SLC4A10 solute carrier family 4 member 10 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC4A10provided by HGNC
Official Full Name: solute carrier family 4 member 10provided by HGNC
Primary source: HGNC:HGNC:13811
See related: Ensembl:ENSG00000144290 MIM:605556; AllianceGenome:HGNC:13811
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: NCBE; NBCn2
Summary: This gene belongs to a small family of sodium-coupled bicarbonate transporters (NCBTs) that regulate the intracellular pH of neurons, the secretion of bicarbonate ions across the choroid plexus, and the pH of the brain extracellular fluid. The protein encoded by this gene was initially identified as a sodium-driven chloride bicarbonate exchanger (NCBE) though there is now evidence that its sodium/bicarbonate cotransport activity is independent of any chloride ion countertransport under physiological conditions. This gene is now classified as a member A10 of the SLC4 family of transmembrane solute carriers. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, May 2010]
Expression: Biased expression in brain (RPKM 21.0) and adrenal (RPKM 1.0) See more
Orthologs: mouse all
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Genomic context

Location:: 2q24.2

Exon count:: 32

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (161624416..161985270)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (162077534..162441869)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (162480926..162841780)

Chromosome 2 - NC_000002.12 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?

Biallelic variants in SLC4A10 encoding a sodium-dependent bicarbonate transporter lead to a neurodevelopmental disorder.
Title: Biallelic variants in SLC4A10 encoding a sodium-dependent bicarbonate transporter lead to a neurodevelopmental disorder.
SLC4A10 mutation causes a neurological disorder associated with impaired GABAergic transmission.
Title: SLC4A10 mutation causes a neurological disorder associated with impaired GABAergic transmission.
genetic variation in SLC4A10 expression and function in the central nervous system may affect the regulation of systemic water balance
Title: NFAT5 and SLC4A10 Loci Associate with Plasma Osmolality.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Observational study of gene-disease association. (HuGE Navigator)
Title: Large-scale candidate gene analysis of spontaneous clearance of hepatitis C virus.
There was no association between common sequence variants in the AQP1 or SLC4A10 genes and primary open-angle glaucoma in the Caucasian population.
Title: AQP1 and SLC4A10 as candidate genes for primary open-angle glaucoma.
propose to rename NCBE as the second electroneutral Na/HCO(3) cotransporter, NBCn2
Title: Characterization of human SLC4A10 as an electroneutral Na/HCO3 cotransporter (NBCn2) with Cl- self-exchange activity.
SLC4A10 (OMIM 605556), a sodium bicarbonate transporter gene with high expression in the cerebral cortex and hippocampus, was disrupted by the translocation breakpoint on chromosome 2q24.
Title: Disruption of sodium bicarbonate transporter SLC4A10 in a patient with complex partial epilepsy and mental retardation.

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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
Neurodevelopmental disorder with hypotonia and characteristic brain abnormalities MedGen: CN377037 OMIM: 620746 GeneReviews: Not available	not available

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2012-04-11) ClinGen Genome Curation Page Haploinsufficency Little evidence for dosage pathogenicity (Last evaluated 2012-04-11) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

G63448 (e-PCR)
- UniSTS:140560

SHGC-77777 (e-PCR)
- UniSTS:101003

SHGC-78023 (e-PCR)
- UniSTS:101556

RH104176 (e-PCR)
- UniSTS:98501

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables sodium,bicarbonate:chloride antiporter activity	IEA Inferred from Electronic Annotation more info
enables sodium:bicarbonate symporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables sodium:bicarbonate symporter activity	IDA Inferred from Direct Assay more info	PubMed
enables sodium:bicarbonate symporter activity	ISS Inferred from Sequence or Structural Similarity more info
enables solute:inorganic anion antiporter activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
involved_in bicarbonate transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in bicarbonate transport	NAS Non-traceable Author Statement more info	PubMed
involved_in bicarbonate transport	TAS Traceable Author Statement more info
involved_in brain morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in chloride transport	NAS Non-traceable Author Statement more info	PubMed
involved_in locomotory exploration behavior	IEA Inferred from Electronic Annotation more info
involved_in monoatomic anion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in multicellular organism growth	IEA Inferred from Electronic Annotation more info
involved_in post-embryonic development	IEA Inferred from Electronic Annotation more info
involved_in proton transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in pyramidal neuron development	IEA Inferred from Electronic Annotation more info
involved_in regulation of intracellular pH	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of short-term neuronal synaptic plasticity	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to light stimulus	IEA Inferred from Electronic Annotation more info
involved_in sodium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in visual perception	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in CA3 pyramidal cell dendrite	IEA Inferred from Electronic Annotation more info
located_in GABA-ergic synapse	ISS Inferred from Sequence or Structural Similarity more info
located_in apical dendrite	IEA Inferred from Electronic Annotation more info
located_in apical plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in axon terminus	ISS Inferred from Sequence or Structural Similarity more info
located_in basal dendrite	IEA Inferred from Electronic Annotation more info
is_active_in basolateral plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in basolateral plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in dendrite	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	NAS Non-traceable Author Statement more info	PubMed
located_in neuronal cell body	ISS Inferred from Sequence or Structural Similarity more info
located_in perikaryon	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in postsynapse	IEA Inferred from Electronic Annotation more info
located_in somatodendritic compartment	ISS Inferred from Sequence or Structural Similarity more info
located_in synapse	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: sodium-driven chloride bicarbonate exchanger

Names: solute carrier family 4, sodium bicarbonate cotransporter-like, member 10; solute carrier family 4, sodium bicarbonate transporter, member 10

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_021401.1 RefSeqGene

Range

5082..365936

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001178015.2 → NP_001171486.1 sodium-driven chloride bicarbonate exchanger isoform 1

See identical proteins and their annotated locations for NP_001171486.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform 1.

Source sequence(s)

AL832525, BC051190, BC143714, DC337667

Consensus CDS

CCDS54411.1

UniProtKB/Swiss-Prot

B7Z1R0, B7Z2J0, B7ZLC5, B9EG69, F8W675, Q4ZFX6, Q6U841, Q8TCP2, Q9HCQ6

UniProtKB/TrEMBL

E7EW28

Related

ENSP00000393066.1, ENST00000446997.6

Conserved Domains (3) summary

TIGR00834
Location:118 → 1061

ae; anion exchange protein

pfam00955
Location:476 → 989

HCO3_cotransp; HCO3- transporter family

pfam07565
Location:146 → 435

Band_3_cyto; Band 3 cytoplasmic domain
NM_001178016.2 → NP_001171487.1 sodium-driven chloride bicarbonate exchanger isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) has multiple differences in the 5' coding region, compared to variant 1, which result in a shorter protein (3) with a novel N-terminus, compared to isoform 1.

Source sequence(s)

AK293793, AL832525, BC051190, BC143714, DC337667

Consensus CDS

CCDS54412.1

UniProtKB/TrEMBL

E7EW28

Related

ENSP00000364664.5, ENST00000375514.9

Conserved Domains (3) summary

TIGR00834
Location:129 → 1042

ae; anion exchange protein

pfam00955
Location:457 → 970

HCO3_cotransp; HCO3- transporter family

pfam07565
Location:157 → 416

Band_3_cyto; Band 3 cytoplasmic domain
NM_001354440.2 → NP_001341369.1 sodium-driven chloride bicarbonate exchanger isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) encodes the longest isoform (4).

Source sequence(s)

AC008063, AC062022, AC092841, AC096654

UniProtKB/TrEMBL

E7EW28

Related

ENSP00000404486.1, ENST00000421911.1

Conserved Domains (1) summary

cl26877
Location:118 → 1061

Band_3_cyto; Band 3 cytoplasmic domain
NM_001354441.2 → NP_001341370.1 sodium-driven chloride bicarbonate exchanger isoform 5

Status: REVIEWED

Source sequence(s)

AC008063, AC062022, AC092841, AC096654

UniProtKB/TrEMBL

E7EW28

Conserved Domains (1) summary

cl26877
Location:129 → 1072

Band_3_cyto; Band 3 cytoplasmic domain
NM_001354442.2 → NP_001341371.1 sodium-driven chloride bicarbonate exchanger isoform 6

Status: REVIEWED

Source sequence(s)

AC008063, AC062022, AC092841, AC096654

UniProtKB/TrEMBL

E7EW28

Conserved Domains (1) summary

cl26877
Location:129 → 1072

Band_3_cyto; Band 3 cytoplasmic domain
NM_001354443.2 → NP_001341372.1 sodium-driven chloride bicarbonate exchanger isoform 7

Status: REVIEWED

Source sequence(s)

AC008063, AC062022, AC092841, AC096654

UniProtKB/TrEMBL

E7EW28

Conserved Domains (1) summary

cl26877
Location:130 → 1043

Band_3_cyto; Band 3 cytoplasmic domain
NM_001354444.2 → NP_001341373.1 sodium-driven chloride bicarbonate exchanger isoform 8

Status: REVIEWED

Source sequence(s)

AC008063, AC062022, AC092841, AC096654

UniProtKB/TrEMBL

E7EW28

Conserved Domains (1) summary

cl26877
Location:118 → 1060

Band_3_cyto; Band 3 cytoplasmic domain
NM_001354445.2 → NP_001341374.1 sodium-driven chloride bicarbonate exchanger isoform 9

Status: REVIEWED

Source sequence(s)

AC008063, AC062022, AC092841, AC096654

UniProtKB/TrEMBL

E7EW28

Conserved Domains (1) summary

cl26877
Location:129 → 1042

Band_3_cyto; Band 3 cytoplasmic domain
NM_001354446.2 → NP_001341375.1 sodium-driven chloride bicarbonate exchanger isoform 10

Status: REVIEWED

Source sequence(s)

AC008063, AC062022, AC092841, AC096654

Consensus CDS

CCDS86888.1

UniProtKB/TrEMBL

C9J240, E7EW28

Related

ENSP00000272716.5, ENST00000272716.9

Conserved Domains (1) summary

cl26877
Location:118 → 1031

Band_3_cyto; Band 3 cytoplasmic domain
NM_001354447.2 → NP_001341376.1 sodium-driven chloride bicarbonate exchanger isoform 11

Status: REVIEWED

Source sequence(s)

AC008063, AC062022, AC092841, AC096654

UniProtKB/TrEMBL

E7EW28

Conserved Domains (1) summary

cl26877
Location:130 → 1043

Band_3_cyto; Band 3 cytoplasmic domain
NM_001354448.2 → NP_001341377.1 sodium-driven chloride bicarbonate exchanger isoform 12

Status: REVIEWED

Source sequence(s)

AC008063, AC062022, AC092841, AC096654

UniProtKB/TrEMBL

E7EW28

Conserved Domains (1) summary

cl26877
Location:129 → 1041

Band_3_cyto; Band 3 cytoplasmic domain
NM_001354449.2 → NP_001341378.1 sodium-driven chloride bicarbonate exchanger isoform 13

Status: REVIEWED

Source sequence(s)

AC008063, AC062022, AC092841, AC096654

UniProtKB/TrEMBL

E7EW28

Conserved Domains (1) summary

cl26877
Location:118 → 1030

Band_3_cyto; Band 3 cytoplasmic domain
NM_001354450.2 → NP_001341379.1 sodium-driven chloride bicarbonate exchanger isoform 14

Status: REVIEWED

Source sequence(s)

AC008063, AC062022, AC092841, AC096654

UniProtKB/TrEMBL

E7EW28

Conserved Domains (1) summary

cl26877
Location:118 → 1031

Band_3_cyto; Band 3 cytoplasmic domain
NM_001354451.2 → NP_001341380.1 sodium-driven chloride bicarbonate exchanger isoform 15

Status: REVIEWED

Source sequence(s)

AC008063, AC062022, AC092841, AC096654

UniProtKB/TrEMBL

E7EW28

Conserved Domains (1) summary

cl26877
Location:118 → 1030

Band_3_cyto; Band 3 cytoplasmic domain
NM_001354453.2 → NP_001341382.1 sodium-driven chloride bicarbonate exchanger isoform 16

Status: REVIEWED

Source sequence(s)

AC008063, AC062022, AC092841, AC096654

UniProtKB/TrEMBL

E7EW28

Conserved Domains (1) summary

cl26877
Location:69 → 982

Band_3_cyto; Band 3 cytoplasmic domain
NM_001354455.2 → NP_001341384.1 sodium-driven chloride bicarbonate exchanger isoform 17

Status: REVIEWED

Source sequence(s)

AC008063, AC062022, AC092841, AC096654

Conserved Domains (1) summary

cl26877
Location:1 → 838

Band_3_cyto; Band 3 cytoplasmic domain
NM_001354460.2 → NP_001341389.1 sodium-driven chloride bicarbonate exchanger isoform 18

Status: REVIEWED

Description

Transcript Variant: This variant (18), as well as variant 19, encodes isoform 18.

Source sequence(s)

AC008063, AC062022, AC092841, AC096654

UniProtKB/TrEMBL

E7EW28

Conserved Domains (1) summary

cl26877
Location:130 → 1073

Band_3_cyto; Band 3 cytoplasmic domain
NM_001354461.2 → NP_001341390.1 sodium-driven chloride bicarbonate exchanger isoform 18

Status: REVIEWED

Description

Transcript Variant: This variant (19), as well as variant 18, encodes isoform 18.

Source sequence(s)

AC008063, AC062022, AC092841, AC096654

UniProtKB/TrEMBL

E7EW28

Conserved Domains (1) summary

cl26877
Location:130 → 1073

Band_3_cyto; Band 3 cytoplasmic domain
NM_022058.4 → NP_071341.2 sodium-driven chloride bicarbonate exchanger isoform 2

See identical proteins and their annotated locations for NP_071341.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region, compared to variant 1, and encodes a shorter protein (2), compared to isoform 1.

Source sequence(s)

AC062022, AC092841, AL832525, BC038298, CA841736

Consensus CDS

CCDS46438.1

UniProtKB/TrEMBL

E7EW28

Related

ENSP00000395797.2, ENST00000415876.6

Conserved Domains (3) summary

TIGR00834
Location:118 → 1031

ae; anion exchange protein

pfam00955
Location:446 → 959

HCO3_cotransp; HCO3- transporter family

pfam07565
Location:146 → 405

Band_3_cyto; Band 3 cytoplasmic domain

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_000002.12 Reference GRCh38.p14 Primary Assembly

Range

161624416..161985270

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005246694.4 → XP_005246751.1 sodium-driven chloride bicarbonate exchanger isoform X4

UniProtKB/TrEMBL

E7EW28

Conserved Domains (3) summary

TIGR00834
Location:129 → 1072

ae; anion exchange protein

pfam00955
Location:487 → 1000

HCO3_cotransp; HCO3- transporter family

pfam07565
Location:157 → 446

Band_3_cyto; Band 3 cytoplasmic domain
XM_011511509.4 → XP_011509811.1 sodium-driven chloride bicarbonate exchanger isoform X1

UniProtKB/TrEMBL

E7EW28

Conserved Domains (3) summary

TIGR00834
Location:118 → 1060

ae; anion exchange protein

pfam00955
Location:475 → 988

HCO3_cotransp; HCO3- transporter family

pfam07565
Location:146 → 434

Band_3_cyto; Band 3 cytoplasmic domain
XM_011511512.4 → XP_011509814.1 sodium-driven chloride bicarbonate exchanger isoform X2

UniProtKB/TrEMBL

E7EW28

Conserved Domains (3) summary

TIGR00834
Location:118 → 1030

ae; anion exchange protein

pfam00955
Location:445 → 958

HCO3_cotransp; HCO3- transporter family

pfam07565
Location:146 → 404

Band_3_cyto; Band 3 cytoplasmic domain
XM_011511513.3 → XP_011509815.1 sodium-driven chloride bicarbonate exchanger isoform X3

See identical proteins and their annotated locations for XP_011509815.1

UniProtKB/TrEMBL

E7EW28

Conserved Domains (1) summary

cl26877
Location:130 → 1073

Band_3_cyto; Band 3 cytoplasmic domain
XM_017004546.2 → XP_016860035.1 sodium-driven chloride bicarbonate exchanger isoform X5

UniProtKB/TrEMBL

E7EW28

Conserved Domains (1) summary

cl26877
Location:130 → 1043

Band_3_cyto; Band 3 cytoplasmic domain
XM_024453016.2 → XP_024308784.1 sodium-driven chloride bicarbonate exchanger isoform X3

UniProtKB/TrEMBL

E7EW28

Conserved Domains (1) summary

cl26877
Location:130 → 1073

Band_3_cyto; Band 3 cytoplasmic domain
XM_017004551.2 → XP_016860040.1 sodium-driven chloride bicarbonate exchanger isoform X6

UniProtKB/TrEMBL

E7EW28
XM_047445156.1 → XP_047301112.1 sodium-driven chloride bicarbonate exchanger isoform X7

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

162077534..162441869

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054343125.1 → XP_054199100.1 sodium-driven chloride bicarbonate exchanger isoform X9
XM_054343118.1 → XP_054199093.1 sodium-driven chloride bicarbonate exchanger isoform X8
XM_054343121.1 → XP_054199096.1 sodium-driven chloride bicarbonate exchanger isoform X4
XM_054343119.1 → XP_054199094.1 sodium-driven chloride bicarbonate exchanger isoform X3
XM_054343122.1 → XP_054199097.1 sodium-driven chloride bicarbonate exchanger isoform X5
XM_054343120.1 → XP_054199095.1 sodium-driven chloride bicarbonate exchanger isoform X3
XM_054343123.1 → XP_054199098.1 sodium-driven chloride bicarbonate exchanger isoform X6
XM_054343124.1 → XP_054199099.1 sodium-driven chloride bicarbonate exchanger isoform X7