SLC34A1 (solute carrier family 34 member 1)

Gene

• Entrez ID: 6569
• Gene name: Solute carrier family 34 member 1
• Gene symbol: SLC34A1
• Synonyms: FRTS2, HCINF2, NAPI-3, NPHLOP1, NPT2, NPTIIa, SLC11, SLC17A2
• 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,

SNPs

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

miRNA

miRTarBase ID	miRNA	Experiments	Reference
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

Gene ontology (GO)

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	21873635
GO:0005436	Function	Sodium:phosphate symporter activity	IDA	8327470, 8898024, 9530108
GO:0005436	Function	Sodium:phosphate symporter activity	IMP	26047794
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	TAS
GO:0005887	Component	Integral component of plasma membrane	NAS	8327470
GO:0005903	Component	Brush border	IBA	21873635
GO:0006817	Process	Phosphate ion transport	IDA	8327470, 8898024, 9530108
GO:0009100	Process	Glycoprotein metabolic process	IEA
GO:0009986	Component	Cell surface	IEA
GO:0010288	Process	Response to lead ion	IDA	8898024
GO:0016324	Component	Apical plasma membrane	IBA	21873635
GO:0016324	Component	Apical plasma membrane	IDA	26047794
GO:0016607	Component	Nuclear speck	IDA
GO:0030165	Function	PDZ domain binding	IEA
GO:0030643	Process	Cellular phosphate ion homeostasis	IBA	21873635
GO:0031526	Component	Brush border membrane	ISS
GO:0031526	Component	Brush border membrane	NAS	8693007
GO:0031982	Component	Vesicle	IBA	21873635
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:0042493	Process	Response to drug	IEA
GO:0042802	Function	Identical protein binding	IEA
GO:0044267	Process	Cellular protein metabolic process	TAS
GO:0044341	Process	Sodium-dependent phosphate transport	IBA	21873635
GO:0044877	Function	Protein-containing complex binding	IEA
GO:0045121	Component	Membrane raft	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: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: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

Other IDs

• MIM: 182309
• HGNC: 11019
• e!Ensembl: ENSG00000131183

Protein

• UniProt ID: 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

• Sequence:

  MLSYGERLGSPAVSPLPVRGGHVMRGTAFAYVPSPQVLHRIPGTSAYAFPSLGPVALAEH
  TCPCGEVLERHEPLPAKLALEEEQKPESRLVPKLRQAGAMLLKVPLMLTFLYLFVCSLDM
  LSSAFQLAGGKVAGDIFKDNAILSNPVAGLVVGILVTVLVQSSSTSTSIIVSMVSSGLLE
  VSSAIPIIMGSNIGTSVTNTIVALMQAGDRTDFRRAFAGATVHDCFNWLSVLVLLPLEAA
  TGYLHHITRLVVASFNIHGGRDAPDLLKIITEPFTKLIIQLDESVITSIATGDESLRNHS
  LIQIWCHPDSLQAPTSMSRAEANSSQTLGNATMEKCNHIFVDTGLPDLAVGLILLAGSLV
  LLCTCLILLVKMLNSLLKGQVAKVIQKVINTDFPAPFTWVTGYFAMVVGASMTFVVQSSS
  VFTSAITPLIGLGVISIERAYPLTLGSNIGTTTTAILAALASPREKLSSAFQIALCHFFF
  NISGILLWYPVPCTRLPIRMAKALGKRTAKYRWFAVLYLLVCFLLLPSLVFGISMAGWQV
  MVGVGTPFGALLAFVVLINVLQSRSPGHLPKWLQTWDFLPRWMHSLKPLDHLITRATLCC
  ARPEPRSPPLPPRVFLEELPPATPSPRLALPAHHNATRL

• Sequence length: 639

Pathways

KEGG:

Parathyroid hormone synthesis, secretion and action
Mineral absorption

Reactome:

Type II Na+/Pi cotransporters
Defective SLC34A1 causes hypophosphatemic nephrolithiasis/osteoporosis 1 (NPHLOP1)
Surfactant metabolism

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Fanconi syndrome	De Toni-Debre-Fanconi Syndrome, FANCONI RENOTUBULAR SYNDROME 2, FANCONI RENOTUBULAR SYNDROME 1, Fanconi Syndrome, Adult Fanconi syndrome, Primary Fanconi renotubular syndrome	rs398124646	20335586
Diabetes	Diabetes	rs80356611	31451708
Diabetes mellitus	Diabetes Mellitus	rs587776515, rs61730328, rs606231121, rs606231122, rs79020217, rs77625743, rs78378398, rs606231123, rs4402960, rs1362648752, rs3745368, rs3792267, rs3842570, rs5030952, rs2975760, rs119489103, rs7903146, rs12255372, rs11196205, rs104893649, rs80356624, rs80356616, rs80356625, rs80356611, rs104894237, rs80356613, rs137852740, rs137852786, rs387906407, rs151344623, rs28938469, rs28936371, rs137852672, rs80356637, rs80356642, rs80356653, rs137852673, rs137852674, rs80356634, rs80356651, rs193929360, rs137853334, rs137853335, rs137853336, rs1600731198, rs137853338, rs121964882, rs121964883, rs387906511, rs121964884, rs121964885, rs2147483647, rs387906512, rs121964887, rs121964888, rs121964889, rs121964890, rs121964891, rs28934878, rs74315383, rs121964893, rs886037620, rs886037621, rs80356663, rs121434593, rs121913150, rs587776825, rs137853236, rs2135842335, rs137853237, rs137853238, rs2135818776, rs1566092470, rs1463923467, rs137853243, rs137853244, rs2135839114, rs137853245, rs2135847417, rs121918407, rs104894005, rs104894006, rs80356655, rs104894008, rs104894009, rs104894010, rs104894011, rs80356654, rs104894016, rs193929376, rs193929374, rs193929375, rs193929373, rs80356666, rs80356669, rs80356664, rs193929366, rs1048095, rs193929355, rs193929356, rs1259467443, rs104893642, rs387906777, rs387906779, rs141804752, rs182349376, rs184917682, rs193922396, rs193922400, rs193922401, rs137852676, rs193922407, rs193922638, rs193922257, rs193922258, rs193922259, rs193922260, rs193922261, rs193922262, rs193922263, rs193922264, rs193922265, rs193922268, rs193921338, rs193922269, rs193922272, rs193922273, rs193922275, rs193922278, rs193922279, rs193922280, rs193922281, rs193922282, rs193922283, rs193922284, rs193922286, rs193922287, rs193922289, rs193922291, rs193922295, rs193922297, rs193922300, rs193922302, rs193922303, rs193922308, rs193922313, rs193922314, rs144723656, rs193922315, rs193922316, rs193922317, rs148311934, rs193922319, rs193922320, rs193922326, rs193922329, rs193922330, rs193922331, rs193922335, rs193922336, rs193922338, rs193922340, rs193922341, rs193922471, rs193922475, rs193922476, rs193922479, rs193922355, rs193922356, rs193922576, rs193922578, rs193922582, rs193922588, rs193922592, rs193922594, rs193922596, rs386134267, rs193922598, rs193922599, rs193922600, rs193922604, rs193922605, rs397514580, rs397515519, rs267601516, rs587780343, rs587780345, rs587780346, rs587780347, rs587780357, rs148954387, rs61736969, rs587783673, rs587783672, rs587783669, rs786204676, rs794727236, rs151344624, rs794727775, rs794727839, rs199946797, rs869320673, rs796065047, rs759072800, rs797045595, rs797045209, rs797045207, rs797045213, rs797045623, rs863225280, rs149703259, rs864321656, rs139964066, rs777870079, rs878853246, rs769268803, rs886039380, rs886041392, rs886041391, rs886042610, rs143064649, rs1057516192, rs746480424, rs1057516281, rs576684889, rs754728827, rs1057520291, rs1057520779, rs893256143, rs1057520504, rs1057524790, rs1057524902, rs1057524904, rs1057524905, rs764232985, rs1064793998, rs1064794268, rs769086289, rs369429452, rs1085307913, rs1131691416, rs765432081, rs1131692182, rs748749585, rs1554335441, rs762263694, rs1312678560, rs767565869, rs1375656631, rs1554335391, rs1360415315, rs1554335616, rs1554335752, rs1554909277, rs769518471, rs757171524, rs768951263, rs762703502, rs1555212248, rs1555212359, rs1555813319, rs1555816654, rs1553638903, rs1553638909, rs948820149, rs371977235, rs1553784995, rs76474829, rs200998587, rs1415041911, rs1554334894, rs1260178539, rs1554335421, rs1555211904, rs779184183, rs1554335564, rs200670692, rs1400535021, rs1554334872, rs1555212749, rs1553876668, rs1553878211, rs954727530, rs1554924035, rs372307320, rs925231098, rs1554913069, rs1554933565, rs766431403, rs746714109, rs751279984, rs770664202, rs1008906426, rs758844607, rs1554924540, rs1566092307, rs753998395, rs1565885935, rs1167124132, rs1376796469, rs556436603, rs1562715657, rs1486280029, rs1564869850, rs755259997, rs769569410, rs1172328722, rs1286294151, rs1375557127, rs1568731279, rs1562715426, rs556581174, rs1564865302, rs1565886545, rs776793516, rs1568724014, rs1392795567, rs781260712, rs1562719705, rs1382448285, rs1564977373, rs750586210, rs1598842892, rs1583592247, rs780612692, rs1593060859, rs1476637197, rs751279776, rs1593060890, rs1191912908, rs1167675604, rs1583601110, rs1593058932, rs778611627, rs753296261	31451708
Fanconi-bickel syndrome	Fanconi-Bickel Syndrome	rs121909742, rs121909743, rs121909744, rs121909745, rs1715390589, rs780067980, rs771477447, rs28928874, rs1576838294, rs121909746, rs121909747, rs1114167428, rs371977235, rs1553785033, rs769888108, rs756874949, rs1553784980, rs1553785722, rs1553786361, rs1560035336, rs1560033414, rs1447936042, rs1318756243
Hypercalcemia	Hypercalcemia, Hypercalcemia, Idiopathic, of Infancy, Hypercalcemia, Infantile, 1, Hypercalcemia, infantile, 2, Autosomal recessive infantile hypercalcemia	rs876657376, rs387907322, rs777676129, rs387907323, rs114368325, rs6068812, rs387907324, rs777947329, rs201304511, rs769409705, rs200095793, rs876661338, rs1554095500, rs139763321, rs774432244, rs781367354	9560283, 26047794, 26047794, 20335586
Hypophosphatemia with nephrolithiasis or osteoporosis	Dominant hypophosphatemia with nephrolithiasis or osteoporosis	rs121918610, rs200893951, rs1554095568
Kidney disease	Chronic Kidney Diseases	rs74315342, rs749740335, rs757649673, rs112417755, rs35138315	22479191, 20383146
Leukemia	Leukemia, Myelocytic, Acute	rs121909646, rs121913488, rs587776834, rs752746786, rs869312821, rs767454740, rs1554564297, rs11978267, rs4132601	27903959
Osteoporosis	Osteoporosis	rs72658152, rs72667023, rs587776916, rs72656370, rs768615287
Renal insufficiency	Renal Insufficiency	rs1596536873

Unknown
Disease name	Disease term	dbSNP ID	References
Bone disease	Bone Diseases, Developmental		9560283
Dwarfism	Dwarfism
Kidney failure	Kidney Failure, Chronic		20383146, 26831199, 31152163
Medullary nephrocalcinosis	Medullary nephrocalcinosis
Milk-alkali syndrome	Milk-Alkali Syndrome		9560283
Nephrocalcinosis	Nephrocalcinosis		28893421
Nephrolithiasis	Nephrolithiasis		28893421
Nephrolithiasis-osteoporosis, hypophosphatemic	Nephrolithiasis-Osteoporosis, Hypophosphatemic, 1		20335586, 12324554, 25050900
Osteopenia	Osteopenia
Phosphate diabetes	Phosphate Diabetes
Rickets	Rickets