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    SLC25A25 solute carrier family 25 member 25 [ Homo sapiens (human) ]

    Gene ID: 114789, updated on 3-Nov-2024

    Summary

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    Official Symbol
    SLC25A25provided by HGNC
    Official Full Name
    solute carrier family 25 member 25provided by HGNC
    Primary source
    HGNC:HGNC:20663
    See related
    Ensembl:ENSG00000148339 MIM:608745; AllianceGenome:HGNC:20663
    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
    MCSC; PCSCL; SCAMC2; SCAMC-2
    Summary
    The protein encoded by this gene belongs to the family of calcium-binding mitochondrial carriers, with a characteristic mitochondrial carrier domain at the C-terminus. These proteins are found in the inner membranes of mitochondria, and function as transport proteins. They shuttle metabolites, nucleotides and cofactors through the mitochondrial membrane and thereby connect and/or regulate cytoplasm and matrix functions. This protein may function as an ATP-Mg/Pi carrier that mediates the transport of Mg-ATP in exchange for phosphate, and likely responsible for the net uptake or efflux of adenine nucleotides into or from the mitochondria. Alternatively spliced transcript variants encoding different isoforms with a common C-terminus but variable N-termini have been described for this gene. [provided by RefSeq, Jul 2012]
    Expression
    Ubiquitous expression in liver (RPKM 17.5), gall bladder (RPKM 17.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC25A25 in Genome Data Viewer
    Location:
    9q34.11
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (128068232..128109245)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (140276208..140317210)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (130830511..130871524)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130704889-130705418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130708322-130708822 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130708823-130709323 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130717798-130718764 Neighboring gene estrogen-induced osteoclastogenesis regulator 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130723095-130723703 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130723748-130724584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130724585-130725420 Neighboring gene Sharpr-MPRA regulatory region 6856 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130730939-130731467 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130735756-130736498 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130736499-130737242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29063 Neighboring gene conserved acetylation island sequence 15 enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20319 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29064 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130763335-130763870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130763871-130764404 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29065 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29067 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20320 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29068 Neighboring gene Sharpr-MPRA regulatory region 5179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130817345-130818242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20323 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29070 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:130835790-130836290 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:130836291-130836791 Neighboring gene nuclear apoptosis inducing factor 1 Neighboring gene Sharpr-MPRA regulatory region 4771 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130853709-130854229 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:130854230-130854750 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130859824-130860560 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130860561-130861298 Neighboring gene SLC25A25 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 4689 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29071 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29072 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20324 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29073 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20325 Neighboring gene prostaglandin E synthase 2

    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 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. Exome sequencing identifies a disease variant of the mitochondrial ATP-Mg/Pi carrier SLC25A25 in two families with kidney stones. Jabalameli MR, et al. Mol Genet Genomic Med, 2021 Dec. PMID 34346195, Free PMC Article
    2. A novel mitochondrial Ca2+-dependent solute carrier in the liver identified by mRNA differential display. Mashima H, et al. J Biol Chem, 2003 Mar 14. PMID 12645546
    3. FOXD3 acts as a repressor of the mitochondrial S-adenosylmethionine carrier (SLC25A26) gene expression in cancer cells. Cianciulli A, et al. Biochimie, 2018 Nov. PMID 30076902
    4. Identification of the mitochondrial ATP-Mg/Pi transporter. Bacterial expression, reconstitution, functional characterization, and tissue distribution. Fiermonte G, et al. J Biol Chem, 2004 Jul 16. PMID 15123600
    5. Identification of a novel human subfamily of mitochondrial carriers with calcium-binding domains. del Arco A, et al. J Biol Chem, 2004 Jun 4. PMID 15054102

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Exome sequencing identifies a disease variant of the mitochondrial ATP-Mg/Pi carrier SLC25A25 in two families with kidney stones.
      Title: Exome sequencing identifies a disease variant of the mitochondrial ATP-Mg/Pi carrier SLC25A25 in two families with kidney stones.
    2. FOXD3 acts as a repressor of the mitochondrial S-adenosylmethionine carrier (SLC25A26) gene expression in cancer cells.
      Title: FOXD3 acts as a repressor of the mitochondrial S-adenosylmethionine carrier (SLC25A26) gene expression in cancer cells.
    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. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    5. may play an important role in regulating the function of hepatocytes rather than in differentiation in vivo
      Title: A novel mitochondrial Ca2+-dependent solute carrier in the liver identified by mRNA differential display.
    6. SCaMC-2, has four variants generated by alternative splicing, resulting in proteins with a common C terminus but with variations in their N-terminal halves, including the loss of one to three EF-hand motifs
      Title: Identification of a novel human subfamily of mitochondrial carriers with calcium-binding domains.
    7. identification of three isoforms of the mitochondrial ATP-Mg/Pi carrier APC1, APC2 and APC3; they are most likely responsible for the net uptake or efflux of adenine nucleotides into or from the mitochondria [APC3]
      Title: Identification of the mitochondrial ATP-Mg/Pi transporter. Bacterial expression, reconstitution, functional characterization, and tissue distribution.
    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

    • KIAA1896, MGC105138, MGC119514, MGC119515, MGC119516, MGC119517

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ATP:phosphate antiporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in ADP transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ATP metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ATP transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in adipose tissue development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in calcium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in camera-type eye development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular respiration IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in multicellular organism growth IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to dietary excess IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to food IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrial inner membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion HTP PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    mitochondrial adenyl nucleotide antiporter SLC25A25
    Names
    calcium-binding mitochondrial carrier protein SCaMC-2
    mitochondrial ATP-Mg/Pi carrier protein 3
    mitochondrial Ca(2+)-dependent solute carrier protein 3
    short calcium-binding mitochondrial carrier 2
    short calcium-binding mitochondrial carrier protein 2
    small calcium-binding mitochondrial carrier 2
    solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 25

    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_032871.2 RefSeqGene

      Range
      5002..46015
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001006641.4 → NP_001006642.1  mitochondrial adenyl nucleotide antiporter SLC25A25 isoform b

      See identical proteins and their annotated locations for NP_001006642.1

      Status: REVIEWED

      Source sequence(s)
      AL360268, AL590708
      Consensus CDS
      CCDS35151.1
      UniProtKB/Swiss-Prot
      Q6KCM7
      Related
      ENSP00000362159.2, ENST00000373068.6
      Conserved Domains (3) summary
      cd00051
      Location:116 → 175
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam00153
      Location:310 → 402
      Mito_carr; Mitochondrial carrier protein
      pfam13499
      Location:52 → 110
      EF-hand_7; EF-hand domain pair

    2. NM_001006642.4 → NP_001006643.1  mitochondrial adenyl nucleotide antiporter SLC25A25 isoform c precursor

      See identical proteins and their annotated locations for NP_001006643.1

      Status: REVIEWED

      Source sequence(s)
      AL360268, AL590708
      Consensus CDS
      CCDS48031.1
      UniProtKB/TrEMBL
      A0A804HLB0
      Related
      ENSP00000410053.2, ENST00000432073.6
      Conserved Domains (4) summary
      cd00051
      Location:102 → 161
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam00153
      Location:296 → 388
      Mito_carr; Mitochondrial carrier protein
      pfam13499
      Location:103 → 158
      EF-hand_7; EF-hand domain pair
      cl08302
      Location:63 → 97
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    3. NM_001265614.3 → NP_001252543.1  mitochondrial adenyl nucleotide antiporter SLC25A25 isoform 5 precursor

      See identical proteins and their annotated locations for NP_001252543.1

      Status: REVIEWED

      Source sequence(s)
      AL360268, AL590708
      Consensus CDS
      CCDS59146.1
      UniProtKB/TrEMBL
      A0A804HLB0
      Related
      ENSP00000362157.5, ENST00000373066.9
      Conserved Domains (4) summary
      cd00051
      Location:102 → 173
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam00153
      Location:308 → 400
      Mito_carr; Mitochondrial carrier protein
      pfam13499
      Location:103 → 170
      EF-hand_7; EF-hand domain pair
      cl08302
      Location:63 → 97
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    4. NM_001330988.2 → NP_001317917.1  mitochondrial adenyl nucleotide antiporter SLC25A25 isoform e

      Status: REVIEWED

      Source sequence(s)
      AL360268, AL590708
      Consensus CDS
      CCDS83420.1
      UniProtKB/Swiss-Prot
      Q6KCM7
      Related
      ENSP00000362160.5, ENST00000373069.10

    5. NM_001387057.1 → NP_001373986.1  mitochondrial adenyl nucleotide antiporter SLC25A25 isoform f

      Status: REVIEWED

      Source sequence(s)
      AL360268, AL590708
      Conserved Domains (5) summary
      PTZ00169
      Location:203 → 457
      PTZ00169; ADP/ATP transporter on adenylate translocase; Provisional
      cd15898
      Location:82 → 111
      EFh_PI-PLC; EF-hand motif [structural motif]
      cd15897
      Location:53 → 77
      EFh_PEF; EF-hand motif [structural motif]
      cl28895
      Location:82 → 171
      EFh_PI-PLC; EF-hand motif found in eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) isozymes
      cl25352
      Location:53 → 125
      EFh_PEF; The penta-EF hand (PEF) family

    6. NM_052901.5 → NP_443133.2  mitochondrial adenyl nucleotide antiporter SLC25A25 isoform a

      See identical proteins and their annotated locations for NP_443133.2

      Status: REVIEWED

      Source sequence(s)
      AL360268, AL590708
      Consensus CDS
      CCDS6890.1
      UniProtKB/Swiss-Prot
      Q5SYW7, Q5SYW8, Q5SYX3, Q5VWU2, Q5VWU3, Q5VWU4, Q6KCM4, Q6KCM6, Q6KCM7, Q6UX48, Q705K2, Q96PZ1, Q9BSA6
      Related
      ENSP00000362155.5, ENST00000373064.9
      Conserved Domains (3) summary
      cd15897
      Location:53 → 77
      EFh_PEF; EF-hand motif [structural motif]
      cl25352
      Location:53 → 139
      EFh_PEF; The penta-EF hand (PEF) family
      cl28162
      Location:191 → 445
      Mito_carr; Mitochondrial carrier protein

    RNA

    1. NR_049766.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL360268, AL590708
      Related
      ENST00000683206.1

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      128068232..128109245
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      140276208..140317210
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001006643.1: Suppressed sequence

      Description
      NM_001006643.1: 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
    Q6KCM7.1 GenPept UniProtKB/Swiss-Prot:Q6KCM7

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