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    SLC25A3 solute carrier family 25 member 3 [ Homo sapiens (human) ]

    Gene ID: 5250, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SLC25A3provided by HGNC
    Official Full Name
    solute carrier family 25 member 3provided by HGNC
    Primary source
    HGNC:HGNC:10989
    See related
    Ensembl:ENSG00000075415 MIM:600370; AllianceGenome:HGNC:10989
    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
    PHC; PTP; PiC; OK/SW-cl.48
    Summary
    The protein encoded by this gene catalyzes the transport of phosphate into the mitochondrial matrix, either by proton cotransport or in exchange for hydroxyl ions. The protein contains three related segments arranged in tandem which are related to those found in other characterized members of the mitochondrial carrier family. Both the N-terminal and C-terminal regions of this protein protrude toward the cytosol. Multiple alternatively spliced transcript variants have been isolated. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in heart (RPKM 179.1), kidney (RPKM 125.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC25A3 in Genome Data Viewer
    Location:
    12q23.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (98593686..98606367)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (98566653..98579332)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (98987464..99000145)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6844 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4753 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:98922080-98922246 Neighboring gene TMPO antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6845 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:98987254-98987878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6847 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:98987879-98988503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6848 Neighboring gene MPRA-validated peak1907 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4754 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_31387 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:99037284-99037911 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:99037912-99038538 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:99038539-99039166 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4756 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:99043141-99044340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:99072005-99072576 Neighboring gene thymopoietin Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_31421 Neighboring gene small nucleolar RNA, H/ACA box 53 Neighboring gene peptidylprolyl isomerase A pseudogene 8 Neighboring gene MPRA-validated peak1909 silencer Neighboring gene IKBKB interacting protein Neighboring gene apoptotic peptidase activating factor 1 Neighboring gene ankyrin repeat and sterile alpha motif domain containing 1B

    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. Nucleotide sequence of a human heart cDNA encoding the mitochondrial phosphate carrier. Dolce V, et al. DNA Seq, 1991. PMID 1777677
    2. Chromosomal localization of the mitochondrial phosphate carrier gene PHC to 12q23. Marsh S, et al. Genomics, 1995 Oct 10. PMID 8575787
    3. Functional analysis of the promoter of the mitochondrial phosphate carrier human gene: identification of activator and repressor elements and their transcription factors. Iacobazzi V, et al. Biochem J, 2005 Nov 1. PMID 15984930, Free PMC Article
    4. Pathologic Variants of the Mitochondrial Phosphate Carrier SLC25A3: Two New Patients and Expansion of the Cardiomyopathy/Skeletal Myopathy Phenotype With and Without Lactic Acidosis. Bhoj EJ, et al. JIMD Rep, 2015. PMID 25681081, Free PMC Article
    5. Natural and Induced Mitochondrial Phosphate Carrier Loss: DIFFERENTIAL DEPENDENCE OF MITOCHONDRIAL METABOLISM AND DYNAMICS AND CELL SURVIVAL ON THE EXTENT OF DEPLETION. Seifert EL, et al. J Biol Chem, 2016 Dec 9. PMID 27780865, Free PMC Article

    See all (250) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. METTL14-mediated methylation of SLC25A3 mitigates mitochondrial damage in osteoblasts, leading to the improvement of osteoporosis.
      Title: METTL14-mediated methylation of SLC25A3 mitigates mitochondrial damage in osteoblasts, leading to the improvement of osteoporosis.
    2. SLC25A3 negatively regulates NLRP3 inflammasome activation by restricting the function of NLRP3.
      Title: SLC25A3 negatively regulates NLRP3 inflammasome activation by restricting the function of NLRP3.
    3. Getting out what you put in: Copper in mitochondria and its impacts on human disease.
      Title: Getting out what you put in: Copper in mitochondria and its impacts on human disease.
    4. SLC25A3 is a mitochondrial copper transporter.
      Title: The mammalian phosphate carrier SLC25A3 is a mitochondrial copper transporter required for cytochrome c oxidase biogenesis.
    5. these results indicate that PiC depletion may need to be profound (>85%) to substantially affect maximal oxphos and that pathogenesis associated with PiC depletion or loss of function may be independent of phosphate limitation when ATP requirements are not high.
      Title: Natural and Induced Mitochondrial Phosphate Carrier Loss: DIFFERENTIAL DEPENDENCE OF MITOCHONDRIAL METABOLISM AND DYNAMICS AND CELL SURVIVAL ON THE EXTENT OF DEPLETION.
    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. This protein has been found differentially expressed in the Wernicke's Area from patients with schizophrenia.
      Title: Proteome analysis of schizophrenia patients Wernicke's area reveals an energy metabolism dysregulation.
    9. An analysis of the promoter region of the human mitochondrial phosphate transporter, including its activation and inhibition domains, is reported.
      Title: Functional analysis of the promoter of the mitochondrial phosphate carrier human gene: identification of activator and repressor elements and their transcription factors.
    10. SLC25A3 protein deficiency is associated with lactic acidosis, hypertrophic cardiomyopathy, and muscular hypotonia
      Title: Mitochondrial phosphate-carrier deficiency: a novel disorder of oxidative phosphorylation.
    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
    Cardiomyopathy-hypotonia-lactic acidosis syndrome
    MedGen: C1835845 OMIM: 610773 GeneReviews: Not available
    		Compare labs

    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 phosphate transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphate:proton symporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-containing complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mitochondrial phosphate ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phosphate ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in proton transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    located_in membrane HDA PubMed 
    is_active_in mitochondrial inner membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrial inner membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in mitochondrion HTP PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    solute carrier family 25 member 3
    Names
    phosphate transport protein
    solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3

    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_011702.2 RefSeqGene

      Range
      5002..17683
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_002635.4 → NP_002626.1  solute carrier family 25 member 3 isoform b precursor

      See identical proteins and their annotated locations for NP_002626.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents the predominant transcript. Variants 2 and 3 encode the same isoform (b).
      Source sequence(s)
      AC013283, BI458030, BX647062, X60036
      Consensus CDS
      CCDS9065.1
      UniProtKB/TrEMBL
      A0A024RBE8, B2RE88, Q53HC3, Q8NCF7
      Related
      ENSP00000448708.2, ENST00000552981.6
      Conserved Domains (2) summary
      pfam00153
      Location:60 → 151
      Mito_carr; Mitochondrial carrier protein
      cl28162
      Location:262 → 340
      Mito_carr; Mitochondrial carrier protein

    2. NM_005888.4 → NP_005879.1  solute carrier family 25 member 3 isoform a precursor

      See identical proteins and their annotated locations for NP_005879.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) has an alternate exon in the 5' coding region, compared to variant 2. It encodes isoform a, which has an internal segment that differs from isoform b.
      Source sequence(s)
      AC013283, AK092689, BI458030, BX647062
      Consensus CDS
      CCDS9066.1
      UniProtKB/Swiss-Prot
      B3KS34, Q00325, Q7Z7N7, Q96A03
      UniProtKB/TrEMBL
      A0A024RBH9, B2RE88, Q53HC3, Q8NCF7
      Related
      ENSP00000228318.3, ENST00000228318.8
      Conserved Domains (2) summary
      pfam00153
      Location:64 → 152
      Mito_carr; Mitochondrial carrier protein
      cl28162
      Location:263 → 341
      Mito_carr; Mitochondrial carrier protein

    3. NM_213611.3 → NP_998776.1  solute carrier family 25 member 3 isoform b precursor

      See identical proteins and their annotated locations for NP_998776.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 2. Variants 2 and 3 both encode isoform b.
      Source sequence(s)
      AC013283, BC001328, BI458030, BX647062
      Consensus CDS
      CCDS9065.1
      UniProtKB/TrEMBL
      A0A024RBE8, B2RE88, Q53HC3, Q8NCF7
      Related
      ENSP00000188376.5, ENST00000188376.9
      Conserved Domains (2) summary
      pfam00153
      Location:60 → 151
      Mito_carr; Mitochondrial carrier protein
      cl28162
      Location:262 → 340
      Mito_carr; Mitochondrial carrier protein

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      98593686..98606367
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      98566653..98579332
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_213612.1: Suppressed sequence

      Description
      NM_213612.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q00325.2 GenPept UniProtKB/Swiss-Prot:Q00325

    Gene LinkOut

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

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