IEA Inferred from Electronic Annotation more info
involved_in protein metabolic process	TAS Traceable Author Statement more info
involved_in response to cadmium ion	IDA Inferred from Direct Assay more info	PubMed
involved_in response to estradiol	IEA Inferred from Electronic Annotation more info
involved_in response to growth hormone	IEA Inferred from Electronic Annotation more info
involved_in response to lead ion	IDA Inferred from Direct Assay more info	PubMed
involved_in response to magnesium ion	IEA Inferred from Electronic Annotation more info
involved_in response to mercury ion	IDA Inferred from Direct Assay more info	PubMed
involved_in response to potassium ion	IEA Inferred from Electronic Annotation more info
involved_in response to thyroid hormone	IEA Inferred from Electronic Annotation more info
involved_in response to vitamin A	IEA Inferred from Electronic Annotation more info
involved_in response to xenobiotic stimulus	IEA Inferred from Electronic Annotation more info
involved_in sodium ion import across plasma membrane	IEA Inferred from Electronic Annotation more info
involved_in sodium-dependent phosphate transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in tricarboxylic acid metabolic process	IEA Inferred from Electronic Annotation 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	IDA Inferred from Direct Assay 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 brush border membrane	NAS Non-traceable Author Statement more info	PubMed
located_in cell surface	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in endosome	IEA Inferred from Electronic Annotation more info
located_in mitotic spindle	IDA Inferred from Direct Assay more info
located_in nuclear speck	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed
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 2A

Names: Na(+)-dependent phosphate cotransporter 2A; Na(+)/Pi cotransporter 2A; Na+-phosphate cotransporter type II; naPi-2a; renal sodium-dependent phosphate transporter; sodium-phosphate transport protein 2A; sodium/phosphate co-transporter; sodium/phosphate cotransporter 2A; solute carrier family 17 (sodium phosphate), member 2; solute carrier family 34 (sodium phosphate), member 1; solute carrier family 34 (type II sodium/phosphate cotransporter), 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

NG_016223.2 RefSeqGene

Range

5002..19416

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001167579.2 → NP_001161051.1 sodium-dependent phosphate transport protein 2A isoform 2

See identical proteins and their annotated locations for NP_001161051.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 3' UTR and has multiple coding region differences compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AC145098, AI650347, AK298299, BI759164

Consensus CDS

CCDS54953.1

UniProtKB/Swiss-Prot

Q06495

Related

ENSP00000423022.1, ENST00000512593.5

Conserved Domains (2) summary

TIGR01013
Location:108 → 310

2a58; Phosphate:Na+ Symporter (PNaS) Family

pfam02690
Location:113 → 204

Na_Pi_cotrans; Na+/Pi-cotransporter
NM_003052.5 → NP_003043.3 sodium-dependent phosphate transport protein 2A isoform 1

See identical proteins and their annotated locations for NP_003043.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).

Source sequence(s)

BC050385, BC053349, BP275443

Consensus CDS

CCDS4418.1

UniProtKB/Swiss-Prot

B4DPE3, Q06495

UniProtKB/TrEMBL

Q86VN6

Related

ENSP00000321424.4, ENST00000324417.6

Conserved Domains (2) summary

TIGR01013
Location:108 → 590

2a58; Phosphate:Na+ Symporter (PNaS) Family

pfam02690
Location:113 → 204

Na_Pi_cotrans; Na+/Pi-cotransporter