SLC13A5 solute carrier family 13 member 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC13A5provided by HGNC
Official Full Name: solute carrier family 13 member 5provided by HGNC
Primary source: HGNC:HGNC:23089
See related: Ensembl:ENSG00000141485 MIM:608305; AllianceGenome:HGNC:23089
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: INDY; NACT; DEE25; mIndy; EIEE25
Summary: This gene encodes a protein belonging to the solute carrier family 13 group of proteins. This family member is a sodium-dependent citrate cotransporter that may regulate metabolic processes. Mutations in this gene cause early infantile epileptic encephalopathy 25. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2014]
Expression: Biased expression in liver (RPKM 61.1) and salivary gland (RPKM 7.3) See more
Orthologs: mouse all
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Genomic context

Location:: 17p13.1

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (6684719..6713369, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (6585350..6614003, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (6588038..6616688, complement)

Chromosome 17 - NC_000017.11 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
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?

Novel Homozygous Variants of SLC13A5 Expand the Functional Heterogeneity of a Homogeneous Syndrome of Early Infantile Epileptic Encephalopathy.
Title: Novel Homozygous Variants of SLC13A5 Expand the Functional Heterogeneity of a Homogeneous Syndrome of Early Infantile Epileptic Encephalopathy.
The citrate transporters SLC13A5 and SLC25A1 elicit different metabolic responses and phenotypes in the mouse.
Title: The citrate transporters SLC13A5 and SLC25A1 elicit different metabolic responses and phenotypes in the mouse.
NaCT/SLC13A5 facilitates citrate import and metabolism under nutrient-limited conditions.
Title: NaCT/SLC13A5 facilitates citrate import and metabolism under nutrient-limited conditions.
A novel homozygous SLC13A5 whole-gene deletion generated by Alu/Alu-mediated rearrangement in an Iraqi family with epileptic encephalopathy.
Title: A novel homozygous SLC13A5 whole-gene deletion generated by Alu/Alu-mediated rearrangement in an Iraqi family with epileptic encephalopathy.
Regulation on Citrate Influx and Metabolism through Inhibiting SLC13A5 and ACLY: A Novel Mechanism Mediating the Therapeutic Effects of Curcumin on NAFLD.
Title: Regulation on Citrate Influx and Metabolism through Inhibiting SLC13A5 and ACLY: A Novel Mechanism Mediating the Therapeutic Effects of Curcumin on NAFLD.
Adult phenotype of the homozygous missense mutation c.655G>A, p.Gly219Arg in SLC13A5: A case report.
Title: Adult phenotype of the homozygous missense mutation c.655G>A, p.Gly219Arg in SLC13A5: A case report.
Consequences of NaCT/SLC13A5/mINDY deficiency: good versus evil, separated only by the blood-brain barrier.
Title: Consequences of NaCT/SLC13A5/mINDY deficiency: good versus evil, separated only by the blood-brain barrier.
Neonatal developmental and epileptic encephalopathy due to autosomal recessive variants in SLC13A5 gene.
Title: Neonatal developmental and epileptic encephalopathy due to autosomal recessive variants in SLC13A5 gene.
Structure and inhibition mechanism of the human citrate transporter NaCT.
Title: Structure and inhibition mechanism of the human citrate transporter NaCT.
A dynamic anchor domain in slc13 transporters controls metabolite transport.
Title: A dynamic anchor domain in slc13 transporters controls metabolite transport.

Submit: New GeneRIF Correction See all GeneRIFs (25)

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
Developmental and epileptic encephalopathy, 25 MedGen: C4014621 OMIM: 615905 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
An atlas of genetic influences on human blood metabolites. EBI GWAS Catalog EBI GWAS CatalogPubMed
The genetic architecture of economic and political preferences. 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

D11S2921 (e-PCR)
- UniSTS:152074

RH46267 (e-PCR)
- UniSTS:91155

WI-18574 (e-PCR)
- UniSTS:34925

MARC_3679-3680:966881428:1 (e-PCR)
- UniSTS:231036

MARC_3679-3680:991937315:1 (e-PCR)
- UniSTS:231036

Clone Names

FLJ42326, MGC138356, DKFZp686E17257, DKFZp686K21244

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables citrate transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables citrate transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables citrate transmembrane transporter activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables citrate transmembrane transporter activity	TAS Traceable Author Statement more info
enables organic acid:sodium symporter activity	IDA Inferred from Direct Assay more info	PubMed
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 succinate transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in alpha-ketoglutarate transport	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to lithium ion	IDA Inferred from Direct Assay more info	PubMed
involved_in citrate transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in citrate transport	IDA Inferred from Direct Assay more info	PubMed
involved_in citrate transport	IMP Inferred from Mutant Phenotype 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 oxaloacetate transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in oxaloacetate 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	IEA Inferred from Electronic Annotation more info
involved_in succinate transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in succinate transport	IDA Inferred from Direct Assay more info	PubMed
involved_in transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in tricarboxylic acid transmembrane transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytosol	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: Na(+)/citrate cotransporter

Names: Na+-coupled citrate transporter protein; mammalian INDY homolog; sodium-dependent dicarboxylate transporter; solute carrier family 13 (sodium-dependent citrate transporter), member 5

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_034220.1 RefSeqGene

Range

5001..33709

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1020

mRNA and Protein(s)

NM_001143838.3 → NP_001137310.1 Na(+)/citrate cotransporter isoform b

See identical proteins and their annotated locations for NP_001137310.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region compared to variant 1. This results in a shorter protein (isoform b), compared to isoform a.

Source sequence(s)

AK127797, BC143689, CR749584, H29568

Consensus CDS

CCDS45593.1

UniProtKB/Swiss-Prot

Q86YT5

UniProtKB/TrEMBL

Q68D44

Related

ENSP00000459372.1, ENST00000573648.5

Conserved Domains (2) summary

COG0471
Location:31 → 497

CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]

cl21473
Location:31 → 482

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_001284509.2 → NP_001271438.1 Na(+)/citrate cotransporter isoform c

See identical proteins and their annotated locations for NP_001271438.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform c), compared to isoform a.

Source sequence(s)

AK127797, CR749584, H29568

Consensus CDS

CCDS67137.1

UniProtKB/Swiss-Prot

Q86YT5

UniProtKB/TrEMBL

Q68D44

Related

ENSP00000293800.6, ENST00000293800.10

Conserved Domains (2) summary

COG0471
Location:31 → 530

CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]

cl21473
Location:31 → 535

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_001284510.2 → NP_001271439.1 Na(+)/citrate cotransporter isoform d

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. This results in a shorter protein (isoform d), compared to isoform a.

Source sequence(s)

AK127797, AK297612, CR749584, DA187094, H29568

Consensus CDS

CCDS67136.1

UniProtKB/Swiss-Prot

Q86YT5

UniProtKB/TrEMBL

Q68D44

Related

ENSP00000370464.4, ENST00000381074.8

Conserved Domains (2) summary

COG0471
Location:45 → 504

CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]

cl21473
Location:35 → 509

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_177550.5 → NP_808218.1 Na(+)/citrate cotransporter isoform a

See identical proteins and their annotated locations for NP_808218.1

Status: REVIEWED

Description

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

Source sequence(s)

AK127797, BC104795, CR749584, H29568

Consensus CDS

CCDS11079.1

UniProtKB/Swiss-Prot

B3KXR0, B7Z4P2, B7ZLB4, F8W7N2, Q6ZMG1, Q86YT5

Related

ENSP00000406220.2, ENST00000433363.7

Conserved Domains (1) summary

cl21473
Location:31 → 552

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 ...

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

6684719..6713369 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011523795.4 → XP_011522097.1 Na(+)/citrate cotransporter isoform X1

Conserved Domains (2) summary

COG0471
Location:31 → 478

CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]

cl21473
Location:31 → 479

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 ...