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	6557
Gene name	Solute carrier family 12 member 1
Gene symbol	SLC12A1
Synonyms (NCBI Gene)	BSCBSC-1BSC1CCC2NKCC2
Chromosome	15
Chromosome location	15q21.1
Summary	This gene encodes a kidney-specific sodium-potassium-chloride cotransporter that is expressed on the luminal membrane of renal epithelial cells of the thick ascending limb of Henle`s loop and the macula densa. It plays a key role in concentrating urine an

Show/Hide all (5)

SNP ID	Visualize variation	Clinical significance	Consequence
rs34819316	G>A,C	Likely-benign, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs142646329	A>G	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs779588655	T>-	Pathogenic, likely-pathogenic	Frameshift variant, coding sequence variant
rs1057519608	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs1057520300	C>-	Pathogenic	Coding sequence variant, frameshift variant

Show/Hide all (30)

miRTarBase ID	miRNA	Experiments
MIRT1351875	hsa-miR-2052	CLIP-seq
MIRT1351876	hsa-miR-23a	CLIP-seq
MIRT1351877	hsa-miR-23b	CLIP-seq
MIRT1351878	hsa-miR-23c	CLIP-seq
MIRT1351879	hsa-miR-323-5p	CLIP-seq
MIRT1351880	hsa-miR-3646	CLIP-seq
MIRT1351881	hsa-miR-3662	CLIP-seq
MIRT1351882	hsa-miR-433	CLIP-seq
MIRT1351883	hsa-miR-4424	CLIP-seq
MIRT1351884	hsa-miR-4742-3p	CLIP-seq
MIRT1351885	hsa-miR-548c-3p	CLIP-seq
MIRT1351886	hsa-miR-561	CLIP-seq
MIRT1351887	hsa-miR-876-3p	CLIP-seq
MIRT2104285	hsa-miR-1305	CLIP-seq
MIRT1351876	hsa-miR-23a	CLIP-seq
MIRT1351877	hsa-miR-23b	CLIP-seq
MIRT1351878	hsa-miR-23c	CLIP-seq
MIRT2104286	hsa-miR-944	CLIP-seq
MIRT2104285	hsa-miR-1305	CLIP-seq
MIRT1351876	hsa-miR-23a	CLIP-seq
MIRT1351877	hsa-miR-23b	CLIP-seq
MIRT1351878	hsa-miR-23c	CLIP-seq
MIRT2104286	hsa-miR-944	CLIP-seq
MIRT2394603	hsa-miR-1231	CLIP-seq
MIRT2394604	hsa-miR-4288	CLIP-seq
MIRT2394605	hsa-miR-4434	CLIP-seq
MIRT2394606	hsa-miR-4516	CLIP-seq
MIRT2394607	hsa-miR-4531	CLIP-seq
MIRT2394608	hsa-miR-516b	CLIP-seq
MIRT2394609	hsa-miR-632	CLIP-seq

Show/Hide all (31)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS	7929272
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006811	Process	Monoatomic ion transport	TAS
GO:0006813	Process	Potassium ion transport	IEA
GO:0006814	Process	Sodium ion transport	IEA
GO:0006884	Process	Cell volume homeostasis	IBA
GO:0006884	Process	Cell volume homeostasis	IDA	21321328
GO:0008511	Function	Sodium:potassium:chloride symporter activity	IBA
GO:0008511	Function	Sodium:potassium:chloride symporter activity	IDA	21321328
GO:0008511	Function	Sodium:potassium:chloride symporter activity	IEA
GO:0008511	Function	Sodium:potassium:chloride symporter activity	TAS	8640224
GO:0015293	Function	Symporter activity	IEA
GO:0015377	Function	Chloride:monoatomic cation symporter activity	IEA
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	TAS	7929272
GO:0016324	Component	Apical plasma membrane	IBA
GO:0016324	Component	Apical plasma membrane	IDA	21321328
GO:0016324	Component	Apical plasma membrane	IEA
GO:0016324	Component	Apical plasma membrane	ISS
GO:0022857	Function	Transmembrane transporter activity	IEA
GO:0034220	Process	Monoatomic ion transmembrane transport	ISS
GO:0035725	Process	Sodium ion transmembrane transport	IBA
GO:0055064	Process	Chloride ion homeostasis	IBA
GO:0055075	Process	Potassium ion homeostasis	IBA
GO:0055078	Process	Sodium ion homeostasis	IBA
GO:0055085	Process	Transmembrane transport	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867, 23533145
GO:0070062	Component	Extracellular exosome	IDA	15326289, 21082674
GO:1902476	Process	Chloride transmembrane transport	IBA
GO:1990573	Process	Potassium ion import across plasma membrane	IBA

MIM	HGNC	e!Ensembl
600839	10910	ENSG00000074803

Q13621

Protein name

Solute carrier family 12 member 1 (Bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1) (BSC1) (Kidney-specific Na-K-Cl symporter) (Na-K-2Cl cotransporter 2) (NKCC2)

Protein function

Renal sodium, potassium and chloride ion cotransporter that mediates the transepithelial NaCl reabsorption in the thick ascending limb and plays an essential role in the urinary concentration and volume regulation (PubMed:21321328). Electrically

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF08403	AA_permease_N	90 → 157	Amino acid permease N-terminal	Family
PF00324	AA_permease	182 → 686	Amino acid permease	Family
PF03522	SLC12	694 → 1099	Solute carrier family 12	Family

Tissue specificity

TISSUE SPECIFICITY: Kidney; localizes to the thick ascending limbs (at protein level). {ECO:0000269|PubMed:29993276}.

Sequence

MSLNNSSNVFLDSVPSNTNRFQVSVINENHESSAAADDNTDPPHYEETSFGDEAQKRLRI
SFRPGNQECYDNFLQSGETAKTDASFHAYDSHTNTYYLQTFGHNTMDAVPKIEYYRNTGS
ISGPKVNRPSLLEIHEQLAKNVAVTPSSADRVANGDGIPGDEQAENKEDDQAGVVKFGWV
KGVLVRCMLNIWGVMLFIRLSWIVGEAGIGLGVLIILLSTMVTSITGLSTSAIATNGFVR
GGGAYYLISRSLGPEFGGSIGLIFAFANAVAVAMYVVGFAETVVDLLKESDSMMVDPTND
IRIIGSITVVILLGISVAGMEWEAKAQVILLVILLIAIANFFIGTVIPSNNEKKSRGFFN
YQASIFAENFGPRFTKGEGFFSVFAIFFPAATGILAGANISGDLEDPQDAIPRGTMLAIF
ITTVAYLGVAICVGACVVRDATGNMNDTIISGMNCNGSAACGLGYDFSRCRHEPCQYGLM
NNFQVMSMVSGFGPLITAGIFSATLSSALASLVSAPKVFQALCKDNIYKALQFFAKGYGK
NNEPLRGYILTFLIAMAFILIAELNTIAPIISNFFLASYALINFSCFHASYAKSPGWRPA
YGIYNMWVSLFGAVLCCAVMFVINWWAAVITYVIEFFLYVYVTCKKPDVNWGSSTQALSY
VSALDNALELTTVEDHVKNFRPQCIVLTGGPMTRPALLDITHAFTKNSGLCICCEVFVGP
RKLCVKEMNSGMAKKQAWLIKNKIKAFYAAVAADCFRDGVRSLLQASGLGRMKPNTLVIG
YKKNWRKAPLTEIENYVGIIHDAFDFEIGVVIVRISQGFDISQVLQVQEELERLEQERLA
LEATIKDNECEEESGGIRGLFKKAGKLNITKTTPKKDGSINTSQSMHVGEFNQKLVEAST
QFKKKQEKGTIDVWWLFDDGGLTLLIPYILTLRKKWKDCKLRIYVGGKINRIEEEKIVMA
SLLSKFRIKFADIHIIGDINIRPNKESWKVFEEMIEPYRLHESCKDLTTAEKLKRETPWK
ITDAELEAVKEKSYRQVRLNELLQEHSRAANLIVLSLPVARKGSISDLLYMAWLEILTKN
LPPVLLVRGNHKNVLTFYS

Sequence length

1099

Interactions

View interactions

	Reactome
			Cation-coupled Chloride cotransporters Defective SLC12A1 causes Bartter syndrome 1 (BS1)

322

Show/Hide Causal Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Bartter disease type 1	Likely pathogenic; Pathogenic	rs2041650191, rs756057922, rs1597456179, rs1318795841, rs776749406, rs1370120380, rs773855120, rs1400209959, rs2141064916, rs1048935147, rs780619649, rs758166864, rs1366101480, rs758291275, rs770400317 View all (30 more)	RCV001329192 RCV001535850 RCV005005233 RCV005395065 RCV001730161 RCV001775425 RCV001775431 RCV001784972 RCV001808289 RCV001837610 RCV001843848 RCV003225202 RCV005002930 RCV005002967 RCV003340526 RCV000779167 RCV000009296 RCV000009297 RCV000009298 RCV000009299 RCV005003019 RCV003225609 RCV000256371 RCV000256407 RCV005356468 RCV005003664 RCV005003672 RCV005013040 RCV005013079 RCV005003701 RCV005003729 RCV005871350 RCV003986049 RCV005006450 RCV000427573 RCV000420163 RCV000430820 RCV000438920 RCV000418206 RCV005624419 RCV005004319 RCV000761354 RCV004559830 RCV005012490 RCV002482169
Bartter syndrome	Likely pathogenic; Pathogenic	rs2041199779, rs1366101480, rs2042079691, rs770400317, rs199877869, rs2505190299, rs2505087791	RCV002469972 RCV004765639 RCV002510404 RCV003994449 RCV004765754 RCV003226665 RCV004586296
Nephrocalcinosis	Pathogenic; Likely pathogenic	rs779588655, rs896545456, rs1555466999	RCV000662326 RCV000662324 RCV000662325
Nephrolithiasis	Pathogenic; Likely pathogenic	rs779588655, rs896545456, rs1555466999	RCV000662326 RCV000662324 RCV000662325
See cases	Likely pathogenic	rs2505026310, rs2505192006	RCV004584282 RCV004584283
SLC12A1-related disorder	Pathogenic; Likely pathogenic	rs137853159, rs1380626543, rs2505225672, rs776346805	RCV003934814 RCV003400437 RCV003408738 RCV003393127

Show/Hide Unknown Diseases (9)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
-	no classification for the single variant	rs863224920, rs1369681529	-
Bartter disease type 3	Uncertain significance	rs2042078431	RCV003338029
Cervical cancer	Likely benign	rs143862365	RCV005917900
Clear cell carcinoma of kidney	Conflicting classifications of pathogenicity	rs142360465	RCV005893391
Familial hypokalemia-hypomagnesemia	Uncertain significance	rs137853157, rs1442023118, rs2041701051	RCV001328098 RCV001328097 RCV001328100
Gastric cancer	Benign; Likely benign	rs34047900	RCV005893393
Sarcoma	Likely benign	rs143862365	RCV005917901
Thymoma	Likely benign; Benign	rs143862365, rs78648980	RCV005917902 RCV005893392
Uterine corpus endometrial carcinoma	Likely benign	rs143862365	RCV005917903

Show/Hide Text Mining Associations (28)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Acute Kidney Injury	Associate	36285332
Adenoma	Associate	28544176, 37074453
Bartter Syndrome	Associate	12472765, 12589089, 12911530, 15287206, 17998760, 21631963, 26963954, 28000888, 33607471, 35348259, 36305432, 37537162
Bartter syndrome antenatal type 1	Associate	26963954
Bartter syndrome type 3	Associate	19056867, 34461850, 36361553
Bloom Syndrome	Associate	32506365
Breast Neoplasms	Associate	38003293
Carcinoma Renal Cell	Associate	26831905, 27766950, 39348357
Colorectal Neoplasms	Associate	25165391
Disease	Associate	18391953
Dwarfism Pituitary	Associate	25157616
Esophageal Squamous Cell Carcinoma	Associate	24944475
Gitelman Syndrome	Associate	32506365
Glioma	Associate	24555568
Hyperparathyroidism Neonatal Severe Primary	Associate	26963954
Hypertension	Associate	18391953, 30113482, 30248150
Hypotension	Associate	30113482
Kidney Diseases	Associate	33095447, 36361553
Multiple System Atrophy	Associate	27900370
Neoplasms	Associate	20420713, 25165391
Nephrocalcinosis	Associate	17998760, 28893421
Nephrolithiasis	Associate	28893421
Pre Eclampsia	Associate	30248150
Retinitis Pigmentosa	Associate	27297950
Sleep Initiation and Maintenance Disorders	Associate	33530007
Stomach Neoplasms	Associate	17052386
Urinary Retention	Associate	23387299
Wilms Tumor	Associate	37904849

SLC12A1 (solute carrier family 12 member 1)