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SLC25A39 solute carrier family 25 member 39 [ Homo sapiens (human) ]

Gene ID: 51629, updated on 3-Apr-2024

Summary

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Official Symbol
SLC25A39provided by HGNC
Official Full Name
solute carrier family 25 member 39provided by HGNC
Primary source
HGNC:HGNC:24279
See related
Ensembl:ENSG00000013306 MIM:610820; AllianceGenome:HGNC:24279
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
CGI69; CGI-69
Summary
This gene encodes a member of the SLC25 transporter or mitochondrial carrier family of proteins. Members of this family are encoded by the nuclear genome while their protein products are usually embedded in the inner mitochondrial membrane and exhibit wide-ranging substrate specificity. Although the encoded protein is currently considered an orphan transporter, this protein is related to other carriers known to transport amino acids. This protein may play a role in iron homeostasis. [provided by RefSeq, Mar 2016]
Expression
Ubiquitous expression in bone marrow (RPKM 112.9), kidney (RPKM 47.3) and 25 other tissues See more
Orthologs
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Genomic context

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See SLC25A39 in Genome Data Viewer
Location:
17q21.31
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (44319628..44324823, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (45172706..45177911, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (42396996..42402191, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene RUNDC3A antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8587 Neighboring gene RNA, U6 small nuclear 453, pseudogene Neighboring gene RUN domain containing 3A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8588 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8589 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12255 Neighboring gene uncharacterized LOC124904009 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12257 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42403114-42403965 Neighboring gene CRISPRi-validated cis-regulatory element chr17.2878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42420716-42421641 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12260 Neighboring gene Sharpr-MPRA regulatory region 15390 Neighboring gene granulin precursor

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. Overexpression of the human 2-oxoglutarate carrier lowers mitochondrial membrane potential in HEK-293 cells: contrast with the unique cold-induced mitochondrial carrier CGI-69. Yu XX, et al. Biochem J, 2001 Jan 15. PMID 11139402, Free PMC Article
  2. Combinatorial GxGxE CRISPR screen identifies SLC25A39 in mitochondrial glutathione transport linking iron homeostasis to OXPHOS. Shi X, et al. Nat Commun, 2022 May 5. PMID 35513392, Free PMC Article
  3. Germinal GLT8D1, GATAD2A and SLC25A39 mutations in a patient with a glomangiopericytal tumor and five different sarcomas over a 10-year period. Beddok A, et al. Sci Rep, 2021 May 7. PMID 33963205, Free PMC Article
  4. SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells. Wang Y, et al. Nature, 2021 Nov. PMID 34707288, Free PMC Article
  5. Fourteen novel human members of mitochondrial solute carrier family 25 (SLC25) widely expressed in the central nervous system. Haitina T, et al. Genomics, 2006 Dec. PMID 16949250

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SLC25A39 links mitochondrial GSH sensing with iron metabolism.
    Title: SLC25A39 links mitochondrial GSH sensing with iron metabolism.
  2. Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis.
    Title: Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis.
  3. Autoregulatory control of mitochondrial glutathione homeostasis.
    Title: Autoregulatory control of mitochondrial glutathione homeostasis.
  4. SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells.
    Title: SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells.
  5. Germinal GLT8D1, GATAD2A and SLC25A39 mutations in a patient with a glomangiopericytal tumor and five different sarcomas over a 10-year period.
    Title: Germinal GLT8D1, GATAD2A and SLC25A39 mutations in a patient with a glomangiopericytal tumor and five different sarcomas over a 10-year period.
  6. Compares and contrasts all the known human SLC25A* genes and includes functional information.
    Title: The mitochondrial transporter family SLC25: identification, properties and physiopathology.
  7. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  8. Required for functional heme biosynthesis in erythroid cells. Possibly regulate ALAS2 through iron-sulfur cluster biogenesis.
    Title: Discovery of genes essential for heme biosynthesis through large-scale gene expression analysis.
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

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ22407

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in glutathione import into mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in glutathione import into mitochondrion IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in heme biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in transport IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in mitochondrial inner membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
probable mitochondrial glutathione transporter SLC25A39

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_001143780.3 → NP_001137252.1  probable mitochondrial glutathione transporter SLC25A39 isoform a

    See identical proteins and their annotated locations for NP_001137252.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AK289357, BC096819
    Consensus CDS
    CCDS45700.1
    UniProtKB/Swiss-Prot
    A8JZZ2, D3DX51, D3DX54, Q4V9M1, Q9BZJ4, Q9P182, Q9UF66, Q9Y379
    Related
    ENSP00000366299.4, ENST00000377095.10
    Conserved Domains (1) summary
    pfam00153
    Location:251 → 350
    Mito_carr; Mitochondrial carrier protein

  2. NM_001321240.2 → NP_001308169.1  probable mitochondrial glutathione transporter SLC25A39 isoform c

    Status: REVIEWED

    Source sequence(s)
    AK294085, BU678976
    Consensus CDS
    CCDS82138.1
    UniProtKB/TrEMBL
    B4DFG5
    Related
    ENSP00000444540.1, ENST00000537904.6
    Conserved Domains (2) summary
    PTZ00169
    Location:16 → 308
    PTZ00169; ADP/ATP transporter on adenylate translocase; Provisional
    pfam00153
    Location:9 → 129
    Mito_carr; Mitochondrial carrier protein

  3. NM_001321241.2 → NP_001308170.1  probable mitochondrial glutathione transporter SLC25A39 isoform d

    Status: REVIEWED

    Source sequence(s)
    AC003043, BU678976, CB960224
    Conserved Domains (1) summary
    pfam00153
    Location:9 → 144
    Mito_carr; Mitochondrial carrier protein

  4. NM_001366726.1 → NP_001353655.1  probable mitochondrial glutathione transporter SLC25A39 isoform e

    Status: REVIEWED

    Source sequence(s)
    AC003043
    UniProtKB/TrEMBL
    K7EMW3
    Conserved Domains (1) summary
    pfam00153
    Location:150 → 249
    Mito_carr; Mitochondrial carrier protein

  5. NM_016016.4 → NP_057100.1  probable mitochondrial glutathione transporter SLC25A39 isoform b

    See identical proteins and their annotated locations for NP_057100.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the coding region compared to variant 1. The encoded isoform (b) is shorter but has the same N- and C-termini compared to isoform a.
    Source sequence(s)
    BC001398, CB960224
    Consensus CDS
    CCDS11482.1
    UniProtKB/Swiss-Prot
    Q9BZJ4
    Related
    ENSP00000225308.8, ENST00000225308.12
    Conserved Domains (1) summary
    pfam00153
    Location:9 → 144
    Mito_carr; Mitochondrial carrier protein

RNA

  1. NR_159401.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC003043

  2. NR_159402.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC003043

  3. NR_159403.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC003043

  4. NR_159404.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC003043

  5. NR_159405.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC003043

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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    44319628..44324823 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011524880.4 → XP_011523182.1  probable mitochondrial glutathione transporter SLC25A39 isoform X1

    Conserved Domains (1) summary
    pfam00153
    Location:257 → 356
    Mito_carr; Mitochondrial carrier protein

  2. XM_047436237.1 → XP_047292193.1  probable mitochondrial glutathione transporter SLC25A39 isoform X8

    UniProtKB/TrEMBL
    B4DFG5

  3. XM_047436236.1 → XP_047292192.1  probable mitochondrial glutathione transporter SLC25A39 isoform X2

  4. XM_047436235.1 → XP_047292191.1  probable mitochondrial glutathione transporter SLC25A39 isoform X7

  5. XM_047436234.1 → XP_047292190.1  probable mitochondrial glutathione transporter SLC25A39 isoform X1

  6. XM_047436240.1 → XP_047292196.1  probable mitochondrial glutathione transporter SLC25A39 isoform X3

    Related
    ENSP00000466615.1, ENST00000588767.5

  7. XM_047436238.1 → XP_047292194.1  probable mitochondrial glutathione transporter SLC25A39 isoform X3

  8. XM_047436241.1 → XP_047292197.1  probable mitochondrial glutathione transporter SLC25A39 isoform X4

    Related
    ENSP00000466676.1, ENST00000586016.5

  9. XM_047436239.1 → XP_047292195.1  probable mitochondrial glutathione transporter SLC25A39 isoform X3

  10. XM_047436242.1 → XP_047292198.1  probable mitochondrial glutathione transporter SLC25A39 isoform X5

  11. XM_047436244.1 → XP_047292200.1  probable mitochondrial glutathione transporter SLC25A39 isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    45172706..45177911 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054316407.1 → XP_054172382.1  probable mitochondrial glutathione transporter SLC25A39 isoform X2

  2. XM_054316406.1 → XP_054172381.1  probable mitochondrial glutathione transporter SLC25A39 isoform X1

  3. XM_054316408.1 → XP_054172383.1  probable mitochondrial glutathione transporter SLC25A39 isoform X3

  4. XM_054316410.1 → XP_054172385.1  probable mitochondrial glutathione transporter SLC25A39 isoform X4

  5. XM_054316409.1 → XP_054172384.1  probable mitochondrial glutathione transporter SLC25A39 isoform X3

  6. XM_054316412.1 → XP_054172387.1  probable mitochondrial glutathione transporter SLC25A39 isoform X6

  7. XM_054316411.1 → XP_054172386.1  probable mitochondrial glutathione transporter SLC25A39 isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BZJ4.2 GenPept UniProtKB/Swiss-Prot:Q9BZJ4

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