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

Gene ID: 153328, updated on 3-Apr-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 acyl carnitine transmembrane transporter activity. Predicted to be involved in acyl carnitine transport and amino acid transport. Predicted to be located in mitochondrial inner membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in kidney (RPKM 2.6), skin (RPKM 1.9) and 10 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (135579172..135888637)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (136106315..136411134)
105.20220307 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
  • 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. The mitochondrial transporter family SLC25: identification, properties and physiopathology. Palmieri F. Mol Aspects Med, 2013 Apr-Jun. PMID 23266187
  2. 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
  3. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. Comuzzie AG, et al. PLoS One, 2012. PMID 23251661, Free PMC Article
  4. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. Hendrickson SL, et al. PLoS One, 2010 Sep 21. PMID 20877624, Free PMC Article
  5. Cell cycle-dependent phosphorylation regulates RECQL4 pathway choice and ubiquitination in DNA double-strand break repair. Lu H, et al. Nat Commun, 2017 Dec 11. PMID 29229926, Free PMC Article

See all (13) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Compares and contrasts all the known human SLC25A* genes and includes functional information.
    Title: The mitochondrial transporter family SLC25: identification, properties and physiopathology.
  2. 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
  
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
solute carrier family 25 member 48
Names
CTC-321K16.1

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_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_2023_10

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

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