Gene Gene information from NCBI Gene database.
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
SNPs SNP information provided by dbSNP.
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
miRNA miRNA information provided by mirtarbase database.
30
miRTarBase ID miRNA Experiments Reference
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
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
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
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
600839 10910 ENSG00000074803
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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
ISGPKVNRPSLLEIHEQLAKNVAVTPSSADRVANGDG
IPGDEQAENKEDDQAGVVKFGWV
KGVLVRCMLNIWGVMLFIRLSWIVGEAGIGLGVLIILLSTMVTSITGLSTSAIATNGFVR
GGGAYYLISRSLGPEFGGSIGLIFAFANAVAVAMYVVGFAETVVDLLKESDSMMVDPTND
IRIIGSITVVILLGISVAGMEWEAKAQVILLVILLIAIANFFIGTVIPSNNEKKSRGFFN
YQASIFAENFGPRFTKGEGFFSVFAIFFPAATGILAGANISGDLEDPQDAIPRGTMLAIF
ITTVAYLGVAICVGACVVRDATGNMNDTIISGMNCNGSAACGLGYDFSRCRHEPCQYGLM
NNFQVMSMVSGFGPLITAGIFSATLSSALASLVSAPKVFQALCKDNIYKALQFFAKGYGK
NNEPLRGYILTFLIAMAFILIAELNTIAPIISNFFLASYALINFSCFHASYAKSPGWRPA
YGIYNMWVSLFGAVLCCAVMFVINWWAAVITYVIEFFLYVYVTCKKPDVNWGSSTQALSY
VSALDNALELTTVEDHVKNFRPQCIV
LTGGPMTRPALLDITHAFTKNSGLCICCEVFVGP
RKLCVKEMNSGMAKKQAWLIKNKIKAFYAAVAADCFRDGVRSLLQASGLGRMKPNTLVIG
YKKNWRKAPLTEIENYVGIIHDAFDFEIGVVIVRISQGFDISQVLQVQEELERLEQERLA
LEATIKDNECEEESGGIRGLFKKAGKLNITKTTPKKDGSINTSQSMHVGEFNQKLVEAST
QFKKKQEKGTIDVWWLFDDGGLTLLIPYILTLRKKWKDCKLRIYVGGKINRIEEEKIVMA
SLLSKFRIKFADIHIIGDINIRPNKESWKVFEEMIEPYRLHESCKDLTTAEKLKRETPWK
ITDAELEAVKEKSYRQVRLNELLQEHSRAANLIVLSLPVARKGSISDLLYMAWLEILTKN
LPPVLLVRGNHKNVLTFYS
Sequence length 1099
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    Cation-coupled Chloride cotransporters
Defective SLC12A1 causes Bartter syndrome 1 (BS1)
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
24
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
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
View all (40 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Bartter syndrome Likely pathogenic; Pathogenic rs2041199779, rs1366101480, rs2042079691, rs770400317, rs199877869, rs2505190299, rs2505087791 RCV002469972
RCV004765639
RCV002510404
RCV003994449
RCV004765754
View all (2 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nephrocalcinosis Pathogenic; Likely pathogenic rs779588655, rs896545456, rs1555466999 RCV000662326
RCV000662324
RCV000662325
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Nephrolithiasis Pathogenic; Likely pathogenic rs779588655, rs896545456, rs1555466999 RCV000662326
RCV000662324
RCV000662325
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
ANTENATAL BARTTER SYNDROME GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BARTTER DISEASE Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Bartter disease type 3 Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BARTTER SYNDROME, ANTENATAL TYPE 1 CTD, Disgenet
CTD, Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Adenocarcinoma Adenocarcinoma BEFREE 26559081
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 26559081
★☆☆☆☆
Found in Text Mining only
Adenoma Adenoma BEFREE 25165391, 28544176
★☆☆☆☆
Found in Text Mining only
Antenatal Bartter syndrome Antenatal Bartter Syndrome Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Bartter Disease Bartter syndrome CTD_human_DG 10561751
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Bartter Disease Bartter syndrome BEFREE 11826289, 12589089, 12761241, 15980941, 16807401, 17998760, 18830715, 21071987, 21631963, 21865213, 22211456, 25631355, 26721884, 27748541, 28000888
View all (8 more)
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Bartter Disease Bartter syndrome LHGDN 12761241, 16807401, 17998760
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Bartter Syndrome Bartter syndrome Pubtator 12472765, 12589089, 12911530, 15287206, 17998760, 21631963, 26963954, 28000888, 33607471, 35348259, 36305432, 37537162 Associate
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Bartter syndrome antenatal type 1 Bartter syndrome Pubtator 26963954 Associate
★☆☆☆☆
Found in Text Mining only
Bartter syndrome type 3 Bartter syndrome Pubtator 19056867, 34461850, 36361553 Associate
★☆☆☆☆
Found in Text Mining only