Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	6569
Gene name	Solute carrier family 34 member 1
Gene symbol	SLC34A1
Synonyms (NCBI Gene)	FRTS2HCINF2NAPI-3NPHLOP1NPT2NPTIIaSLC11SLC17A2
Chromosome	5
Chromosome location	5q35.3
Summary	This gene encodes a member of the type II sodium-phosphate cotransporter family. Mutations in this gene are associated with hypophosphatemia nephrolithiasis/osteoporosis 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq,

Show/Hide all (18)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121918610	GC>TT	Pathogenic	Missense variant, coding sequence variant, genic upstream transcript variant, non coding transcript variant
rs121918611	G>A,C	Pathogenic	Missense variant, coding sequence variant, genic upstream transcript variant, non coding transcript variant
rs142772770	T>C	Likely-pathogenic	Missense variant, coding sequence variant, genic upstream transcript variant, non coding transcript variant
rs146919762	G>A	Likely-pathogenic	Coding sequence variant, genic upstream transcript variant, missense variant, non coding transcript variant
rs148976897	C>T	Likely-benign, likely-pathogenic	Coding sequence variant, genic upstream transcript variant, missense variant, non coding transcript variant
rs150592440	G>A,C	Pathogenic, likely-benign	Coding sequence variant, genic upstream transcript variant, synonymous variant, non coding transcript variant
rs200095793	G>A,T	Pathogenic	Splice donor variant, genic downstream transcript variant
rs200893951	C>A,T	Likely-pathogenic	Coding sequence variant, synonymous variant, genic upstream transcript variant, non coding transcript variant, stop gained
rs201304511	G>A	Pathogenic, likely-pathogenic	Splice donor variant, genic upstream transcript variant
rs201331677	C>T	Likely-pathogenic	Coding sequence variant, genic downstream transcript variant, missense variant, non coding transcript variant, intron variant
rs376131751	G>C	Likely-pathogenic	Non coding transcript variant, genic downstream transcript variant, coding sequence variant, missense variant
rs769409705	G>C,T	Pathogenic, likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant, non coding transcript variant
rs876661296	TCCCCAAGCTGCGCCAGGCTG>-	Benign, pathogenic-likely-pathogenic	Coding sequence variant, non coding transcript variant, genic upstream transcript variant, inframe deletion
rs876661338	T>G	Pathogenic	Genic downstream transcript variant, non coding transcript variant, missense variant, coding sequence variant
rs1554095263	->ATCCTGGTGACCGTGCTGGTG	Pathogenic	Coding sequence variant, inframe insertion, non coding transcript variant, genic upstream transcript variant
rs1554095500	A>C	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant, genic upstream transcript variant
rs1554095568	C>T	Pathogenic	Stop gained, upstream transcript variant, coding sequence variant, genic upstream transcript variant, non coding transcript variant
rs1581634382	GGGCCCTGTGGCCCTTGCTG>A	Likely-pathogenic	Coding sequence variant, non coding transcript variant, genic upstream transcript variant, frameshift variant

Show/Hide all (46)

miRTarBase ID	miRNA	Experiments
MIRT1359987	hsa-miR-1269	CLIP-seq
MIRT1359988	hsa-miR-1269b	CLIP-seq
MIRT1359989	hsa-miR-146b-3p	CLIP-seq
MIRT1359990	hsa-miR-153	CLIP-seq
MIRT1359991	hsa-miR-3152-5p	CLIP-seq
MIRT1359992	hsa-miR-3160-5p	CLIP-seq
MIRT1359993	hsa-miR-3173-5p	CLIP-seq
MIRT1359994	hsa-miR-3183	CLIP-seq
MIRT1359995	hsa-miR-4254	CLIP-seq
MIRT1359996	hsa-miR-4287	CLIP-seq
MIRT1359997	hsa-miR-4292	CLIP-seq
MIRT1359998	hsa-miR-4308	CLIP-seq
MIRT1359999	hsa-miR-4469	CLIP-seq
MIRT1360000	hsa-miR-4529-3p	CLIP-seq
MIRT1360001	hsa-miR-4685-3p	CLIP-seq
MIRT1360002	hsa-miR-4723-3p	CLIP-seq
MIRT1360003	hsa-miR-4725-5p	CLIP-seq
MIRT1360004	hsa-miR-4786-5p	CLIP-seq
MIRT1360005	hsa-miR-504	CLIP-seq
MIRT1360006	hsa-miR-548q	CLIP-seq
MIRT1360007	hsa-miR-670	CLIP-seq
MIRT1360008	hsa-miR-769-5p	CLIP-seq
MIRT1360009	hsa-miR-874	CLIP-seq
MIRT1360010	hsa-miR-1912	CLIP-seq
MIRT1360011	hsa-miR-1915	CLIP-seq
MIRT1360012	hsa-miR-3130-5p	CLIP-seq
MIRT1360013	hsa-miR-4269	CLIP-seq
MIRT1360014	hsa-miR-4482	CLIP-seq
MIRT1360015	hsa-miR-4751	CLIP-seq
MIRT1360016	hsa-miR-487a	CLIP-seq
MIRT1360017	hsa-miR-492	CLIP-seq
MIRT2394724	hsa-miR-2355-5p	CLIP-seq
MIRT1359992	hsa-miR-3160-5p	CLIP-seq
MIRT2394725	hsa-miR-3679-3p	CLIP-seq
MIRT1359987	hsa-miR-1269	CLIP-seq
MIRT1359988	hsa-miR-1269b	CLIP-seq
MIRT1359991	hsa-miR-3152-5p	CLIP-seq
MIRT1359994	hsa-miR-3183	CLIP-seq
MIRT1359996	hsa-miR-4287	CLIP-seq
MIRT1359997	hsa-miR-4292	CLIP-seq
MIRT1359998	hsa-miR-4308	CLIP-seq
MIRT1359999	hsa-miR-4469	CLIP-seq
MIRT1360000	hsa-miR-4529-3p	CLIP-seq
MIRT1360001	hsa-miR-4685-3p	CLIP-seq
MIRT1360002	hsa-miR-4723-3p	CLIP-seq
MIRT1360006	hsa-miR-548q	CLIP-seq

Show/Hide all (69)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001503	Process	Ossification	IEA
GO:0001822	Process	Kidney development	IEA
GO:0005436	Function	Sodium:phosphate symporter activity	IBA
GO:0005436	Function	Sodium:phosphate symporter activity	IDA	8327470, 8898024, 9530108
GO:0005436	Function	Sodium:phosphate symporter activity	IEA
GO:0005436	Function	Sodium:phosphate symporter activity	IMP	12324554, 20335586, 26047794
GO:0005436	Function	Sodium:phosphate symporter activity	TAS
GO:0005515	Function	Protein binding	IPI	17895247, 22506049
GO:0005654	Component	Nucleoplasm	IDA
GO:0005768	Component	Endosome	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005886	Component	Plasma membrane	IDA	26047794
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	IMP	20335586
GO:0005886	Component	Plasma membrane	NAS	8327470
GO:0005886	Component	Plasma membrane	TAS
GO:0005903	Component	Brush border	IBA
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006814	Process	Sodium ion transport	IEA
GO:0006817	Process	Phosphate ion transport	IDA	8327470, 8898024, 9530108
GO:0007584	Process	Response to nutrient	IEA
GO:0009100	Process	Glycoprotein metabolic process	IEA
GO:0009410	Process	Response to xenobiotic stimulus	IEA
GO:0009986	Component	Cell surface	IEA
GO:0010288	Process	Response to lead ion	IDA	8898024
GO:0015293	Function	Symporter activity	IEA
GO:0016020	Component	Membrane	IEA
GO:0016036	Process	Cellular response to phosphate starvation	IEA
GO:0016324	Component	Apical plasma membrane	IBA
GO:0016324	Component	Apical plasma membrane	IDA	26047794
GO:0016324	Component	Apical plasma membrane	IEA
GO:0016607	Component	Nuclear speck	IDA
GO:0030165	Function	PDZ domain binding	IEA
GO:0030643	Process	Intracellular phosphate ion homeostasis	IBA
GO:0031526	Component	Brush border membrane	IEA
GO:0031526	Component	Brush border membrane	ISS
GO:0031526	Component	Brush border membrane	NAS	8693007
GO:0031982	Component	Vesicle	IBA
GO:0032026	Process	Response to magnesium ion	IEA
GO:0032355	Process	Response to estradiol	IEA
GO:0033189	Process	Response to vitamin A	IEA
GO:0035435	Process	Phosphate ion transmembrane transport	IEA
GO:0035864	Process	Response to potassium ion	IEA
GO:0042431	Process	Indole metabolic process	IEA
GO:0042802	Function	Identical protein binding	IEA
GO:0043434	Process	Response to peptide hormone	IEA
GO:0044341	Process	Sodium-dependent phosphate transport	IBA
GO:0044341	Process	Sodium-dependent phosphate transport	IEA
GO:0044877	Function	Protein-containing complex binding	IEA
GO:0045838	Process	Positive regulation of membrane potential	IEA
GO:0046686	Process	Response to cadmium ion	IDA	8898024
GO:0046689	Process	Response to mercury ion	IDA	8898024
GO:0048471	Component	Perinuclear region of cytoplasm	IEA
GO:0055062	Process	Phosphate ion homeostasis	IDA	8327470, 8898024, 9530108
GO:0060416	Process	Response to growth hormone	IEA
GO:0071107	Process	Response to parathyroid hormone	IEA
GO:0071248	Process	Cellular response to metal ion	IEA
GO:0071374	Process	Cellular response to parathyroid hormone stimulus	IEA
GO:0072350	Process	Tricarboxylic acid metabolic process	IEA
GO:0072686	Component	Mitotic spindle	IDA
GO:0072734	Process	Cellular response to staurosporine	IEA
GO:0097066	Process	Response to thyroid hormone	IEA
GO:0097187	Process	Dentinogenesis	IEA
GO:0098719	Process	Sodium ion import across plasma membrane	IEA
GO:1901128	Process	Gentamycin metabolic process	IEA
GO:1901652	Process	Response to peptide	IEA
GO:1901684	Process	Arsenate ion transmembrane transport	IEA
GO:2000120	Process	Positive regulation of sodium-dependent phosphate transport	IEA
GO:2000187	Process	Positive regulation of phosphate transmembrane transport	IEA

MIM	HGNC	e!Ensembl
182309	11019	ENSG00000131183

Q06495

Protein name

Sodium-dependent phosphate transport protein 2A (Sodium-phosphate transport protein 2A) (Na(+)-dependent phosphate cotransporter 2A) (NaPi-3) (Sodium/phosphate cotransporter 2A) (Na(+)/Pi cotransporter 2A) (NaPi-2a) (Solute carrier family 34 member 1)

Protein function

Involved in actively transporting phosphate into cells via Na(+) cotransport in the renal brush border membrane (PubMed:12324554, PubMed:20335586, PubMed:26047794, PubMed:8327470). The cotransport has a Na(+):Pi stoichiometry of 3:1 and is elect

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02690	Na_Pi_cotrans	113 → 252	Na+/Pi-cotransporter	Family
PF02690	Na_Pi_cotrans	361 → 551	Na+/Pi-cotransporter	Family

Tissue specificity

TISSUE SPECIFICITY: Kidney and lung. {ECO:0000269|PubMed:8327470}.

Sequence

MLSYGERLGSPAVSPLPVRGGHVMRGTAFAYVPSPQVLHRIPGTSAYAFPSLGPVALAEH
TCPCGEVLERHEPLPAKLALEEEQKPESRLVPKLRQAGAMLLKVPLMLTFLYLFVCSLDM
LSSAFQLAGGKVAGDIFKDNAILSNPVAGLVVGILVTVLVQSSSTSTSIIVSMVSSGLLE
VSSAIPIIMGSNIGTSVTNTIVALMQAGDRTDFRRAFAGATVHDCFNWLSVLVLLPLEAA
TGYLHHITRLVVASFNIHGGRDAPDLLKIITEPFTKLIIQLDESVITSIATGDESLRNHS
LIQIWCHPDSLQAPTSMSRAEANSSQTLGNATMEKCNHIFVDTGLPDLAVGLILLAGSLV
LLCTCLILLVKMLNSLLKGQVAKVIQKVINTDFPAPFTWVTGYFAMVVGASMTFVVQSSS
VFTSAITPLIGLGVISIERAYPLTLGSNIGTTTTAILAALASPREKLSSAFQIALCHFFF
NISGILLWYPVPCTRLPIRMAKALGKRTAKYRWFAVLYLLVCFLLLPSLVFGISMAGWQV
MVGVGTPFGALLAFVVLINVLQSRSPGHLPKWLQTWDFLPRWMHSLKPLDHLITRATLCC
ARPEPRSPPLPPRVFLEELPPATPSPRLALPAHHNATRL

Sequence length

639

Interactions

View interactions

	KEGG		Reactome
	Parathyroid hormone synthesis, secretion and action Mineral absorption		Type II Na+/Pi cotransporters Defective SLC34A1 causes hypophosphatemic nephrolithiasis/osteoporosis 1 (NPHLOP1) Surfactant metabolism

396

Show/Hide Causal Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autosomal recessive infantile hypercalcemia	Likely pathogenic; Pathogenic	rs1426432774	RCV001195304
Fanconi renotubular syndrome 2	Likely pathogenic; Pathogenic	rs770557903, rs1174958403, rs2481014114, rs201304511, rs769409705, rs188409125, rs200893951, rs1426432774, rs777543926	RCV001843687 RCV005624498 RCV002466290 RCV005044463 RCV002500742 RCV005036835 RCV002481520 RCV002484062 RCV006249730
Hypercalcemia, infantile, 2	Pathogenic; Likely pathogenic	rs1174958403, rs201304511, rs769409705, rs200095793, rs876661338, rs757124444, rs188409125, rs200893951, rs1554095500, rs1426432774, rs777543926	RCV003326007 RCV000223675 RCV000223664 RCV000223671 RCV000223677 RCV000223665 RCV003152853 RCV005036835 RCV002481520 RCV000505687 RCV002484062 RCV001251504
Hypophosphatemic nephrolithiasis/osteoporosis 1	Pathogenic; Likely pathogenic	rs1174958403, rs201304511, rs769409705, rs121918610, rs1272063335, rs188409125, rs2481008620, rs200893951, rs1554095568, rs1426432774, rs777543926	RCV005624498 RCV005044463 RCV002500742 RCV000013794 RCV004577630 RCV005036835 RCV003992018 RCV004787785 RCV000503372 RCV002484062 RCV006249730
Nephrocalcinosis	Pathogenic	rs201304511	RCV000662327
Nephrolithiasis	Pathogenic	rs201304511	RCV000662327
Osteogenesis imperfecta type III	Likely pathogenic	rs1581634382	RCV000860017
SLC34A1-related disorder	Pathogenic; Likely pathogenic	rs201304511, rs769409705, rs200095793, rs1298448088	RCV004532819 RCV000778761 RCV005431563 RCV004554040

Show/Hide Unknown Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Cervical cancer	Benign	rs73804338	RCV005918253
Decreased total lymphocyte count	Benign; Likely benign	rs145798898	RCV002227462
Decreased total neutrophil count	Benign; Likely benign	rs145798898	RCV002227462
Gastric cancer	Conflicting classifications of pathogenicity	rs561557630	RCV005912749
Nephrolithiasis/osteoporosis, hypophosphatemic	Uncertain significance	rs768911630	RCV000276194
Nonpapillary renal cell carcinoma	Likely benign	rs771178295	RCV005913931
Prostate cancer	Uncertain significance	rs193920767	RCV000149142
Thymoma	Benign	rs73804338	RCV005918254

Show/Hide Text Mining Associations (35)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Acute Kidney Injury	Associate	38139117
Bone Diseases Metabolic	Associate	38139117, 39461557
Carcinoma Renal Cell	Inhibit	32461965
Carcinoma Renal Cell	Associate	36978048
Constipation	Associate	39461557
Epilepsy	Associate	40225330
Failure to Thrive	Associate	39461557
Familial Hypophosphatemic Rickets	Associate	18996815
Fanconi Syndrome	Associate	29924459, 40225330
Hypercalcemia	Associate	28470390, 39461557
Hypercalcemia Infantile	Associate	28304097, 28470390, 29924459, 34125233, 34721296
Hypercalciuria	Associate	18996815, 28470390, 32311027, 39461557
Hypophosphatemia	Associate	25050900, 31096470, 37132631, 37432176, 39461557
Hypophosphatemic Rickets Autosomal Dominant	Associate	31096470, 32311027
Hypophosphatemic Rickets with Hypercalciuria Hereditary	Associate	16358214, 32311027
Kidney Calculi	Associate	26272126, 29924459, 32216560, 37432176, 40372791, 40759569
Metabolic Diseases	Associate	18996815
Nephrocalcinosis	Associate	25050900, 28893421, 37559368, 39461557
Nephrolithiasis	Associate	22396660, 28893421, 32311027, 38139117
Nephrolithiasis Osteoporosis Hypophosphatemic 1	Associate	29924459, 38139117
Osteomalacia	Associate	39461557
Osteoporosis	Associate	32216560, 39461557
Paraparesis	Associate	31096470
Polyuria	Associate	39461557
Pulmonary Alveolar Microlithiasis	Associate	17601973
Pulmonary Alveolar Microlithiasis	Inhibit	36864068
Renal Colic	Associate	38139117
Renal Insufficiency Chronic	Associate	20383146, 21980298
Rickets	Associate	39461557
Rickets Hypophosphatemic	Associate	32311027
Testicular Microlithiasis	Associate	38139117
Thrombosis	Associate	34668383
Vitamin D Deficiency	Associate	28470390, 40225330
Vomiting	Associate	39461557
Wasting Syndrome	Associate	32311027, 39461557

SLC34A1 (solute carrier family 34 member 1)