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

    Gene ID: 10165, updated on 10-Dec-2024

    Summary

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    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

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    See SLC25A13 in Genome Data Viewer
    Location:
    7q21.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (96120220..96322098, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (97356097..97557993, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (95749532..95951410, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene dynein cytoplasmic 1 intermediate chain 1 Neighboring gene uncharacterized LOC124901700 Neighboring gene uncharacterized LOC124901701 Neighboring gene eDlx#24 enhancer in SHFM1 region Neighboring gene eExon 15 DLX5/6 limb enhancer Neighboring gene eExon 17 DLX5/6 limb enhancer Neighboring gene eDlx#23 enhancer in SHFM1 region Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:95772367-95773202 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:95773203-95774037 Neighboring gene CYCS pseudogene 18 Neighboring gene VISTA enhancer hs1642 Neighboring gene microRNA 591 Neighboring gene ribosomal protein L21 pseudogene 74 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:95943579-95944241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18384 Neighboring gene Sharpr-MPRA regulatory region 3069 Neighboring gene RNA, U6 small nuclear 532, pseudogene Neighboring gene RNA, U6 small nuclear 364, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Homozygous SLC25A13 mutation in a Taiwanese patient with adult-onset citrullinemia complicated with steatosis and hepatocellular carcinoma. Tsai CW, et al. J Formos Med Assoc, 2006 Oct. PMID 17000460
    2. Infantile cholestatic jaundice associated with adult-onset type II citrullinemia. Tazawa Y, et al. J Pediatr, 2001 May. PMID 11343052
    3. SLC25A13 cDNA cloning analysis using peripheral blood lymphocytes facilitates the identification of a large deletion mutation: Molecular diagnosis of an infant with neonatal intrahepatic cholestasis caused by citrin deficiency. Zeng HS, et al. Mol Med Rep, 2016 Dec. PMID 27779681
    4. [Analysis of clinical features and SLC25A13 gene mutations in a family affected with neonatal intrahepatic cholestasis]. Wang L, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2016 Oct. PMID 27577219
    5. [Analysis of SLC25A13 gene variants in 16 infants with intrahepatic cholestasis caused by citrin protein deficiency]. Liu W, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2022 Feb 10. PMID 35076907

    See all (267) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Features of liver injury in 138 Chinese patients with NICCD.
      Title: Features of liver injury in 138 Chinese patients with NICCD.
    2. 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.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. [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].
    8. 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.
    9. 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.
    10. 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

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    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 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 
    enables protein binding IPI
    Inferred from Physical Interaction
    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 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 IEA
    Inferred from Electronic Annotation
    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 malate-aspartate shuttle IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in mitochondrial transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    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 HTP PubMed 
    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

    1. NG_012247.2 RefSeqGene

      Range
      5050..206928
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. 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

    2. 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

    1. 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_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      96120220..96322098 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047419712.1 → XP_047275668.1  electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X2

      UniProtKB/TrEMBL
      Q53GR7

    2. XM_017011663.2 → XP_016867152.2  electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X1

      UniProtKB/TrEMBL
      Q53GR7

    3. XM_047419715.1 → XP_047275671.1  electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X5

    4. XM_047419714.1 → XP_047275670.1  electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X4

    5. XM_047419713.1 → XP_047275669.1  electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      97356097..97557993 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356990.1 → XP_054212965.1  electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X2

      UniProtKB/TrEMBL
      Q53GR7

    2. XM_054356989.1 → XP_054212964.1  electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X1

      UniProtKB/TrEMBL
      Q53GR7

    3. XM_054356991.1 → XP_054212966.1  electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X6

      UniProtKB/TrEMBL
      B7Z2E2

    4. XM_054356994.1 → XP_054212969.1  electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X5

    5. XM_054356993.1 → XP_054212968.1  electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X4

    6. XM_054356992.1 → XP_054212967.1  electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UJS0.2 GenPept UniProtKB/Swiss-Prot:Q9UJS0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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