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

Summary

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

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_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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).
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.
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.
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.
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.
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.
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.
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.
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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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	not available
Corneal dystrophy, Fuchs endothelial, 4 MedGen: C2750450 OMIM: 613268 GeneReviews: Not available	not available
Corneal dystrophy-perceptive deafness syndrome MedGen: C1857572 OMIM: 217400 GeneReviews: Not available	not available

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

D20S179 (e-PCR), detects polymorphism
- UniSTS:24596

D20S113 (e-PCR), detects polymorphism
- UniSTS:60446

D20S889 (e-PCR)
- UniSTS:55855

D20S882 (e-PCR), detects polymorphism
- UniSTS:20066

D20S482 (e-PCR), detects polymorphism
- UniSTS:13445

ksks428 (e-PCR)
- UniSTS:514484

SLC4A11_8111 (e-PCR)
- UniSTS:467901

Slc4a11 (e-PCR), detects polymorphism
- UniSTS:546014

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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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

NG_017072.1 RefSeqGene

Range

5052..16820

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Status: REVIEWED

Source sequence(s)

AL109976
NM_001400278.1 → NP_001387207.1 solute carrier family 4 member 11 isoform 5

Status: REVIEWED

Source sequence(s)

AL109976

Related

ENSP00000493824.1, ENST00000644692.1
NM_001400279.1 → NP_001387208.1 solute carrier family 4 member 11 isoform 5

Status: REVIEWED

Source sequence(s)

AL109976
NM_001400280.1 → NP_001387209.1 solute carrier family 4 member 11 isoform 6

Status: REVIEWED

Source sequence(s)

AL109976
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

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
NR_174470.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL109976
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

NC_000020.11 Reference GRCh38.p14 Primary Assembly

Range

3227417..3239559 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047440543.1 → XP_047296499.1 solute carrier family 4 member 11 isoform X6
XM_047440542.1 → XP_047296498.1 solute carrier family 4 member 11 isoform X5
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 ...
XM_047440540.1 → XP_047296496.1 solute carrier family 4 member 11 isoform X2
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 ...
XM_017028093.2 → XP_016883582.2 solute carrier family 4 member 11 isoform X1
XM_047440541.1 → XP_047296497.1 solute carrier family 4 member 11 isoform X3
XM_047440544.1 → XP_047296500.1 solute carrier family 4 member 11 isoform X7
XM_017028097.2 → XP_016883586.2 solute carrier family 4 member 11 isoform X8