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Atlas / Gene / SLC25A48

SLC25A48

gene
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Also known as FLJ44862

Summary

SLC25A48 (solute carrier family 25 member 48, HGNC:30451) is a protein-coding gene on chromosome 5q31.1, encoding Solute carrier family 25 member 48 (Q6ZT89). Mitochondrial transporter that transports choline across the inner mitochondrial membrane.

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.

Source: NCBI Gene 153328 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 28 total
  • MANE Select transcript: NM_001349336

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30451
Approved symbolSLC25A48
Namesolute carrier family 25 member 48
Location5q31.1
Locus typegene with protein product
StatusApproved
AliasesFLJ44862
Ensembl geneENSG00000145832
Ensembl biotypeprotein_coding
OMIM616150
Entrez153328

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 14 protein_coding, 4 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000274513, ENST00000412661, ENST00000425402, ENST00000433282, ENST00000462340, ENST00000471980, ENST00000510147, ENST00000646290, ENST00000647391, ENST00000650267, ENST00000681962, ENST00000698885, ENST00000698886, ENST00000868041, ENST00000868042, ENST00000868043, ENST00000868044, ENST00000919114, ENST00000919115

RefSeq mRNA: 4 — MANE Select: NM_001349336 NM_001349335, NM_001349336, NM_001349345, NM_145282

CCDS: CCDS43366, CCDS87323, CCDS93786

Canonical transcript exons

ENST00000681962 — 8 exons

ExonStartEnd
ENSE00001600103135874021135874154
ENSE00001628402135871461135871718
ENSE00003601434135842416135842459
ENSE00003614465135850425135850496
ENSE00003756625135852563135852821
ENSE00003828531135879968135880097
ENSE00003918361135888032135888637
ENSE00003918648135834663135834893

Expression profiles

Bgee: expression breadth ubiquitous, 169 present calls, max score 93.70.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.9275 / max 186.4196, expressed in 177 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
586620.5135115
586560.230886
586570.074131
586590.047316
586580.032512
586550.029410

Top tissues by expression

246 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
tibial nerveUBERON:000132393.70gold quality
sural nerveUBERON:001548890.98gold quality
amygdalaUBERON:000187686.68gold quality
tibiaUBERON:000097985.65gold quality
hypothalamusUBERON:000189884.84gold quality
caudate nucleusUBERON:000187384.68gold quality
putamenUBERON:000187483.59gold quality
anterior cingulate cortexUBERON:000983583.15gold quality
right frontal lobeUBERON:000281082.66gold quality
Brodmann (1909) area 9UBERON:001354082.03gold quality
prefrontal cortexUBERON:000045181.75gold quality
C1 segment of cervical spinal cordUBERON:000646981.66gold quality
substantia nigraUBERON:000203881.23gold quality
spinal cordUBERON:000224080.68gold quality
nucleus accumbensUBERON:000188280.49gold quality
Ammon’s hornUBERON:000195479.98gold quality
dorsolateral prefrontal cortexUBERON:000983479.57gold quality
metanephros cortexUBERON:001053379.44gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047379.28silver quality
midbrainUBERON:000189178.64gold quality
pancreatic ductal cellCL:000207978.48silver quality
neocortexUBERON:000195078.10gold quality
frontal cortexUBERON:000187078.08gold quality
oocyteCL:000002377.82gold quality
temporal lobeUBERON:000187177.45gold quality
cerebral cortexUBERON:000095677.11gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099175.84gold quality
forebrainUBERON:000189075.49gold quality
ileal mucosaUBERON:000033174.75gold quality
corpus callosumUBERON:000233674.69gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.65

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting SLC25A48, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-569699.9872.364487
HSA-MIR-3605-5P99.9667.12932
HSA-MIR-472999.6972.184233
HSA-MIR-6797-5P99.6166.552084
HSA-MIR-3191-5P99.2466.521722
HSA-MIR-544B99.1867.411632
HSA-MIR-519099.1567.761234
HSA-MIR-3117-5P99.0467.93618
HSA-MIR-509498.6367.111062
HSA-MIR-446398.5666.051071
HSA-MIR-444398.0266.251928
HSA-MIR-432-5P98.0068.13989
HSA-MIR-219B-5P97.9165.80531
HSA-MIR-6515-5P97.0865.481219
HSA-MIR-3194-5P96.8064.901027
HSA-MIR-390796.7665.04662

Literature-anchored findings (GeneRIF, showing 4)

  • Compares and contrasts all the known human SLC25A* genes and includes functional information. (PMID:23266187)
  • Metabolic gene function discovery platform GeneMAP identifies SLC25A48 as necessary for mitochondrial choline import. (PMID:38977856)
  • SLC25A48 influences plasma levels of choline and localizes to the inner mitochondrial membrane. (PMID:39047301)
  • SLC25A48 controls mitochondrial choline import and metabolism. (PMID:39111307)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioslc25a48ENSDARG00000021250
mus_musculusSlc25a48ENSMUSG00000021509
rattus_norvegicusSlc25a48ENSRNOG00000012040

Paralogs (49): SLC25A13 (ENSG00000004864), SLC25A5 (ENSG00000005022), SLC25A39 (ENSG00000013306), SLC25A40 (ENSG00000075303), SLC25A3 (ENSG00000075415), SLC25A43 (ENSG00000077713), SLC25A24 (ENSG00000085491), SLC25A1 (ENSG00000100075), SLC25A17 (ENSG00000100372), SLC25A14 (ENSG00000102078), SLC25A15 (ENSG00000102743), SLC25A11 (ENSG00000108528), UCP1 (ENSG00000109424), SLC25A36 (ENSG00000114120), SLC25A12 (ENSG00000115840), SLC25A2 (ENSG00000120329), SLC25A51 (ENSG00000122696), SLC25A16 (ENSG00000122912), SLC25A35 (ENSG00000125434), SLC25A19 (ENSG00000125454), SLC25A23 (ENSG00000125648), SLC25A47 (ENSG00000140107), SLC25A52 (ENSG00000141437), SLC25A38 (ENSG00000144659), SLC25A26 (ENSG00000144741), SLC25A37 (ENSG00000147454), SLC25A25 (ENSG00000148339), SLC25A31 (ENSG00000151475), SLC25A4 (ENSG00000151729), SLC25A27 (ENSG00000153291), SLC25A28 (ENSG00000155287), SLC25A44 (ENSG00000160785), SLC25A45 (ENSG00000162241), SLC25A34 (ENSG00000162461), SLC25A32 (ENSG00000164933), SLC25A6 (ENSG00000169100), SLC25A33 (ENSG00000171612), SLC25A30 (ENSG00000174032), UCP3 (ENSG00000175564), UCP2 (ENSG00000175567)

Protein

Protein identifiers

Solute carrier family 25 member 48 — Q6ZT89 (reviewed: Q6ZT89)

All UniProt accessions (6): A0A3B3IRS1, A0A3B3IS12, C9JM56, D6RFW8, Q6ZT89, J3KQI1

UniProt curated annotations — full annotation on UniProt →

Function. Mitochondrial transporter that transports choline across the inner mitochondrial membrane.

Subcellular location. Mitochondrion membrane. Mitochondrion inner membrane.

Similarity. Belongs to the mitochondrial carrier (TC 2.A.29) family.

Isoforms (3)

UniProt IDNamesCanonical?
Q6ZT89-11yes
Q6ZT89-22
Q6ZT89-33

RefSeq proteins (4): NP_001336264, NP_001336265, NP_001336274, NP_660325 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002067MCPFamily
IPR018108MCP_transmembraneRepeat
IPR023395MCP_dom_sfHomologous_superfamily
IPR050567Mitochondrial_CarrierFamily

Pfam: PF00153

Catalyzed reactions (Rhea), 1 shown:

  • choline(out) = choline(in) (RHEA:32751)

UniProt features (16 total): transmembrane region 6, splice variant 3, mutagenesis site 3, repeat 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6ZT89-F175.590.01

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Mutagenesis-validated functional residues (3):

PositionPhenotype
27does not affect mitochondrion membrane localization. impairs mitochondrial choline uptake.
64does not affect mitochondrion membrane localization. impairs mitochondrial choline uptake.
179reduction of mitochondrial localization. impairs mitochondrial choline uptake.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 51 (showing top): YAO_HOXA10_TARGETS_VIA_PROGESTERONE_UP, MARTINEZ_RB1_TARGETS_UP, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_ORGANIC_CATION_TRANSPORT, MARTINEZ_RB1_AND_TP53_TARGETS_UP, GOBP_TRANSMEMBRANE_TRANSPORT, chr5q31, GOCC_ORGANELLE_INNER_MEMBRANE, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_7, GOMF_TRANSPORTER_ACTIVITY, GOCC_ORGANELLE_ENVELOPE, GOBP_CHOLINE_TRANSPORT, MAFG_TARGET_GENES, ZNF257_TARGET_GENES, ZSCAN31_TARGET_GENES

GO Biological Process (2): choline transport (GO:0015871), transmembrane transport (GO:0055085)

GO Molecular Function (3): choline transmembrane transporter activity (GO:0015220), transmembrane transporter activity (GO:0022857), protein binding (GO:0005515)

GO Cellular Component (4): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), membrane (GO:0016020), mitochondrial membrane (GO:0031966)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
nitrogen compound transport1
transport1
cellular process1
choline transport1
transmembrane transporter activity1
transporter activity1
transmembrane transport1
binding1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
cellular anatomical structure1
mitochondrion1
mitochondrial envelope1
organelle membrane1

Protein interactions and networks

STRING

754 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SLC25A48SLC25A52Q3SY17494
SLC25A48SLC25A51Q9H1U9479
SLC25A48SLC25A46Q96AG3467
SLC25A48SLC16A9Q7RTY1457
SLC25A48TXNDC15Q96J42452
SLC25A48SLC16A5O15375447
SLC25A48SLC25A53Q5H9E4430
SLC25A48TTC23Q5W5X9422
SLC25A48CATSPER3Q86XQ3410
SLC25A48SNAPC1Q16533373
SLC25A48BCKDKO14874357
SLC25A48ABTB3A6QL63349
SLC25A48MLF1P58340340
SLC25A48PDPRQ8NCN5336
SLC25A48MIOXQ9UGB7329

IntAct

22 interactions, top by confidence:

ABTypeScore
KRTAP10-7SLC25A48psi-mi:“MI:0915”(physical association)0.560
TRAF1SLC25A48psi-mi:“MI:0915”(physical association)0.560
SLC25A48PNMA1psi-mi:“MI:0915”(physical association)0.560
UBASH3BSLC25A48psi-mi:“MI:0915”(physical association)0.560
SLC25A48MID2psi-mi:“MI:0915”(physical association)0.560
SLC25A48psi-mi:“MI:0915”(physical association)0.560
SLC25A48KRTAP10-7psi-mi:“MI:0915”(physical association)0.560
MID2SLC25A48psi-mi:“MI:0915”(physical association)0.560
SLC25A48psi-mi:“MI:0915”(physical association)0.560
SLC25A48UBASH3Bpsi-mi:“MI:0915”(physical association)0.560
PNMA1SLC25A48psi-mi:“MI:0915”(physical association)0.560
HMGA1SLC25A48psi-mi:“MI:0915”(physical association)0.400
SLC25A48TPM2psi-mi:“MI:0914”(association)0.350
SLC25A48TXNDC9psi-mi:“MI:0914”(association)0.350

BioGRID (39): SLC25A48 (Two-hybrid), SLC25A48 (Two-hybrid), SLC25A48 (Two-hybrid), SLC25A48 (Two-hybrid), KRTAP10-7 (Two-hybrid), KRTAP10-3 (Two-hybrid), TPM2 (Affinity Capture-MS), RNF11 (Affinity Capture-MS), EEF2 (Affinity Capture-MS), ANKRD40 (Affinity Capture-MS), SLC25A48 (Affinity Capture-MS), SLC25A48 (Two-hybrid), SLC25A48 (Two-hybrid), SLC25A48 (Two-hybrid), SLC25A48 (Two-hybrid)

ESM2 similar proteins: A0A0U2IR85, A0A3G9HRV8, A4RF23, A5DIS9, F4HW79, G3YC86, G3YD89, G3YFS7, K3VFR5, K7VYZ9, O13844, O60029, O81845, O94370, P04710, P23500, P31692, P32331, P32332, P38152, P38921, P40035, Q03028, Q06143, Q10248, Q12289, Q12375, Q18P97, Q54B67, Q54BM3, Q54FE6, Q55GE2, Q6C107, Q6FTN2, Q6ZT89, Q7DNC3, Q84UC7, Q86AV5, Q8BW66, Q8CFJ7

Diamond homologs: A0A0G2K5L2, A2ADF7, A4QNX2, B0G143, F1LX07, F1LZW6, F1RFX9, O13844, O43772, O75746, P16261, P39953, Q02978, Q08DK4, Q0II44, Q12482, Q1DRJ3, Q21153, Q26365, Q3KQZ1, Q3TZX3, Q4V8K4, Q505J6, Q54QN2, Q54RB9, Q552L9, Q58DS3, Q5B717, Q5RBC8, Q5RD81, Q5SWT3, Q5XIF9, Q5ZKP7, Q66L49, Q68F18, Q6ZT89, Q75AH6, Q7PQV7, Q86AV5, Q8BH59

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

28 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance18
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1986 predictions. Top by Δscore:

VariantEffectΔscore
5:135574566:GCGTA:Gdonor_loss1.0000
5:135574567:CGTA:Cdonor_loss1.0000
5:135574568:GTAC:Gdonor_loss1.0000
5:135574569:TACC:Tdonor_loss1.0000
5:135574570:A:Cdonor_loss1.0000
5:135574571:CCTGC:Cdonor_loss1.0000
5:135578428:ACTC:Adonor_loss1.0000
5:135578430:TCA:Tdonor_loss1.0000
5:135578432:A:ACdonor_gain1.0000
5:135578433:C:CCdonor_gain1.0000
5:135578433:CATAA:Cdonor_gain1.0000
5:135578437:A:Cdonor_gain1.0000
5:135578536:GACCC:Gacceptor_loss1.0000
5:135578540:C:CCacceptor_gain1.0000
5:135578540:CTGC:Cacceptor_loss1.0000
5:135578541:T:Aacceptor_loss1.0000
5:135834890:GGAG:Gdonor_gain1.0000
5:135834891:GAG:Gdonor_gain1.0000
5:135834891:GAGG:Gdonor_gain1.0000
5:135834894:G:Cdonor_loss1.0000
5:135834894:G:GGdonor_gain1.0000
5:135850423:A:AGacceptor_gain1.0000
5:135850424:G:GGacceptor_gain1.0000
5:135850493:GAGT:Gdonor_gain1.0000
5:135850495:GT:Gdonor_gain1.0000
5:135850497:G:GGdonor_gain1.0000
5:135852817:GGACG:Gdonor_gain1.0000
5:135852818:GACG:Gdonor_gain1.0000
5:135852818:GACGG:Gdonor_gain1.0000
5:135852820:CGGTA:Cdonor_loss1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000011934 (5:135651077 G>A,C), RS1000025653 (5:135776274 G>A,C,T), RS1000030070 (5:135858918 G>C), RS1000035649 (5:135803529 T>C), RS1000040909 (5:135786298 TG>T), RS1000048899 (5:135638210 G>A,T), RS1000057718 (5:135873489 G>A,C), RS1000060347 (5:135808004 T>C), RS1000077787 (5:135790550 G>A), RS1000088330 (5:135701763 A>G), RS1000107383 (5:135834364 A>T), RS1000109610 (5:135873751 A>T), RS1000115875 (5:135599222 C>A,T), RS1000134397 (5:135732504 C>G), RS1000150218 (5:135764809 T>G)

Disease associations

OMIM: gene MIM:616150 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

5 associations (top):

StudyTraitp-value
GCST001762_688Obesity-related traits3.000000e-06
GCST004689_1Resistance to Mycobacterium tuberculosis in HIV-positive individuals measured by a negative tuberculin skin test (continuous)7.000000e-08
GCST004690_1Resistance to Mycobacterium tuberculosis in HIV-positive individuals measured by a negative tuberculin skin test (dichotomous)6.000000e-08
GCST006992_1Cerebrospinal fluid p-tau levels in Alzheimer’s disease dementia8.000000e-07
GCST007007_2Cerebrospinal fluid t-tau levels2.000000e-07

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0004810interleukin-6 measurement
EFO:0008307tuberculin skin test reactivity measurement
EFO:0008322decreased susceptibility to bacterial infection
EFO:0004763p-tau measurement
EFO:0004760t-tau measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs7716492CXCL14, SLC25A480.000

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — Miscellaneous SLC25 mitochondrial transporters

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression3
Methapyrilenedecreases expression, increases methylation2
Valproic Acidincreases expression, increases methylation2
Aflatoxin B1decreases expression, decreases methylation2
benzo(e)pyreneincreases methylation1
aflatoxin B2increases methylation1
maleic acidincreases expression1
Air Pollutantsaffects methylation, increases abundance1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Nicotinedecreases expression1
Nitrogen Dioxideincreases abundance, affects methylation1
Cadmium Chlorideincreases expression1
Particulate Matteraffects methylation, increases abundance1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_D4KDHCT116-SLC25A48-KO-c10Cancer cell lineMale
CVCL_D4KEHCT116-SLC25A48-KO-c11Cancer cell lineMale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 75

This page pulls from 75 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgtopdb_interactiongwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot