SLC25A13 solute carrier family 25 member 13 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC25A13provided by HGNC
Official Full Name: solute carrier family 25 member 13provided by HGNC
Primary source: HGNC:HGNC:10983
See related: Ensembl:ENSG00000004864 MIM:603859; AllianceGenome:HGNC:10983
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: CTLN2; NICCD; CITRIN; ARALAR2
Summary: This gene is a member of the mitochondrial carrier family. The encoded protein contains four EF-hand Ca(2+) binding motifs in the N-terminal domain, and localizes to mitochondria. The protein catalyzes the exchange of aspartate for glutamate and a proton across the inner mitochondrial membrane, and is stimulated by calcium on the external side of the inner mitochondrial membrane. Mutations in this gene result in citrullinemia, type II. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]
Expression: Ubiquitous expression in liver (RPKM 31.0), kidney (RPKM 12.7) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7q21.3

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (96120220..96322098, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (97356097..97557993, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (95749532..95951410, complement)

Chromosome 7 - NC_000007.14 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?

Features of liver injury in 138 Chinese patients with NICCD.
Title: Features of liver injury in 138 Chinese patients with NICCD.
Clinical and genetic analysis of 26 Chinese patients with neonatal intrahepatic cholestasis due to citrin deficiency.
Title: Clinical and genetic analysis of 26 Chinese patients with neonatal intrahepatic cholestasis due to citrin deficiency.
Genetic and clinical features of patients with intrahepatic cholestasis caused by citrin deficiency.
Title: Genetic and clinical features of patients with intrahepatic cholestasis caused by citrin deficiency.
The mutation spectrum of SLC25A13 gene in citrin deficiency: identification of novel mutations in Vietnamese pediatric cohort with neonatal intrahepatic cholestasis.
Title: The mutation spectrum of SLC25A13 gene in citrin deficiency: identification of novel mutations in Vietnamese pediatric cohort with neonatal intrahepatic cholestasis.
NAGS, CPS1, and SLC25A13 (Citrin) at the Crossroads of Arginine and Pyrimidines Metabolism in Tumor Cells.
Title: NAGS, CPS1, and SLC25A13 (Citrin) at the Crossroads of Arginine and Pyrimidines Metabolism in Tumor Cells.
The Overexpression of SLC25A13 Predicts Poor Prognosis and Is Correlated with Immune Cell Infiltration in Patients with Skin Cutaneous Melanoma.
Title: The Overexpression of SLC25A13 Predicts Poor Prognosis and Is Correlated with Immune Cell Infiltration in Patients with Skin Cutaneous Melanoma.
[Analysis of SLC25A13 gene variants in 16 infants with intrahepatic cholestasis caused by citrin protein deficiency].
Title: [Analysis of SLC25A13 gene variants in 16 infants with intrahepatic cholestasis caused by citrin protein deficiency].
Hypoglycemic attacks and growth failure are the most common manifestations of citrin deficiency after 1 year of age.
Title: Hypoglycemic attacks and growth failure are the most common manifestations of citrin deficiency after 1 year of age.
Analysis of daily energy, protein, fat, and carbohydrate intake in citrin-deficient patients: Towards prevention of adult-onset type II citrullinemia.
Title: Analysis of daily energy, protein, fat, and carbohydrate intake in citrin-deficient patients: Towards prevention of adult-onset type II citrullinemia.
Neonatal Intrahepatic Cholestasis caused by Citrin Deficiency: In vivo and in vitro studies of the aberrant transcription arising from two novel splice-site variants in SLC25A13.
Title: Neonatal Intrahepatic Cholestasis caused by Citrin Deficiency: In vivo and in vitro studies of the aberrant transcription arising from two novel splice-site variants in SLC25A13.

Submit: New GeneRIF Correction See all GeneRIFs (72)

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
Citrullinemia type II MedGen: C1863844 GeneReviews: Citrin Deficiency	Compare labs
Citrullinemia, type II, adult-onset MedGen: CN295299 OMIM: 603471 GeneReviews: Citrin Deficiency	Compare labs
Neonatal intrahepatic cholestasis due to citrin deficiency MedGen: C1853942 OMIM: 605814 GeneReviews: Citrin Deficiency	Compare labs

EBI GWAS Catalog

Description
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. 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

SHGC-37627 (e-PCR)
- UniSTS:37639

D7S1812 (e-PCR)
- UniSTS:51995

SHGC-153354 (e-PCR)
- UniSTS:177695

SHGC-35735 (e-PCR)
- UniSTS:70956

D7S2374 (e-PCR)
- UniSTS:70970

SHGC-56158 (e-PCR)
- UniSTS:17813

A006W14 (e-PCR)
- UniSTS:40670

SHGC-53039 (e-PCR)
- UniSTS:26613

REN37691 (e-PCR)
- UniSTS:362491

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 3-sulfino-L-alanine: proton, glutamate antiporter activity	IDA Inferred from Direct Assay more info	PubMed
enables L-aspartate transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables L-glutamate transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables acidic amino acid transmembrane transporter activity	EXP Inferred from Experiment more info	PubMed
enables aspartate:glutamate, proton antiporter activity	IDA Inferred from Direct Assay more info	PubMed
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in ATP biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in L-aspartate transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in L-glutamate transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in L-glutamate transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in aspartate family amino acid metabolic process	TAS Traceable Author Statement more info
involved_in aspartate transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in aspartate transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular respiration	IDA Inferred from Direct Assay more info	PubMed
involved_in gluconeogenesis	TAS Traceable Author Statement more info
involved_in malate-aspartate shuttle	IBA Inferred from Biological aspect of Ancestor more info
involved_in malate-aspartate shuttle	IDA Inferred from Direct Assay more info	PubMed
involved_in mitochondrial transport	NAS Non-traceable Author Statement more info	PubMed
involved_in modified amino acid transport	IEA Inferred from Electronic Annotation more info
involved_in neutral amino acid transport	IEA Inferred from Electronic Annotation more info
involved_in proton transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in response to calcium ion	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in mitochondrial inner membrane	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial inner membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in mitochondrial inner membrane	TAS Traceable Author Statement more info
located_in mitochondrion	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial

Names: ARALAR-related gene 2; calcium-binding mitochondrial carrier protein Aralar2; citrullinemia type II; mitochondrial aspartate glutamate carrier 2; solute carrier family 25 (aspartate/glutamate carrier), member 13

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_012247.2 RefSeqGene

Range

5050..206928

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001160210.2 → NP_001153682.1 electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform 1

See identical proteins and their annotated locations for NP_001153682.1

Status: REVIEWED

Description

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

Source sequence(s)

AJ496569, DA118296, DA696723

Consensus CDS

CCDS55130.1

UniProtKB/TrEMBL

Q53GR7

Related

ENSP00000400101.2, ENST00000416240.6

Conserved Domains (4) summary

pfam00153
Location:517 → 612

Mito_carr; Mitochondrial carrier protein

pfam13499
Location:16 → 81

EF-hand_7; EF-hand domain pair

cd15897
Location:57 → 83

EFh_PEF; EF-hand motif [structural motif]

cl25352
Location:56 → 183

EFh_PEF; The penta-EF hand (PEF) family
NM_014251.3 → NP_055066.1 electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform 2

See identical proteins and their annotated locations for NP_055066.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. The resulting isoform (2) lacks one-aa, compared to isoform 1.

Source sequence(s)

AC004458, BC006566, DA118296

Consensus CDS

CCDS5645.1

UniProtKB/Swiss-Prot

O14566, O14575, Q546F9, Q9NZW1, Q9UJS0, Q9UNI7

UniProtKB/TrEMBL

Q53GR7

Related

ENSP00000265631.6, ENST00000265631.10

Conserved Domains (4) summary

pfam00153
Location:516 → 611

Mito_carr; Mitochondrial carrier protein

pfam13499
Location:16 → 81

EF-hand_7; EF-hand domain pair

cd15897
Location:57 → 83

EFh_PEF; EF-hand motif [structural motif]

cl25352
Location:56 → 183

EFh_PEF; The penta-EF hand (PEF) family

RNA

NR_027662.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate exon in the 5' coding region resulting in a frameshift, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK294629, BC006566, DA118296, DA696723

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_000007.14 Reference GRCh38.p14 Primary Assembly

Range

96120220..96322098 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047419712.1 → XP_047275668.1 electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X2
XM_017011663.2 → XP_016867152.2 electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X1
XM_047419715.1 → XP_047275671.1 electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X5
XM_047419714.1 → XP_047275670.1 electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X4
XM_047419713.1 → XP_047275669.1 electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X3

Alternate T2T-CHM13v2.0

Genomic

NC_060931.1 Alternate T2T-CHM13v2.0

Range

97356097..97557993 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054356990.1 → XP_054212965.1 electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X2
XM_054356989.1 → XP_054212964.1 electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X1
XM_054356991.1 → XP_054212966.1 electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X6
XM_054356994.1 → XP_054212969.1 electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X5
XM_054356993.1 → XP_054212968.1 electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X4
XM_054356992.1 → XP_054212967.1 electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X3