SLC25A13

gene
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Also known as CITRINARALAR2

Summary

SLC25A13 (solute carrier family 25 member 13, HGNC:10983) is a protein-coding gene on chromosome 7q21.3, encoding Electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrial (Q9UJS0). Mitochondrial electrogenic aspartate/glutamate antiporter that favors efflux of aspartate and entry of glutamate and proton within the mitochondria as part of the malate-aspartate shuttle.

This gene is a member of the mitochondrial carrier family. The encoded protein contains four EF-hand Ca(2+) binding motifs in the N-terminal domain, and localizes to mitochondria. The protein catalyzes the exchange of aspartate for glutamate and a proton across the inner mitochondrial membrane, and is stimulated by calcium on the external side of the inner mitochondrial membrane. Mutations in this gene result in citrullinemia, type II. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 10165 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): citrin deficiency (Definitive, ClinGen) — +3 more curated relationships
  • GWAS associations: 5
  • Clinical variants (ClinVar): 991 total — 102 pathogenic, 91 likely-pathogenic
  • Phenotypes (HPO): 97
  • Druggable target: yes
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity unscored
  • MANE Select transcript: NM_014251

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10983
Approved symbolSLC25A13
Namesolute carrier family 25 member 13
Location7q21.3
Locus typegene with protein product
StatusApproved
AliasesCITRIN, ARALAR2
Ensembl geneENSG00000004864
Ensembl biotypeprotein_coding
OMIM603859
Entrez10165

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 11 protein_coding, 5 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000265631, ENST00000416240, ENST00000472162, ENST00000484495, ENST00000487710, ENST00000490072, ENST00000492869, ENST00000494085, ENST00000856214, ENST00000856215, ENST00000856216, ENST00000856217, ENST00000856218, ENST00000856219, ENST00000856220, ENST00000935610, ENST00000948397

RefSeq mRNA: 2 — MANE Select: NM_014251 NM_001160210, NM_014251

CCDS: CCDS55130, CCDS5645

Canonical transcript exons

ENST00000265631 — 18 exons

ExonStartEnd
ENSE000004344799612183996121997
ENSE000007062769618958196189674
ENSE000007062789618929496189378
ENSE000007062879614655696146696
ENSE000007062919613174396131881
ENSE000007063289612165596121745
ENSE000010868089623480296234917
ENSE000010868119619303796193183
ENSE000010868129619110996191247
ENSE000018301809632194296322098
ENSE000019379679612022096121377
ENSE000035117499618492796185011
ENSE000035411659629689896296951
ENSE000035958429627719696277338
ENSE000036341719620883896208977
ENSE000036357029617147296171524
ENSE000036503029617004596170125
ENSE000036683579618427796184435

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 95.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.7957 / max 325.6449, expressed in 1798 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
8499517.88371793
849960.9646674
849940.4754235
849900.4719151

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right lobe of liverUBERON:000111495.60gold quality
liverUBERON:000210795.52gold quality
secondary oocyteCL:000065594.95gold quality
pigmented layer of retinaUBERON:000178293.89gold quality
retinaUBERON:000096693.86gold quality
tibiaUBERON:000097992.79gold quality
adrenal tissueUBERON:001830392.14gold quality
corpus callosumUBERON:000233691.76gold quality
buccal mucosa cellCL:000233691.39gold quality
choroid plexus epitheliumUBERON:000391191.26gold quality
calcaneal tendonUBERON:000370191.08gold quality
endometrium epitheliumUBERON:000481190.48gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099190.30gold quality
esophagus squamous epitheliumUBERON:000692089.95gold quality
inferior vagus X ganglionUBERON:000536389.92gold quality
nephron tubuleUBERON:000123189.71gold quality
rectumUBERON:000105289.33gold quality
C1 segment of cervical spinal cordUBERON:000646989.18gold quality
oocyteCL:000002389.09gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047388.38gold quality
spinal cordUBERON:000224088.30gold quality
spermCL:000001988.16gold quality
jejunal mucosaUBERON:000039988.12gold quality
squamous epitheliumUBERON:000691488.12gold quality
skin of legUBERON:000151188.09gold quality
right adrenal gland cortexUBERON:003582788.04gold quality
right uterine tubeUBERON:000130287.92gold quality
visceral pleuraUBERON:000240187.69gold quality
transverse colonUBERON:000115787.68gold quality
monocyteCL:000057687.54gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-GEOD-100618yes246.31
E-ANND-3yes8.39

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

54 targeting SLC25A13, 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-3120-5P100.0065.56965
HSA-MIR-3646100.0073.565283
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-6888-3P99.9765.951170
HSA-MIR-335-3P99.9373.364958
HSA-MIR-589-3P99.9169.622088
HSA-MIR-548E-5P99.8972.734486
HSA-MIR-990299.8969.152250
HSA-MIR-629-3P99.8567.991875
HSA-MIR-3663-3P99.8470.39798
HSA-MIR-3681-5P99.8266.88387
HSA-MIR-34B-5P99.7867.561175
HSA-MIR-449C-5P99.7867.631168
HSA-MIR-4713-5P99.7867.801794
HSA-MIR-3150A-3P99.7664.441640
HSA-MIR-6763-5P99.7664.681767
HSA-MIR-2682-5P99.7367.381055
HSA-MIR-471999.7372.103329
HSA-MIR-4524A-3P99.7266.852406
HSA-MIR-317599.6566.302031
HSA-MIR-6849-5P99.6466.00352
HSA-MIR-548AV-5P99.6070.842107
HSA-MIR-548K99.6070.842107
HSA-MIR-129099.5969.902079
HSA-MIR-432899.5771.064094
HSA-MIR-4708-3P99.5167.99870
HSA-MIR-1211799.5067.57868
HSA-MIR-805499.4870.812084
HSA-MIR-183-3P99.4169.411598

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity Not yet evaluated (unscored). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

  • 851del4/1638ins23 mutations in a Chinese adult onset type II citrullinaemia patient (PMID:11432966)
  • genetic screening of mutations in early and late onset patients with citrin deficiency and in the Japanese population: identification of two novel mutations and establishment of multiple DNA diagnosis methods for nine mutations (PMID:11793471)
  • Adult-onset type II citrullinemia is caused by mutations of the SLC25A13 gene (PMID:12111366)
  • Adult-onset type II citrullinemia is caused by mutations of the SLC25A13 gene (PMID:16278034)
  • Adult-onset type II citrullinemia is caused by mutations of the SLC25A13 gene (PMID:16928234)
  • Citrullinemia is a metabolic disorder characterized by elevated plasma concentrations of citrulline and ammonia. Adult-onset citrullinemia (type II, CTLN2) has been attributed to citrin deficiency caused by mutations in the SLC25A13 gene. (PMID:17000460)
  • Analysis of citrin protein in peripheral blood lymphocytes is useful to diagnose citrin deficiency in patients without known mutations or hypercitrullinemia. (PMID:17092749)
  • This report describes the clinical characteristics, biochemical findings and molecular analysis of the SLC25A13 gene of patients with citrin deficiency in Korea. (PMID:17982687)
  • report 13 novel SLC25A13 mutations (one insertion, two deletion, three splice site, two nonsense, and five missense) in patients with citrin deficiency from Japan, Israel, UK, and Czech Republic (PMID:18392553)
  • SLC25A13 gene mutations exist in Chinese infants with intrahepatic cholestasis and abnormal blood amino acids. (PMID:18578996)
  • Patients presenting with non-alcoholic fatty liver unrelated to obesity and metabolic syndrome might have citrin deficiency, caused by SLC25A13 gene mutations. (PMID:18620775)
  • Case Report: suggest that the administration of arginine and sodium pyruvate with low-carbohydrate meals may be an effective therapy in patients with citrin deficiency. (PMID:18958581)
  • 5 novel mutations were found in SLC25A13 from three unrelated French-Canadian Citrin deficiency patients. (PMID:19036621)
  • Results of this study showed, even during the silent period, sustained hypercitrullinemia, hypercholesterolemia, and augmented oxidative stress in children with citrin deficiency. (PMID:19232506)
  • The first two cases of NICCD are described in infants from the UK, one of Caucasian and one of Pakistani origin. (PMID:19517266)
  • The historical aspects of citrin and citrin deficiency, characteristic food preference and food aversion of citrin-deficient subjects, and carbohydrate toxicity in relation to ureogenesis, is described. (PMID:20233664)
  • The 851del4, 1638ins23 and IVS6+5G>A mutations are the hot-spot mutations in Chinese patients with neonatal intrahepatic cholestasis caused by citrin deficiency. (PMID:20376801)
  • Four hundred infants with unexplained intrahepatic cholestasis from 18 China were studied for detecting SLC25A13 gene mutation 851del4. Eight homozygous and 30 heterozygous mutations were detected in 46 mutant alleles with a 851del4 mutation rate of 5.8%. (PMID:20458766)
  • We report three unrelated Malay children with genetically confirmed neonatal intrahepatic cholestatic caused by citrin deficiency characterised by an insertion mutation IVS16ins3kb in SLC25A13 gene (PMID:20614727)
  • MDR analysis provided evidence of interaction between the genes for ASS1 and SLC25A13 on the risk of CL/P. (PMID:20739017)
  • SLC25A13 gene mutations play an important role in Chinese infants with intrahepatic cholestasis and various forms of aminoacidemia; 851del4 and 1638ins23 are the most common mutation types (PMID:20927635)
  • The SLC25A13 mutations may not be a major contributor to the pathogenesis of hepatocellular carcinoma in Taiwan. (PMID:21134364)
  • this study expanded the genotypic and phenotypic spectrum of citrin deficiency. (PMID:21424115)
  • individuals with non-viral HCC were more likely to possess SLC25A13 gene mutations compared to healthy subjects (PMID:21470889)
  • Seven genetic variations of SLC25A13, termed as 851del4, 1638ins23, IVS16ins3kb, IVS6+5G>A, c.775C>T (p.Q259X), c.1505C>T (p.P502L) and c.1311C>T (p.C437C), were identified (PMID:21507300)
  • Functional studies, carried out on the recombinant mutant protein containing glutamate at position 437, demonstrated that neonatal intrahepatic cholestasis caused by citrin deficiency is caused by a reduced transport activity of SLC25A13 (PMID:21914561)
  • Mutations in SLC25A13 are associated with citrin deficiency. (PMID:22277121)
  • A protein encoded by this locus was found to be differentially expressed in postmortem brains from patients with atypical frontotemporal lobar degeneration. (PMID:22360420)
  • In 171 suspected patients, seven neonatal intrahepatic cholestasis caused by citrin deficiency patients were detected by HRM. (PMID:22487826)
  • uncovered the marked transcript diversity of SLC25A13 gene in human PBLs, and suggested that cDNA cloning analysis of this gene in human PBLs might be a feasible tool for CD molecular diagno (PMID:23022256)
  • Analysis of the SLC25A13 gene sequence. (PMID:23053473)
  • The objectives were to study the prevalence of neonatal intrahepatic cholestasis caused by citrin deficiency (NICCD) in Thai infants with idiopathic cholestasis, mutation spectrum of SLC25A13 in Thai NICCD, and comparison of clinical manifestations and blood chemistry between NICCD and non-NICCD infants. (PMID:23067347)
  • Compares and contrasts all the known human SLC25A* genes and includes functional information. (PMID:23266187)
  • The SLC25A13 mutation spectra among the three regions of China were different, providing a basis for the improvement of diagnostic strategies and interpretation of genetic diagnosis. (PMID:23901231)
  • Identification of novel SLC25A13 gene mutations in East Asian patients with citrin deficiency. (PMID:24069319)
  • Report frequency SLC25A13 mutations in the Thai population and estimate prevalence of citrin deficiency. (PMID:24282362)
  • we reviewed the English literature on mutations in the SLC25A13 gene, and its genotype-phenotype correlations to provide valuable insights into the molecular genetic background of citrullinemia–{REVIEW} (PMID:24508627)
  • Point mutation of ASS1, ASL and SLC25A13 is associated with citrullinemia. (PMID:24927999)
  • This study aims to screen for five prevalent SLC25A13 mutations, to calculate the mutation carrier rate in Guangdong. (PMID:25110155)
  • Mutation screening of the SLC25A13 gene revealed the compound heterozygous mutations c.1081C>T (p.R361*) and c.74C>A (p. A25E) which confirmed the diagnosis of NICCD. The nonsense mutation c.1081C>T (p.R361*) is novel. (PMID:25365849)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioslc25a13ENSDARG00000099353
mus_musculusSlc25a13ENSMUSG00000015112
rattus_norvegicusSlc25a13ENSRNOG00000009957

Paralogs (49): 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), SLC25A48 (ENSG00000145832), 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

Electrogenic aspartate/glutamate antiporter SLC25A13, mitochondrialQ9UJS0 (reviewed: Q9UJS0)

Alternative names: Calcium-binding mitochondrial carrier protein Aralar2, Citrin, Mitochondrial aspartate glutamate carrier 2, Solute carrier family 25 member 13

All UniProt accessions (2): Q9UJS0, R4GN64

UniProt curated annotations — full annotation on UniProt →

Function. Mitochondrial electrogenic aspartate/glutamate antiporter that favors efflux of aspartate and entry of glutamate and proton within the mitochondria as part of the malate-aspartate shuttle. Substrate exchange across the membrane occurs consecutively with one substrate being transported first, then dissociating from the substrate binding site before the second substrate binds for transport in the opposite direction. Also mediates the uptake of L-cysteinesulfinate (3-sulfino-L-alanine) by mitochondria in exchange for L-glutamate and proton. Can also exchange L-cysteinesulfinate with aspartate in their anionic form without any proton translocation. Lacks transport activity towards gamma-aminobutyric acid (GABA).

Subunit / interactions. Homodimer (via N-terminus).

Subcellular location. Mitochondrion inner membrane.

Tissue specificity. High levels in liver and low levels in kidney, pancreas, placenta, heart and brain.

Disease relevance. Citrin deficiency, adolescent or adult onset (CDAA) [MIM:603471] An autosomal recessive metabolic disorder characterized by elevated serum and urine citrulline levels, ammonia intoxication, and neuropsychiatric symptoms including abnormal behaviors, loss of memory, seizures and coma. Death can result from brain edema. The disease is caused by variants affecting the gene represented in this entry. Citrin deficiency, neonatal or infantile onset (CDNI) [MIM:605814] An autosomal recessive metabolic disorder characterized by increased serum citrulline, poor growth, and neonatal intrahepatic cholestasis with suppression of the bile flow, hepatic fibrosis and variable liver dysfunction. Most patients show spontaneous improvement of symptoms by 1 year of age. However, some affected individuals may develop chronic or fatal liver disease. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. Activated by calcium-binding in the mitochondrial intermembrane space. Inhibited by pyridoxal 5’-phosphate, bathophenathroline, mercurials, diethyl pyrocarbonate and N-ethylmaleimide.

Domain organisation. The EF-hand 2 domain within the regulatory N-terminal domain binds one calcium in the mitochondrial intermembrane space. Calcium triggers the binding of the regulatory N-terminal domain to the C-terminal domain, opening a vestibule which allows the substrates to be translocated through the carrier domain. In the absence of calcium, the linker loop domain may close the vestibule and prevent substrates from entering the carrier domain.

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

Isoforms (2)

UniProt IDNamesCanonical?
Q9UJS0-11yes
Q9UJS0-22

RefSeq proteins (2): NP_001153682, NP_055066* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002048EF_hand_domDomain
IPR002067MCPFamily
IPR011992EF-hand-dom_pairHomologous_superfamily
IPR018108MCP_transmembraneRepeat
IPR023395MCP_dom_sfHomologous_superfamily
IPR051028Mito_Solute_CarrierFamily

Pfam: PF00153

Catalyzed reactions (Rhea), 3 shown:

  • L-aspartate(in) + L-glutamate(out) + H(+)(out) = L-aspartate(out) + L-glutamate(in) + H(+)(in) (RHEA:70783)
  • 3-sulfino-L-alanine(out) + L-glutamate(in) + H(+)(in) = 3-sulfino-L-alanine(in) + L-glutamate(out) + H(+)(out) (RHEA:70967)
  • 3-sulfino-L-alanine(out) + L-aspartate(in) = 3-sulfino-L-alanine(in) + L-aspartate(out) (RHEA:70975)

UniProt features (100 total): mutagenesis site 26, helix 20, modified residue 9, topological domain 7, transmembrane region 6, strand 6, binding site 5, domain 4, region of interest 4, repeat 3, sequence variant 3, sequence conflict 2, turn 2, initiator methionine 1, chain 1, splice variant 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
4P5WX-RAY DIFFRACTION2.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UJS0-F183.090.36

Functional residue map

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

Ligand- & substrate-binding residues (5): 66; 68; 70; 72; 77

Post-translational modifications (9): 2, 353, 372, 453, 484, 484, 580, 662, 666

Mutagenesis-validated functional residues (26):

PositionPhenotype
25reduces transporter activity.
39no effect on mitochondrial localization.
66does not affect transporter activity, folding, dimeric state or mitochondrial localization; when associated with a-68, a
68does not affect transporter activity, folding, dimeric state or mitochondrial localization; when associated with a-66, a
70does not affect transporter activity, folding, dimeric state or mitochondrial localization; when associated with a-66, a
74slightly reduces transporter activity.
77does not affect transporter activity, folding, dimeric state or mitochondrial localization; when associated with a-66, a
85increases transporter activity.
95reduces transporter activity.
139reduces transporter activity.
176reduces transporter activity.
350reduces transporter activity.
355reduces transporter activity.
393reduces transporter activity.
405abolishes transporter activity.
453slightly reduces transporter activity.
455abolishes transporter activity.
489abolishes transporter activity.
493abolishes transporter activity.
500primarily cytoplasmic.
531reduces transporter activity.
546abolishes transporter activity.
585abolishes transporter activity.
588reduces mitochondrial localization.
588abolishes transporter activity.

Function

Pathways and Gene Ontology

Reactome pathways

8 pathways

IDPathway
R-HSA-1268020Mitochondrial protein import
R-HSA-8963693Aspartate and asparagine metabolism
R-HSA-9856872Malate-aspartate shuttle
R-HSA-1428517Aerobic respiration and respiratory electron transport
R-HSA-1430728Metabolism
R-HSA-611105Respiratory electron transport
R-HSA-71291Metabolism of amino acids and derivatives
R-HSA-9609507Protein localization

MSigDB gene sets: 443 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, BROWNE_HCMV_INFECTION_16HR_UP, TGACCTY_ERR1_Q2, GOBP_NUCLEOSIDE_PHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_AMINO_ACID_TRANSMEMBRANE_TRANSPORT, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, SHIPP_DLBCL_CURED_VS_FATAL_DN, GOBP_MITOCHONDRIAL_TRANSPORT, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_NADPLUS_METABOLIC_PROCESS, GOBP_MONOATOMIC_CATION_TRANSPORT, GOBP_ORGANIC_ACID_TRANSPORT, GOBP_RESPONSE_TO_METAL_ION

GO Biological Process (12): gluconeogenesis (GO:0006094), ATP biosynthetic process (GO:0006754), mitochondrial transport (GO:0006839), aspartate transmembrane transport (GO:0015810), L-glutamate transmembrane transport (GO:0015813), malate-aspartate shuttle (GO:0043490), cellular respiration (GO:0045333), response to calcium ion (GO:0051592), neutral amino acid transport (GO:0015804), transmembrane transport (GO:0055085), L-aspartate transmembrane transport (GO:0070778), proton transmembrane transport (GO:1902600)

GO Molecular Function (9): 3-sulfino-L-alanine: proton, glutamate antiporter activity (GO:0000514), aspartate:glutamate, proton antiporter activity (GO:0000515), L-glutamate transmembrane transporter activity (GO:0005313), calcium ion binding (GO:0005509), L-aspartate transmembrane transporter activity (GO:0015183), identical protein binding (GO:0042802), protein binding (GO:0005515), acidic amino acid transmembrane transporter activity (GO:0015172), metal ion binding (GO:0046872)

GO Cellular Component (4): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), plasma membrane (GO:0005886), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-5 pathways:

CategoryPathways
Metabolism2
Protein localization1
Metabolism of amino acids and derivatives1
Respiratory electron transport1
Aerobic respiration and respiratory electron transport1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
L-amino acid transmembrane transporter activity3
acidic amino acid transport2
L-alpha-amino acid transmembrane transport2
dicarboxylic acid transmembrane transporter activity2
acidic amino acid transmembrane transporter activity2
glucose metabolic process1
hexose biosynthetic process1
purine ribonucleotide biosynthetic process1
purine ribonucleoside triphosphate biosynthetic process1
ATP metabolic process1
intracellular transport1
amino acid transmembrane transport1
C4-dicarboxylate transport1
nitrogen compound transport1
carboxylic acid transmembrane transport1
L-glutamate import1
L-aspartate:2-oxoglutarate transaminase activity1
NAD+ metabolic process1
L-malate dehydrogenase (NAD+) activity1
mitochondrial transmembrane transport1
energy derivation by oxidation of organic compounds1
response to metal ion1
amino acid transport1
transport1
cellular process1
aspartate transmembrane transport1
monoatomic cation transmembrane transport1
sulfur amino acid transmembrane transporter activity1
proton transmembrane transporter activity1
neutral L-amino acid transmembrane transporter activity1
modified amino acid transmembrane transporter activity1
amino acid:monoatomic cation antiporter activity1
L-aspartate transmembrane transporter activity1
L-glutamate:proton antiporter activity1
L-glutamate transmembrane transport1
metal ion binding1
C4-dicarboxylate transmembrane transporter activity1
L-aspartate transmembrane transport1
protein binding1
binding1

Protein interactions and networks

STRING

1370 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SLC25A13ASS1P00966946
SLC25A13TIMM13P62206928
SLC25A13TIMM8AO60220872
SLC25A13TIMM23O14925856
SLC25A13TIMM9Q9Y5J7717
SLC25A13TIMM10P62072656
SLC25A13NAGSQ8N159609
SLC25A13RALGAPBQ86X10547
SLC25A13SLC25A11Q02978536
SLC25A13MTCH1Q9NZJ7529
SLC25A13TIMM22Q9Y584519
SLC25A13MCUQ8NE86508
SLC25A13ASLP04424507
SLC25A13OTCP00480506
SLC25A13MIMS1Q96ND0505

IntAct

178 interactions, top by confidence:

ABTypeScore
IKBKBCHUKpsi-mi:“MI:0914”(association)0.960
RAD51DRAD51Bpsi-mi:“MI:0914”(association)0.850
CTSVCTSLpsi-mi:“MI:0914”(association)0.720
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
CFTRESYT2psi-mi:“MI:0914”(association)0.710
IFT27IFT56psi-mi:“MI:0914”(association)0.690
SLC25A13SLC25A12psi-mi:“MI:0915”(physical association)0.690
TIMM10AGKpsi-mi:“MI:0914”(association)0.640
CANXPGRMC1psi-mi:“MI:0914”(association)0.570
ILKHAX1psi-mi:“MI:0914”(association)0.530
IRAK1SEC16Apsi-mi:“MI:0914”(association)0.530
COQ2SLC25A5psi-mi:“MI:0914”(association)0.530
GRB2SH3PXD2Bpsi-mi:“MI:0914”(association)0.530
DDX21MED19psi-mi:“MI:2364”(proximity)0.480
TUBA1ATUBAL3psi-mi:“MI:0914”(association)0.420
SLC25A13APODpsi-mi:“MI:0915”(physical association)0.400
KLK10SLC25A13psi-mi:“MI:0915”(physical association)0.400
AATKDPM1psi-mi:“MI:0914”(association)0.350
ARAFPPP6Cpsi-mi:“MI:0914”(association)0.350
LIMK2CALUpsi-mi:“MI:0914”(association)0.350
SIK2BAG2psi-mi:“MI:0914”(association)0.350
OTUB1psi-mi:“MI:0914”(association)0.350
OTUB1EPM2Apsi-mi:“MI:0914”(association)0.350

BioGRID (347): SLC25A13 (Affinity Capture-MS), SLC25A13 (Affinity Capture-MS), SLC25A13 (Affinity Capture-MS), SLC25A13 (Affinity Capture-MS), SLC25A13 (Affinity Capture-MS), SLC25A13 (Affinity Capture-MS), SLC25A13 (Affinity Capture-MS), SLC25A13 (Affinity Capture-MS), SLC25A13 (Affinity Capture-MS), SLC25A13 (Affinity Capture-MS), SLC25A13 (Affinity Capture-MS), ELAVL1 (Co-fractionation), IMMT (Co-fractionation), SLC25A13 (Affinity Capture-MS), SLC25A13 (Affinity Capture-MS)

ESM2 similar proteins: A2ASZ8, A2CEQ0, A5PJZ1, B4F8I5, B8ZHC9, F1LX07, F1LZW6, F4HW79, F4JU70, K7VYZ9, O13805, O18757, O65023, O75746, P0C546, Q05AQ3, Q0P483, Q0V7M4, Q19529, Q20799, Q21153, Q5PQ27, Q5RBC8, Q5XH95, Q5XHA0, Q628Z2, Q66L49, Q6C107, Q6GQS1, Q6KCM7, Q6NUK1, Q6NYZ6, Q7T0U6, Q7ZY36, Q7ZYD5, Q86VD7, Q8BH59, Q8BMD8, Q8BVN7, Q8HXW2

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

3 interactions.

AEffectBMechanism
calcium(2+)“up-regulates activity”SLC25A13“chemical activation”
SLC25A13“down-regulates quantity”“glutamic acid”relocalization
SLC25A13“up-regulates quantity”“aspartic acid”relocalization

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 212 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Resolution of D-loop Structures through Holliday Junction Intermediates612.1×4e-03
Homology Directed Repair510.4×7e-03
HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)510.4×7e-03
TAK1-dependent IKK and NF-kappa-B activation510.1×7e-03
Selective autophagy59.3×7e-03
Adherens junctions interactions58.3×9e-03
DNA Double-Strand Break Repair58.3×9e-03
Aggrephagy58.3×9e-03

GO biological processes:

GO termPartnersFoldFDR
pre-miRNA processing531.2×5e-04
obsolete protein targeting to mitochondrion516.1×9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic102
Likely pathogenic91
Uncertain significance237
Likely benign419
Benign34

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1068567NM_014251.3(SLC25A13):c.420del (p.Glu141fs)Pathogenic
1069861NC_000007.13:g.(?95906498)(95906660_?)delPathogenic
1070090NM_014251.3(SLC25A13):c.475C>T (p.Gln159Ter)Pathogenic
1070408NM_014251.3(SLC25A13):c.1751-5_1751-4insGATTTCTCCATTTTTTTTTTTTTTTTTNNNNNNNNNNGTCCCCCCGCCCCCCGAGCCCGAACCCCTTTCCACTGCCAACACCTCACCTCGCCCCCGCCGCCATCTTCCTCCTCCCTTGGCAGCCCCGCCCCCCPathogenic
1071593NM_014251.3(SLC25A13):c.1173dup (p.Arg392Ter)Pathogenic
1071972NC_000007.13:g.(?95838140)(95838299_?)delPathogenic
1071973NC_000007.13:g.(?95761045)(95761203_?)dupPathogenic
1073569NM_014251.3(SLC25A13):c.792del (p.Thr265fs)Pathogenic
1075398NM_014251.3(SLC25A13):c.1063C>G (p.Arg355Gly)Pathogenic
1075399NM_014251.3(SLC25A13):c.173_174del (p.Val58fs)Pathogenic
1351050NM_014251.3(SLC25A13):c.1633_1637dup (p.Leu548fs)Pathogenic
1359671NM_014251.3(SLC25A13):c.1603_1609dup (p.Leu537fs)Pathogenic
1361197NM_014251.3(SLC25A13):c.1228dup (p.Thr410fs)Pathogenic
1366582NM_014251.3(SLC25A13):c.132C>G (p.Tyr44Ter)Pathogenic
1379532NM_014251.3(SLC25A13):c.1610del (p.Ser536_Leu537insTer)Pathogenic
1382583NM_014251.3(SLC25A13):c.1486_1489del (p.Phe496fs)Pathogenic
1385282NM_014251.3(SLC25A13):c.1612del (p.Leu537_Val538insTer)Pathogenic
1386444NM_014251.3(SLC25A13):c.94G>T (p.Glu32Ter)Pathogenic
1388183NM_014251.3(SLC25A13):c.1453-2A>TPathogenic
1401121NM_014251.3(SLC25A13):c.848+1G>APathogenic
1405696NM_014251.3(SLC25A13):c.1324C>T (p.Gln442Ter)Pathogenic
1408381NM_014251.3(SLC25A13):c.124del (p.Thr42fs)Pathogenic
1420534NM_014251.3(SLC25A13):c.1416_1419del (p.Val473fs)Pathogenic
1425711NM_014251.3(SLC25A13):c.111del (p.Asn38fs)Pathogenic
1451917NM_014251.3(SLC25A13):c.1095del (p.Phe365fs)Pathogenic
1453939NM_014251.3(SLC25A13):c.457C>T (p.Gln153Ter)Pathogenic
1458599NM_014251.3(SLC25A13):c.640C>T (p.Gln214Ter)Pathogenic
1458843NC_000007.13:g.(?95812693)(95813744_?)delPathogenic
1459235NM_014251.3(SLC25A13):c.1075C>T (p.Gln359Ter)Pathogenic
1459776NC_000007.13:g.(?95749522)(95751319_?)delPathogenic

SpliceAI

4311 predictions. Top by Δscore:

VariantEffectΔscore
7:96121374:TTTT:Tacceptor_gain1.0000
7:96121375:TTT:Tacceptor_gain1.0000
7:96121376:TT:Tacceptor_gain1.0000
7:96121376:TTCTA:Tacceptor_loss1.0000
7:96121377:TC:Tacceptor_loss1.0000
7:96121378:C:CCacceptor_gain1.0000
7:96121379:T:Cacceptor_loss1.0000
7:96121646:GATAC:Gdonor_loss1.0000
7:96121649:AC:Adonor_loss1.0000
7:96121650:CT:Cdonor_loss1.0000
7:96121651:TTAC:Tdonor_loss1.0000
7:96121652:TACAC:Tdonor_loss1.0000
7:96121653:A:ACdonor_gain1.0000
7:96121653:A:Cdonor_loss1.0000
7:96121653:ACACT:Adonor_gain1.0000
7:96121654:C:CAdonor_gain1.0000
7:96121654:CA:Cdonor_gain1.0000
7:96121654:CACT:Cdonor_gain1.0000
7:96121654:CACTC:Cdonor_gain1.0000
7:96121742:CGAG:Cacceptor_gain1.0000
7:96121746:C:CCacceptor_gain1.0000
7:96121747:T:Cacceptor_gain1.0000
7:96121748:T:Cacceptor_gain1.0000
7:96121748:T:TCacceptor_gain1.0000
7:96121834:CATA:Cdonor_loss1.0000
7:96121835:ATACC:Adonor_loss1.0000
7:96121836:TA:Tdonor_loss1.0000
7:96121838:CCA:Cdonor_gain1.0000
7:96121847:C:CAdonor_gain1.0000
7:96121851:T:TAdonor_gain1.0000

AlphaMissense

4364 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:96121717:A:CF593L1.000
7:96121717:A:TF593L1.000
7:96121719:A:GF593L1.000
7:96121894:G:CC565W1.000
7:96121954:C:AK545N1.000
7:96121954:C:GK545N1.000
7:96121965:C:GD542H1.000
7:96131856:T:GD493A1.000
7:96131857:C:GD493H1.000
7:96146649:C:AK453N1.000
7:96146649:C:GK453N1.000
7:96146667:A:CN447K1.000
7:96146667:A:TN447K1.000
7:96184277:C:GG393R1.000
7:96184323:A:CC377W1.000
7:96184383:C:AQ357H1.000
7:96184383:C:GQ357H1.000
7:96184395:T:AK353N1.000
7:96184395:T:GK353N1.000
7:96184402:A:GL351P1.000
7:96184405:T:CD350G1.000
7:96184405:T:GD350A1.000
7:96184406:C:GD350H1.000
7:96184430:C:GG342R1.000
7:96184430:C:TG342R1.000
7:96121715:C:TG594D0.999
7:96121718:A:CF593C0.999
7:96121718:A:GF593S0.999
7:96121720:C:AQ592H0.999
7:96121720:C:GQ592H0.999

dbSNP variants (sampled 300 via entrez): RS1000007122 (7:96295254 C>G), RS1000009566 (7:96122988 C>T), RS1000014049 (7:96152475 G>A), RS1000047320 (7:96309164 C>T), RS1000087678 (7:96159031 T>C), RS1000093526 (7:96288932 T>C,G), RS1000102161 (7:96205292 T>A), RS1000123398 (7:96203911 G>A), RS1000156296 (7:96248035 C>A), RS1000159989 (7:96160438 G>A), RS1000185081 (7:96179031 G>T), RS1000186961 (7:96268025 T>C), RS1000206393 (7:96299975 T>G), RS1000223245 (7:96164767 G>C), RS1000238159 (7:96225383 A>G,T)

Disease associations

OMIM: gene MIM:603859 | disease phenotypes: MIM:215700, MIM:603471, MIM:605814

GenCC curated gene-disease

DiseaseClassificationInheritance
citrullinemia, type II, adult-onsetStrongAutosomal recessive
neonatal intrahepatic cholestasis due to citrin deficiencyStrongAutosomal recessive
citrullinemia type IISupportiveAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
citrin deficiencyDefinitiveAR

Mondo (8): citrin deficiency (MONDO:0016602), citrullinemia (MONDO:0015991), citrullinemia, type II, adult-onset (MONDO:0011326), neonatal intrahepatic cholestasis due to citrin deficiency (MONDO:0011601), citrullinemia type II (MONDO:0016603), adult-onset citrullinemia type I (MONDO:0016601), citrullinemia type I (MONDO:0008988), megacolon (MONDO:0001273)

Orphanet (6): Citrin deficiency (Orphanet:247582), Citrullinemia (Orphanet:187), Citrullinemia type II (Orphanet:247585), Neonatal intrahepatic cholestasis due to citrin deficiency (Orphanet:247598), Late-onset citrullinemia type I (Orphanet:247573), Citrullinemia type I (Orphanet:247525)

HPO phenotypes

97 total (30 of 97 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000518Cataract
HP:0000709Psychosis
HP:0000711Restlessness
HP:0000718Aggressive behavior
HP:0000737Irritability
HP:0000738Hallucinations
HP:0000746Delusion
HP:0000752Hyperactivity
HP:0000805Enuresis
HP:0000952Jaundice
HP:0001250Seizure
HP:0001254Lethargy
HP:0001259Coma
HP:0001263Global developmental delay
HP:0001289Confusion
HP:0001337Tremor
HP:0001394Cirrhosis
HP:0001395Hepatic fibrosis
HP:0001396Cholestasis
HP:0001397Hepatic steatosis
HP:0001402Hepatocellular carcinoma
HP:0001403Macrovesicular hepatic steatosis
HP:0001406Intrahepatic cholestasis
HP:0001414Microvesicular hepatic steatosis
HP:0001433Hepatosplenomegaly
HP:0001508Failure to thrive
HP:0001510Growth delay
HP:0001511Intrauterine growth retardation
HP:0001531Failure to thrive in infancy

GWAS associations

5 associations (top):

StudyTraitp-value
GCST007691_29Femoral neck bone mineral density8.000000e-48
GCST008163_28Height4.000000e-06
GCST010135_40Oily fish consumption1.000000e-08
GCST010140_30Pork consumption1.000000e-08
GCST012332_84Multisite chronic pain6.000000e-09

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0007785femoral neck bone mineral density
EFO:0008111diet measurement
EFO:0010100multisite chronic pain

MeSH disease descriptors (3)

DescriptorNameTree numbers
D020159CitrullinemiaC10.228.140.163.100.937.374; C16.320.565.100.940.374; C16.320.565.189.937.374; C18.452.132.100.937.374; C18.452.648.100.940.374; C18.452.648.189.937.374
D008531MegacolonC06.405.469.158.701
C536398Neonatal-onset citrullinemia type 2 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067317 (SINGLE PROTEIN)

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs768172SLC25A130.000

GtoPdb / IUPHAR curated pharmacology

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

Target class: transporter — Mitochondrial amino acid transporter subfamily

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
5.93Kd1178nMCHEMBL3752910
5.93ED501178nMCHEMBL3752910

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149407: Binding affinity to human SLC25A13 incubated for 45 mins by Kinobead based pull down assaykd1.1779uM

CTD chemical–gene interactions

46 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases expression6
Valproic Acidaffects cotreatment, increases expression, affects expression, decreases methylation4
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression3
sodium arsenitedecreases expression, affects binding, increases reaction2
perfluorooctane sulfonic aciddecreases expression2
Acetaminophendecreases expression2
Cisplatindecreases reaction, increases expression, decreases expression2
Aflatoxin B1affects expression, decreases expression, decreases methylation2
aristolochic acid Idecreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
bisphenol Aincreases expression1
arseniteaffects expression1
cobaltous chloridedecreases expression1
perfluorooctanoic aciddecreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
2,3,5-(triglutathion-S-yl)hydroquinoneincreases ADP-ribosylation1
perfluoro-n-nonanoic aciddecreases expression1
perfluorohexanesulfonic aciddecreases expression1
torcetrapibincreases expression1
bisphenol AFincreases expression1
Resveratrolaffects cotreatment, increases expression1
Acroleinincreases oxidation, increases abundance, affects cotreatment1
Air Pollutantsincreases oxidation, affects cotreatment, increases abundance1
Atrazinedecreases expression1
Cannabidioldecreases expression1
Clozapineincreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5652449BindingBinding affinity to human SLC25A13 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

7 cell lines: 4 cancer cell line, 3 transformed cell line

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

CellosaurusNameCategorySex
CVCL_B2FNAbcam HeLa SLC25A13 KOCancer cell lineFemale
CVCL_BW47GM23989Transformed cell lineMale
CVCL_D4JGHCT116-SLC25A13-KO-c2Cancer cell lineMale
CVCL_D4JHHCT116-SLC25A13-KO-c8Cancer cell lineMale
CVCL_D9RRUbigene HEK293 SLC25A13 KOTransformed cell lineFemale
CVCL_RU03GM26185Transformed cell lineMale
CVCL_TM12HAP1 SLC25A13 (-)Cancer cell lineMale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00718627PHASE2COMPLETEDHuman Heterologous Liver Cells for Infusion in Children With Urea Cycle Disorders
NCT05687474Not specifiedCOMPLETEDBaby Detect : Genomic Newborn Screening
NCT06895746Not specifiedACTIVE_NOT_RECRUITINGMulti-omics Study in Citrin Deficiency
NCT07055269Not specifiedACTIVE_NOT_RECRUITINGLiver Metabolic Functions in Patients With Citrin Deficiency and Healthy Subjects
NCT01421888Not specifiedTERMINATEDThe NIH UNI Study: Urea Cycle Disorders, Nutrition and Immunity
NCT01610089Not specifiedCOMPLETEDNitric Oxide Flux and Ureagenesis in Argininosuccinate Synthetase Deficiency (ASSD)(Citrullinemia I)
NCT04612764Not specifiedACTIVE_NOT_RECRUITINGLiver Disease in Urea Cycle Disorders
NCT04908319Not specifiedRECRUITINGHepatic Histopathology in Urea Cycle Disorders
NCT05910151Not specifiedUNKNOWNSelective Screening of Children for Hereditary Metabolic Diseases by Tandem Mass Spectrometry in Kazakhstan
NCT04340856Not specifiedCOMPLETEDRetrospective, Uncontrolled Cohort Study on the Therapy of Chronic Megalon
NCT07470892Not specifiedNOT_YET_RECRUITINGPreoperative Fish Oil PN and Prognosis After Constipation Surgery