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SLC25A21 solute carrier family 25 member 21 [ Homo sapiens (human) ]

Gene ID: 89874, updated on 5-Mar-2024

Summary

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Official Symbol
SLC25A21provided by HGNC
Official Full Name
solute carrier family 25 member 21provided by HGNC
Primary source
HGNC:HGNC:14411
See related
Ensembl:ENSG00000183032 MIM:607571; AllianceGenome:HGNC:14411
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ODC; ODC1; MTDPS18
Summary
SLC25A21 is a homolog of the S. cerevisiae ODC proteins, mitochondrial carriers that transport C5-C7 oxodicarboxylates across inner mitochondrial membranes. One of the species transported by ODC is 2-oxoadipate, a common intermediate in the catabolism of lysine, tryptophan, and hydroxylysine in mammals. Within mitochondria, 2-oxoadipate is converted into acetyl-CoA.[supplied by OMIM, Apr 2004]
Expression
Biased expression in esophagus (RPKM 5.4), salivary gland (RPKM 2.6) and 13 other tissues See more
Orthologs
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Genomic context

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See SLC25A21 in Genome Data Viewer
Location:
14q13.3
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (36677921..37172606, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (30867261..31362039, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (37147126..37641811, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene RN7SK pseudogene 257 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:37116557-37117386 Neighboring gene uncharacterized LOC105370455 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:37123150-37123888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:37125365-37126102 Neighboring gene PAX9 promoter region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:37131533-37132044 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:37132045-37132554 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:37132555-37133065 Neighboring gene NANOG hESC enhancer GRCh37_chr14:37153788-37154289 Neighboring gene paired box 9 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:37271122-37272321 Neighboring gene NANOG hESC enhancer GRCh37_chr14:37274394-37274895 Neighboring gene uncharacterized LOC107984668 Neighboring gene microRNA 4503 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:37549523-37550722 Neighboring gene Sharpr-MPRA regulatory region 11704 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:37636900-37637452 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:37640926-37641505 Neighboring gene SLC25A21 antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:37641506-37642084 Neighboring gene RNA, U6 small nuclear 273, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr14:37708438-37708614 Neighboring gene VISTA enhancer hs593 Neighboring gene mirror-image polydactyly 1 Neighboring gene uncharacterized LOC107984702

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. Mitochondrial oxodicarboxylate carrier deficiency is associated with mitochondrial DNA depletion and spinal muscular atrophy-like disease. Boczonadi V, et al. Genet Med, 2018 Oct. PMID 29517768, Free PMC Article
  2. Identification of the human mitochondrial oxodicarboxylate carrier. Bacterial expression, reconstitution, functional characterization, tissue distribution, and chromosomal location. Fiermonte G, et al. J Biol Chem, 2001 Mar 16. PMID 11083877
  3. The mitochondrial transporter family SLC25: identification, properties and physiopathology. Palmieri F. Mol Aspects Med, 2013 Apr-Jun. PMID 23266187
  4. Large-scale genotyping identifies 41 new loci associated with breast cancer risk. Michailidou K, et al. Nat Genet, 2013 Apr. PMID 23535729, Free PMC Article
  5. CBFβ stabilizes HIV Vif to counteract APOBEC3 at the expense of RUNX1 target gene expression. Kim DY, et al. Mol Cell, 2013 Feb 21. PMID 23333304, Free PMC Article

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SLC25A21 downregulation promotes KRAS-mutant colorectal cancer progression by increasing glutamine anaplerosis.
    Title: SLC25A21 downregulation promotes KRAS-mutant colorectal cancer progression by increasing glutamine anaplerosis.
  2. We identified a novel pathogenic variant in a patient by whole-exome sequencing. The pathogenicity of the mutation was studied by transport assays, computer modeling, followed by targeted metabolic testing and in vitro studies in human fibroblasts and neurons
    Title: Mitochondrial oxodicarboxylate carrier deficiency is associated with mitochondrial DNA depletion and spinal muscular atrophy-like disease.
  3. Compares and contrasts all the known human SLC25A* genes and includes functional information.
    Title: The mitochondrial transporter family SLC25: identification, properties and physiopathology.
  4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  5. 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.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Submit: New GeneRIF Correction

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
Mitochondrial DNA depletion syndrome 18
MedGen: C5394140 OMIM: 618811 GeneReviews: Not available
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EBI GWAS Catalog

Description
Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
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)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Vif vif HIV-1 Vif downregulates the expression of solute carrier family 25, member 21 (SLC25A21) in Vif-expression T cells PubMed

Go to the HIV-1, Human Interaction Database

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

Clone Names

  • MGC126570

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables alpha-ketoglutarate transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables alpha-ketoglutarate transmembrane transporter activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables alpha-ketoglutarate transmembrane transporter activity TAS
Traceable Author Statement
more info
  
enables antiporter activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in lipid transport IEA
Inferred from Electronic Annotation
more info
  
involved_in lysine catabolic process TAS
Traceable Author Statement
more info
  
involved_in mitochondrial alpha-ketoglutarate transmembrane transport IC
Inferred by Curator
more info
 PubMed 
involved_in mitochondrial alpha-ketoglutarate transmembrane transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
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
  

General protein information

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Preferred Names
mitochondrial 2-oxodicarboxylate carrier
Names
mitochondrial 2-oxoadipate carrier
oxodicarboxylate carrier
solute carrier family 25 (mitochondrial oxoadipate carrier), member 21
solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21

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.

mRNA and Protein(s)

  1. NM_001171170.2 → NP_001164641.1  mitochondrial 2-oxodicarboxylate carrier isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has a split 3' exon, as compared to variant 1. The resulting isoform (2) lacks the last aa, as compared to isoform 1.
    Source sequence(s)
    AJ278148, AK289575, AL079303
    Consensus CDS
    CCDS55913.1
    UniProtKB/Swiss-Prot
    Q9BQT8
    Related
    ENSP00000451873.1, ENST00000555449.5
    Conserved Domains (2) summary
    PTZ00168
    Location:12 → 283
    PTZ00168; mitochondrial carrier protein; Provisional
    pfam00153
    Location:15 → 105
    Mito_carr; Mitochondrial carrier protein

  2. NM_030631.4 → NP_085134.1  mitochondrial 2-oxodicarboxylate carrier isoform 1

    See identical proteins and their annotated locations for NP_085134.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) is the longer transcript and encodes isoform 1.
    Source sequence(s)
    AJ278148, AL079303
    Consensus CDS
    CCDS9663.1
    UniProtKB/Swiss-Prot
    A8K0L0, G3V4L5, Q3MJ99, Q9BQT8
    Related
    ENSP00000329452.5, ENST00000331299.6
    Conserved Domains (1) summary
    pfam00153
    Location:15 → 105
    Mito_carr; Mitochondrial carrier protein

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

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    36677921..37172606 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047431871.1 → XP_047287827.1  mitochondrial 2-oxodicarboxylate carrier isoform X1

  2. XM_011537288.4 → XP_011535590.1  mitochondrial 2-oxodicarboxylate carrier isoform X2

    Conserved Domains (1) summary
    pfam00153
    Location:175 → 268
    Mito_carr; Mitochondrial carrier protein

  3. XM_011537289.4 → XP_011535591.1  mitochondrial 2-oxodicarboxylate carrier isoform X3

    Conserved Domains (1) summary
    pfam00153
    Location:173 → 266
    Mito_carr; Mitochondrial carrier protein

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    30867261..31362039 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054376909.1 → XP_054232884.1  mitochondrial 2-oxodicarboxylate carrier isoform X1

  2. XM_054376910.1 → XP_054232885.1  mitochondrial 2-oxodicarboxylate carrier isoform X2

  3. XM_054376911.1 → XP_054232886.1  mitochondrial 2-oxodicarboxylate carrier isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BQT8.1 GenPept UniProtKB/Swiss-Prot:Q9BQT8

Gene LinkOut

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