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    SLC4A11 solute carrier family 4 member 11 [ Homo sapiens (human) ]

    Gene ID: 83959, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SLC4A11provided by HGNC
    Official Full Name
    solute carrier family 4 member 11provided by HGNC
    Primary source
    HGNC:HGNC:16438
    See related
    Ensembl:ENSG00000088836 MIM:610206; AllianceGenome:HGNC:16438
    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
    BTR1; CHED; CDPD1; CHED2; NABC1; dJ794I6.2
    Summary
    This gene encodes a voltage-regulated, electrogenic sodium-coupled borate cotransporter that is essential for borate homeostasis, cell growth and cell proliferation. Mutations in this gene have been associated with a number of endothelial corneal dystrophies including recessive corneal endothelial dystrophy 2, corneal dystrophy and perceptive deafness, and Fuchs endothelial corneal dystrophy. Multiple transcript variants encoding different isoforms have been described. [provided by RefSeq, Mar 2010]
    Expression
    Biased expression in thyroid (RPKM 6.2), kidney (RPKM 5.1) and 12 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC4A11 in Genome Data Viewer
    Location:
    20p13
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (3227417..3239559, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (3258367..3270505, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (3208063..3220205, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985414 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12614 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:3163335-3163502 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3183418-3184016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17476 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:3189739-3190387 Neighboring gene DDRGK domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12615 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3210499-3211281 Neighboring gene inosine triphosphatase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12616 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12617 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3228779-3229524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3229525-3230269 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3230929-3231429 Neighboring gene dynein axonemal assembly factor 9 Neighboring gene ubiquitin conjugating enzyme E2 F (putative) pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3276431-3276932 Neighboring gene RNA, U6 small nuclear 1019, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Mutation analysis of the SLC4A11 gene in Indian families with congenital hereditary endothelial dystrophy 2 and a review of the literature. Kodaganur SG, et al. Mol Vis, 2013. PMID 23922488, Free PMC Article
    2. Homozygous SLC4A11 mutation in a large Irish CHED2 pedigree. Hand CK, et al. Ophthalmic Genet, 2017 Mar-Apr. PMID 27057589
    3. Borate transporter SLC4A11 mutations cause both Harboyan syndrome and non-syndromic corneal endothelial dystrophy. Desir J, et al. J Med Genet, 2007 May. PMID 17220209, Free PMC Article
    4. Genetic analysis of two Indian families affected with congenital hereditary endothelial dystrophy: two novel mutations in SLC4A11. Kumar A, et al. Mol Vis, 2007 Jan 16. PMID 17262014, Free PMC Article
    5. SLC4A11 and the Pathophysiology of Congenital Hereditary Endothelial Dystrophy. Patel SP, et al. Biomed Res Int, 2015. PMID 26451371, Free PMC Article

    See all (80) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Investigation of the functional impact of CHED- and FECD4-associated SLC4A11 mutations in human corneal endothelial cells.
      Title: Investigation of the functional impact of CHED- and FECD4-associated SLC4A11 mutations in human corneal endothelial cells.
    2. Structural insights into the conformational changes of BTR1/SLC4A11 in complex with PIP2.
      Title: Structural insights into the conformational changes of BTR1/SLC4A11 in complex with PIP(2).
    3. Pathogenicity and Function Analysis of Two Novel SLC4A11 Variants in Patients With Congenital Hereditary Endothelial Dystrophy.
      Title: Pathogenicity and Function Analysis of Two Novel SLC4A11 Variants in Patients With Congenital Hereditary Endothelial Dystrophy.
    4. Compound heterozygous mutations in the SLC4A11 gene associated with congenital hereditary endothelial dystrophy in a Chinese family.
      Title: Compound heterozygous mutations in the SLC4A11 gene associated with congenital hereditary endothelial dystrophy in a Chinese family.
    5. Identification and in silico analysis of a spectrum of SLC4A11 variations in Indian familial and sporadic cases of congenital hereditary endothelial dystrophy.
      Title: Identification and in silico analysis of a spectrum of SLC4A11 variations in Indian familial and sporadic cases of congenital hereditary endothelial dystrophy.
    6. Corneal dystrophy mutations R125H and R804H disable SLC4A11 by altering the extracellular pH dependence of the intracellular pK that governs H(+)(OH(-)) transport.
      Title: Corneal dystrophy mutations R125H and R804H disable SLC4A11 by altering the extracellular pH dependence of the intracellular pK that governs H(+)(OH(-)) transport.
    7. Mutational analysis in sodium-borate cotransporter SLC4A11 in consanguineous families from Punjab, Pakistan.
      Title: Mutational analysis in sodium-borate cotransporter SLC4A11 in consanguineous families from Punjab, Pakistan.
    8. Autosomal recessive congenital hereditary corneal dystrophy associated with a novel SLC4A11 mutation in two consanguineous Tunisian families.
      Title: Autosomal recessive congenital hereditary corneal dystrophy associated with a novel SLC4A11 mutation in two consanguineous Tunisian families.
    9. SLC4A11 mutations causative of congenital hereditary endothelial dystrophy (CHED) progressing to Harboyan syndrome in consanguineous Pakistani families.
      Title: SLC4A11 mutations causative of congenital hereditary endothelial dystrophy (CHED) progressing to Harboyan syndrome in consanguineous Pakistani families.
    10. Harboyan syndrome: novel SLC4A11 mutation, clinical manifestations, and outcome of corneal transplantation.
      Title: Harboyan syndrome: novel SLC4A11 mutation, clinical manifestations, and outcome of corneal transplantation.
    Submit: New GeneRIF Correction See all GeneRIFs (65)

    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
    Congenital hereditary endothelial dystrophy of cornea
    MedGen: C1857569 OMIM: 217700 GeneReviews: Not available
    		Compare labs
    Corneal dystrophy, Fuchs endothelial, 4
    MedGen: C2750450 OMIM: 613268 GeneReviews: Not available
    		Compare labs
    Corneal dystrophy-perceptive deafness syndrome
    MedGen: C1857572 OMIM: 217400 GeneReviews: Not available
    		Compare labs

    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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    Markers

    Homology

    Clone Names

    • MGC126418, MGC126419

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables active borate transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables bicarbonate transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein dimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables proton channel activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables proton transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables sodium channel activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables solute:inorganic anion antiporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables symporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables water transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in bicarbonate transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in borate transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in borate transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cellular hypotonic response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cellular response to oxidative stress IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in fluid transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in intracellular monoatomic cation homeostasis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in monoatomic anion transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in monoatomic ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in proton transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of mesenchymal stem cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of mitochondrial membrane potential IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in sodium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in sodium ion transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in water transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in apical plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in basolateral plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in basolateral plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in basolateral plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in basolateral plasma membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in vesicle membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    solute carrier family 4 member 11
    Names
    bicarbonate transporter related protein 1
    sodium-coupled borate cotransporter 1
    solute carrier family 4, sodium bicarbonate transporter-like, member 11
    solute carrier family 4, sodium borate transporter, member 11

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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

    1. NG_017072.1 RefSeqGene

      Range
      5052..16820
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001174089.2 → NP_001167560.1  solute carrier family 4 member 11 isoform 3

      See identical proteins and their annotated locations for NP_001167560.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and 5' coding region compared to variant 1. The resulting protein (isoform 3) has a distinct N-terminus and is shorter compared to isoform 1.
      Source sequence(s)
      AF336127, AK296760, CA312226, DC341640
      Consensus CDS
      CCDS54446.1
      UniProtKB/Swiss-Prot
      B4DKC8, B4DKX9, G3V1M3, Q2TB62, Q2TB63, Q8NBS3, Q9BXF4, Q9NTW9
      UniProtKB/TrEMBL
      A0A2R8Y7S1
      Related
      ENSP00000493503.1, ENST00000642402.1
      Conserved Domains (1) summary
      pfam00955
      Location:325 → 818
      HCO3_cotransp; HCO3- transporter family

    2. NM_001174090.2 → NP_001167561.1  solute carrier family 4 member 11 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AF336127, AK296508, CA312226
      Consensus CDS
      CCDS54445.1
      UniProtKB/TrEMBL
      A0A2R8Y7S1
      Related
      ENSP00000369399.3, ENST00000380059.7
      Conserved Domains (2) summary
      pfam00955
      Location:369 → 860
      HCO3_cotransp; HCO3- transporter family
      cl00163
      Location:246 → 325
      PTS_IIA_fru; PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This ...

    3. NM_001363745.2 → NP_001350674.1  solute carrier family 4 member 11 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL109976
      Consensus CDS
      CCDS86932.1
      UniProtKB/TrEMBL
      A0A2R8Y7S1, A0A2R8YFD9
      Related
      ENSP00000495050.1, ENST00000647296.1
      Conserved Domains (2) summary
      pfam00955
      Location:326 → 779
      HCO3_cotransp; HCO3- transporter family
      cl00163
      Location:203 → 282
      PTS_IIA_fru; PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This ...

    4. NM_001400277.1 → NP_001387206.1  solute carrier family 4 member 11 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AL109976
      UniProtKB/TrEMBL
      A0A2R8Y7S1

    5. NM_001400278.1 → NP_001387207.1  solute carrier family 4 member 11 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AL109976
      UniProtKB/TrEMBL
      A0A2R8Y7S1
      Related
      ENSP00000493824.1, ENST00000644692.1

    6. NM_001400279.1 → NP_001387208.1  solute carrier family 4 member 11 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AL109976
      UniProtKB/TrEMBL
      A0A2R8Y7S1

    7. NM_001400280.1 → NP_001387209.1  solute carrier family 4 member 11 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AL109976
      UniProtKB/TrEMBL
      A0A2R8Y7S1

    8. NM_032034.4 → NP_114423.1  solute carrier family 4 member 11 isoform 2

      See identical proteins and their annotated locations for NP_114423.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region compared to variant 1. The resulting protein (isoform 2) has a distinct N-terminus and is shorter compared to isoform 1.
      Source sequence(s)
      AF336127, CA312226
      Consensus CDS
      CCDS13052.1
      UniProtKB/TrEMBL
      A0A2R8Y7S1
      Related
      ENSP00000369396.3, ENST00000380056.7
      Conserved Domains (2) summary
      pfam00955
      Location:342 → 833
      HCO3_cotransp; HCO3- transporter family
      cl00163
      Location:219 → 298
      PTS_IIA_fru; PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This ...

    RNA

    1. NR_135000.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) includes an alternate 5' terminal exon and uses an alternate internal splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AF336127, AK091157, AK296508, DA630556, HY211104
      Related
      ENST00000474451.5

    2. NR_174470.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL109976

    3. NR_174471.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL109976

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      3227417..3239559 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047440543.1 → XP_047296499.1  solute carrier family 4 member 11 isoform X6

      UniProtKB/TrEMBL
      A0A2R8Y7S1

    2. XM_047440542.1 → XP_047296498.1  solute carrier family 4 member 11 isoform X5

    3. XM_017028096.2 → XP_016883585.1  solute carrier family 4 member 11 isoform X4

      UniProtKB/TrEMBL
      A0A2R8Y7S1
      Conserved Domains (2) summary
      pfam00955
      Location:307 → 798
      HCO3_cotransp; HCO3- transporter family
      cl00163
      Location:184 → 263
      PTS_IIA_fru; PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This ...

    4. XM_047440540.1 → XP_047296496.1  solute carrier family 4 member 11 isoform X2

      UniProtKB/TrEMBL
      A0A2R8Y7S1

    5. XM_017028094.2 → XP_016883583.1  solute carrier family 4 member 11 isoform X4

      UniProtKB/TrEMBL
      A0A2R8Y7S1
      Conserved Domains (2) summary
      pfam00955
      Location:307 → 798
      HCO3_cotransp; HCO3- transporter family
      cl00163
      Location:184 → 263
      PTS_IIA_fru; PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This ...

    6. XM_017028093.2 → XP_016883582.2  solute carrier family 4 member 11 isoform X1

    7. XM_047440541.1 → XP_047296497.1  solute carrier family 4 member 11 isoform X3

    8. XM_047440544.1 → XP_047296500.1  solute carrier family 4 member 11 isoform X7

      UniProtKB/TrEMBL
      V9GYK6

    9. XM_017028097.2 → XP_016883586.2  solute carrier family 4 member 11 isoform X8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      3258367..3270505 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324115.1 → XP_054180090.1  solute carrier family 4 member 11 isoform X6

      UniProtKB/TrEMBL
      A0A2R8Y7S1

    2. XM_054324114.1 → XP_054180089.1  solute carrier family 4 member 11 isoform X5

    3. XM_054324112.1 → XP_054180087.1  solute carrier family 4 member 11 isoform X4

      UniProtKB/TrEMBL
      A0A2R8Y7S1

    4. XM_054324110.1 → XP_054180085.1  solute carrier family 4 member 11 isoform X2

      UniProtKB/TrEMBL
      A0A2R8Y7S1

    5. XM_054324113.1 → XP_054180088.1  solute carrier family 4 member 11 isoform X4

      UniProtKB/TrEMBL
      A0A2R8Y7S1

    6. XM_054324109.1 → XP_054180084.1  solute carrier family 4 member 11 isoform X1

    7. XM_054324111.1 → XP_054180086.1  solute carrier family 4 member 11 isoform X3

    8. XM_054324116.1 → XP_054180091.1  solute carrier family 4 member 11 isoform X7

      UniProtKB/TrEMBL
      V9GYK6

    9. XM_054324117.1 → XP_054180092.1  solute carrier family 4 member 11 isoform X8

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NBS3.3 GenPept UniProtKB/Swiss-Prot:Q8NBS3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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