SLC13A2 solute carrier family 13 member 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC13A2provided by HGNC
Official Full Name: solute carrier family 13 member 2provided by HGNC
Primary source: HGNC:HGNC:10917
See related: Ensembl:ENSG00000007216 MIM:604148; AllianceGenome:HGNC:10917
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: NaCT; NADC1; SDCT1; NaDC-1
Summary: The protein encoded by this gene is a sodium-coupled citrate transporter that is regulated by the chaperone activity of cyclophilin b. The encoded protein may play a role in the formation of kidney stones. [provided by RefSeq, Oct 2016]
Expression: Biased expression in duodenum (RPKM 49.7), small intestine (RPKM 41.0) and 4 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q11.2

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (28473644..28497781)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (29416661..29440798)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (26800662..26824799)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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?

Cryo-EM structures of the human NaS1 and NaDC1 transporters revealed the elevator transport and allosteric regulation mechanism.
Title: Cryo-EM structures of the human NaS1 and NaDC1 transporters revealed the elevator transport and allosteric regulation mechanism.
SLC26A6 and NADC1: Future direction of nephrolithiasis and calculusrelated hypertension research (Review).
Title: SLC26A6 and NADC‑1: Future direction of nephrolithiasis and calculus‑related hypertension research (Review).
Homozygous GG of rs11567842 SNP in NaDC-1 gene was a protective genotype for hypocitraturia in kidney stone patients
Title: rs11567842 SNP in SLC13A2 gene associates with hypocitraturia in Thai patients with nephrolithiasis.
Results point to an epistatic interaction between the VDR and the SLC13A2 alleles in the pathogenesis of idiopathic hypocitraturia in calcium-oxalate stone formers.
Title: Evidence for epistatic interaction between VDR and SLC13A2 genes in the pathogenesis of hypocitraturia in recurrent calcium oxalate stone formers.
Mapping Functionally Important Residues in the Na(+)/Dicarboxylate Cotransporter, NaDC1.
Title: Mapping Functionally Important Residues in the Na(+)/Dicarboxylate Cotransporter, NaDC1.
NaDC1 is present throughout the entire proximal tubule, but was not detected in kidney tumors.
Title: Expression of sodium-dependent dicarboxylate transporter 1 (NaDC1/SLC13A2) in normal and neoplastic human kidney.
cyclophilin isoform B is likely responsible for down-regulation of carrier expression by CsA and that it does so via its chaperone activity on NaDC1 (by direct interaction) rather than its rotamase activity.
Title: Synthesis, maturation, and trafficking of human Na+-dicarboxylate cotransporter NaDC1 requires the chaperone activity of cyclophilin B.
study concludes most of the naturally occurring nonsynonymous SNPs affect protein processing of NaDC1; several also affect functional properties; mutations are predicted to decrease transport activity
Title: Single nucleotide polymorphisms in the human Na+-dicarboxylate cotransporter affect transport activity and protein expression.
Observational study of gene-disease association. (HuGE Navigator)
Title: L-type voltage-dependent calcium channel alpha subunit 1C is a novel candidate gene associated with secondary hyperparathyroidism: an application of haplotype-based analysis for multiple linked single nucleotide polymorphisms.
The Ser or Thr at position 509 is the most important determinant of functional differences in apparent affinity for substrate and cations. The cation and substrate binding sites are located in close proximity to one another.
Title: Threonine-509 is a determinant of apparent affinity for both substrate and cations in the human Na+/dicarboxylate cotransporter.

Submit: New GeneRIF Correction See all GeneRIFs (14)

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

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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables alpha-ketoglutarate transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables alpha-ketoglutarate transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables fumarate transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables fumarate transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables low-affinity sodium:dicarboxylate symporter activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sodium:dicarboxylate symporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables sodium:dicarboxylate symporter activity	IDA Inferred from Direct Assay more info	PubMed
enables succinate transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables succinate transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in alpha-ketoglutarate transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in alpha-ketoglutarate transport	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to lithium ion	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to lithium ion	IDA Inferred from Direct Assay more info	PubMed
involved_in fumarate transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in fumarate transport	IDA Inferred from Direct Assay more info	PubMed
involved_in sodium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in succinate transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in succinate transmembrane transport	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in apical plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in 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	TAS Traceable Author Statement more info

General protein information

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Preferred Names: solute carrier family 13 member 2

Names: Na(+)-coupled citrate transporter; Na(+)/dicarboxylate cotransporter 1; renal sodium/dicarboxylate cotransporter; solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2

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_051960.1 RefSeqGene

Range

4999..29136

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001145975.2 → NP_001139447.1 solute carrier family 13 member 2 isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (a).

Source sequence(s)

AC015917, AK298388, AK314684, AW024214, BC096277

Consensus CDS

CCDS54098.1

UniProtKB/TrEMBL

B4E1M6

Related

ENSP00000392411.3, ENST00000444914.7

Conserved Domains (1) summary

cl21473
Location:6 → 614

ArsB_NhaD_permease; Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices ...
NM_001346683.2 → NP_001333612.1 solute carrier family 13 member 2 isoform d

Status: REVIEWED

Description

Transcript Variant: This variant (4) includes an alternate internal exon and uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (d) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform a.

Source sequence(s)

AC015917

Consensus CDS

CCDS92282.1

UniProtKB/TrEMBL

B4E1M6, J3QL78

Related

ENSP00000463421.2, ENST00000579281.5
NM_001346684.2 → NP_001333613.1 solute carrier family 13 member 2 isoform e

Status: REVIEWED

Description

Transcript Variant: This variant (5) includes an alternate internal exon and lacks an alternate internal segment compared to variant 1. The resulting isoform (e) has a shorter and distinct N-terminus compared to isoform a.

Source sequence(s)

AC015917

UniProtKB/TrEMBL

B3KRN0
NM_003984.4 → NP_003975.1 solute carrier family 13 member 2 isoform b

See identical proteins and their annotated locations for NP_003975.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the internal coding region compared to variant 1. This results in a shorter isoform (b) compared to isoform a.

Source sequence(s)

AC015917, AW024214, DB320886, U26209

Consensus CDS

CCDS11231.1

UniProtKB/Swiss-Prot

B2RBI9, B4DPL1, E7ETH5, Q13183, Q4VAR7

UniProtKB/TrEMBL

B4E1M6

Related

ENSP00000316202.6, ENST00000314669.10

Conserved Domains (1) summary

pfam00939
Location:6 → 565

Na_sulph_symp; Sodium:sulfate symporter transmembrane region

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

28473644..28497781

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047437011.1 → XP_047292967.1 solute carrier family 13 member 2 isoform X2
XM_011525450.4 → XP_011523752.1 solute carrier family 13 member 2 isoform X1

UniProtKB/TrEMBL

B4E1M6

Conserved Domains (2) summary

TIGR00785
Location:33 → 608

dass; anion transporter

cl21473
Location:6 → 615

ArsB_NhaD_permease; Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices ...
XM_011525453.3 → XP_011523755.1 solute carrier family 13 member 2 isoform X4

UniProtKB/TrEMBL

B4E1M6

Conserved Domains (2) summary

TIGR00785
Location:33 → 535

dass; anion transporter

cl21473
Location:6 → 542

ArsB_NhaD_permease; Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices ...
XM_011525452.2 → XP_011523754.1 solute carrier family 13 member 2 isoform X3

UniProtKB/TrEMBL

B4E1M6

Conserved Domains (2) summary

TIGR00785
Location:33 → 559

dass; anion transporter

pfam00939
Location:6 → 566

Na_sulph_symp; Sodium:sulfate symporter transmembrane region
XM_011525454.4 → XP_011523756.1 solute carrier family 13 member 2 isoform X5

Conserved Domains (1) summary

cl21473
Location:6 → 396

ArsB_NhaD_permease; Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices ...

Alternate T2T-CHM13v2.0

Genomic

NC_060941.1 Alternate T2T-CHM13v2.0

Range

29416661..29440798

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054317707.1 → XP_054173682.1 solute carrier family 13 member 2 isoform X2
XM_054317706.1 → XP_054173681.1 solute carrier family 13 member 2 isoform X1
XM_054317709.1 → XP_054173684.1 solute carrier family 13 member 2 isoform X4
XM_054317708.1 → XP_054173683.1 solute carrier family 13 member 2 isoform X3
XM_054317710.1 → XP_054173685.1 solute carrier family 13 member 2 isoform X5

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001145976.1: Suppressed sequence

Description

NM_001145976.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.