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    SLC25A48 solute carrier family 25 member 48 [ Homo sapiens (human) ]

    Gene ID: 153328, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SLC25A48provided by HGNC
    Official Full Name
    solute carrier family 25 member 48provided by HGNC
    Primary source
    HGNC:HGNC:30451
    See related
    Ensembl:ENSG00000145832 MIM:616150; AllianceGenome:HGNC:30451
    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
    Summary
    Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in mitochondrial inner membrane. Predicted to be active in mitochondrion. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in kidney (RPKM 2.6), skin (RPKM 1.9) and 10 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC25A48 in Genome Data Viewer
    Location:
    5q31.1
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (135579172..135888637)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (136106315..136411134)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (134914862..135224326)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 242 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:134871641-134872156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:134877514-134878015 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:134878708-134879599 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:134879600-134880490 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:134880491-134881382 Neighboring gene neurogenin 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:134900858-134901378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:134904009-134904938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:134905671-134906171 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:134920433-134920934 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:134938767-134939339 Neighboring gene C-X-C motif chemokine ligand 14 Neighboring gene SLC25A48 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:135029067-135029568 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:135029569-135030068 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:135068290-135069074 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:135070567-135071066 Neighboring gene microRNA 5692c-1 Neighboring gene uncharacterized LOC107986453 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:135169317-135169818 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:135213247-135213748 Neighboring gene uncharacterized LOC124901074 Neighboring gene interleukin 9 Neighboring gene F-box and leucine rich repeat protein 21, 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 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. SLC25A48 influences plasma levels of choline and localizes to the inner mitochondrial membrane. Bernard DJ, et al. Mol Genet Metab, 2024 Sep-Oct. PMID 39047301
    2. Metabolic gene function discovery platform GeneMAP identifies SLC25A48 as necessary for mitochondrial choline import. Khan A, et al. Nat Genet, 2024 Aug. PMID 38977856
    3. SLC25A48 controls mitochondrial choline import and metabolism. Verkerke ARP, et al. Cell Metab, 2024 Sep 3. PMID 39111307
    4. The mitochondrial transporter family SLC25: identification, properties and physiopathology. Palmieri F. Mol Aspects Med, 2013 Apr-Jun. PMID 23266187
    5. Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity. Hosgood HD 3rd, et al. Occup Environ Med, 2009 Dec. PMID 19773279, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SLC25A48 influences plasma levels of choline and localizes to the inner mitochondrial membrane.
      Title: SLC25A48 influences plasma levels of choline and localizes to the inner mitochondrial membrane.
    2. Metabolic gene function discovery platform GeneMAP identifies SLC25A48 as necessary for mitochondrial choline import.
      Title: Metabolic gene function discovery platform GeneMAP identifies SLC25A48 as necessary for mitochondrial choline import.
    3. SLC25A48 controls mitochondrial choline import and metabolism.
      Title: SLC25A48 controls mitochondrial choline import and metabolism.
    4. Compares and contrasts all the known human SLC25A* genes and includes functional information.
      Title: The mitochondrial transporter family SLC25: identification, properties and physiopathology.
    5. 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

    EBI GWAS Catalog

    Description
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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

    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in transmembrane transport IEA
    Inferred from Electronic Annotation
    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
    solute carrier family 25 member 48
    Names
    CTC-321K16.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001349335.2 → NP_001336264.1  solute carrier family 25 member 48 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in its 5' UTR, lacks part of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AC011427, AC034206, AC114296, BC025747, BM704498
      Consensus CDS
      CCDS87323.1
      UniProtKB/TrEMBL
      J3KQI1
      Related
      ENSP00000493514.1, ENST00000646290.1
      Conserved Domains (1) summary
      pfam00153
      Location:166 → 242
      Mito_carr; Mitochondrial carrier protein

    2. NM_001349336.2 → NP_001336265.1  solute carrier family 25 member 48 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest isoform (1).
      Source sequence(s)
      AC011427, BC025747, BG700532, BM704498
      Consensus CDS
      CCDS93786.1
      UniProtKB/Swiss-Prot
      Q6ZT89, Q8TAV9
      Related
      ENSP00000506858.1, ENST00000681962.1
      Conserved Domains (1) summary
      pfam00153
      Location:220 → 296
      Mito_carr; Mitochondrial carrier protein

    3. NM_001349345.2 → NP_001336274.1  solute carrier family 25 member 48 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' and 3' UTRs and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at a downstream start codon and cause a frameshift relative to isoform 1. The encoded isoform has a shorter N-terminus and a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC011427, AC034206, AC114296, DB307801, EL949709
      Conserved Domains (1) summary
      cl28162
      Location:53 → 94
      Mito_carr; Mitochondrial carrier protein

    4. NM_145282.5 → NP_660325.4  solute carrier family 25 member 48 isoform 2

      See identical proteins and their annotated locations for NP_660325.4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks several exons and includes an alternate 3' terminal exon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC011427, BC025747, BG700532
      Consensus CDS
      CCDS43366.2
      UniProtKB/Swiss-Prot
      Q6ZT89
      Related
      ENSP00000413049.2, ENST00000412661.3
      Conserved Domains (2) summary
      pfam00153
      Location:6 → 91
      Mito_carr; Mitochondrial carrier protein
      cl28162
      Location:107 → 142
      Mito_carr; Mitochondrial carrier protein

    RNA

    1. NR_146141.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains an alternate internal exon and uses an alternate 3' exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC011427, BC025747, BG700532, DB307801, EL949709

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      135579172..135888637
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006714550.2 → XP_006714613.1  solute carrier family 25 member 48 isoform X6

      Conserved Domains (2) summary
      PTZ00168
      Location:5 → 265
      PTZ00168; mitochondrial carrier protein; Provisional
      pfam00153
      Location:6 → 91
      Mito_carr; Mitochondrial carrier protein

    2. XM_011543199.2 → XP_011541501.1  solute carrier family 25 member 48 isoform X9

      Conserved Domains (1) summary
      pfam00153
      Location:6 → 91
      Mito_carr; Mitochondrial carrier protein

    3. XM_006714544.2 → XP_006714607.1  solute carrier family 25 member 48 isoform X2

      UniProtKB/TrEMBL
      A0A3B3IRS1
      Related
      ENSP00000496992.1, ENST00000510147.2
      Conserved Domains (1) summary
      pfam00153
      Location:6 → 91
      Mito_carr; Mitochondrial carrier protein

    4. XM_005271903.2 → XP_005271960.1  solute carrier family 25 member 48 isoform X8

      Conserved Domains (1) summary
      pfam00153
      Location:6 → 91
      Mito_carr; Mitochondrial carrier protein

    5. XM_017009091.2 → XP_016864580.1  solute carrier family 25 member 48 isoform X10

    6. XM_047416806.1 → XP_047272762.1  solute carrier family 25 member 48 isoform X11

    7. XM_047416807.1 → XP_047272763.1  solute carrier family 25 member 48 isoform X12

    8. XM_006714552.3 → XP_006714615.1  solute carrier family 25 member 48 isoform X13

      Conserved Domains (1) summary
      pfam00153
      Location:6 → 91
      Mito_carr; Mitochondrial carrier protein

    9. XM_017009088.2 → XP_016864577.1  solute carrier family 25 member 48 isoform X3

      UniProtKB/Swiss-Prot
      Q6ZT89, Q8TAV9
      Related
      ENSP00000497060.1, ENST00000650267.1
      Conserved Domains (1) summary
      pfam00153
      Location:220 → 296
      Mito_carr; Mitochondrial carrier protein

    10. XM_017009089.2 → XP_016864578.1  solute carrier family 25 member 48 isoform X5

    11. XM_011543196.2 → XP_011541498.1  solute carrier family 25 member 48 isoform X7

      Conserved Domains (1) summary
      pfam00153
      Location:6 → 91
      Mito_carr; Mitochondrial carrier protein

    12. XM_017009087.2 → XP_016864576.1  solute carrier family 25 member 48 isoform X3

      UniProtKB/Swiss-Prot
      Q6ZT89, Q8TAV9
      Related
      ENSP00000399834.3, ENST00000433282.6
      Conserved Domains (1) summary
      pfam00153
      Location:220 → 296
      Mito_carr; Mitochondrial carrier protein

    13. XM_047416804.1 → XP_047272760.1  solute carrier family 25 member 48 isoform X1

    14. XM_047416805.1 → XP_047272761.1  solute carrier family 25 member 48 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      136106315..136411134
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351778.1 → XP_054207753.1  solute carrier family 25 member 48 isoform X6

    2. XM_054351781.1 → XP_054207756.1  solute carrier family 25 member 48 isoform X9

    3. XM_054351773.1 → XP_054207748.1  solute carrier family 25 member 48 isoform X2

    4. XM_054351780.1 → XP_054207755.1  solute carrier family 25 member 48 isoform X8

    5. XM_054351782.1 → XP_054207757.1  solute carrier family 25 member 48 isoform X10

    6. XM_054351783.1 → XP_054207758.1  solute carrier family 25 member 48 isoform X11

    7. XM_054351784.1 → XP_054207759.1  solute carrier family 25 member 48 isoform X12

    8. XM_054351785.1 → XP_054207760.1  solute carrier family 25 member 48 isoform X13

    9. XM_054351775.1 → XP_054207750.1  solute carrier family 25 member 48 isoform X3

      UniProtKB/Swiss-Prot
      Q6ZT89, Q8TAV9

    10. XM_054351777.1 → XP_054207752.1  solute carrier family 25 member 48 isoform X5

    11. XM_054351779.1 → XP_054207754.1  solute carrier family 25 member 48 isoform X7

    12. XM_054351774.1 → XP_054207749.1  solute carrier family 25 member 48 isoform X3

      UniProtKB/Swiss-Prot
      Q6ZT89, Q8TAV9

    13. XM_054351772.1 → XP_054207747.1  solute carrier family 25 member 48 isoform X1

    14. XM_054351776.1 → XP_054207751.1  solute carrier family 25 member 48 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZT89.2 GenPept UniProtKB/Swiss-Prot:Q6ZT89

    Gene LinkOut

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

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