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Aliases for SLC25A1 Gene

Aliases for SLC25A1 Gene

  • Solute Carrier Family 25 Member 1 2 3 4 5
  • Solute Carrier Family 25 (Mitochondrial Carrier; Citrate Transporter), Member 1 2 3
  • Solute Carrier Family 20 (Mitochondrial Citrate Transporter), Member 3 2 3
  • Tricarboxylate Carrier Protein 3 4
  • Citrate Transport Protein 3 4
  • SLC20A3 3 4
  • CTP 3 4
  • Tricarboxylate Transport Protein, Mitochondrial 3
  • D2L2AD 3
  • SEA 3

External Ids for SLC25A1 Gene

Previous HGNC Symbols for SLC25A1 Gene

  • SLC20A3

Previous GeneCards Identifiers for SLC25A1 Gene

  • GC22M016103
  • GC22M017537
  • GC22M002784

Summaries for SLC25A1 Gene

Entrez Gene Summary for SLC25A1 Gene

  • This gene encodes a member of the mitochondrial carrier subfamily of solute carrier proteins. Members of this family include nuclear-encoded transporters that translocate small metabolites across the mitochondrial membrane. This protein regulates the movement of citrate across the inner membranes of the mitochondria. Mutations in this gene have been associated with combined D-2- and L-2-hydroxyglutaric aciduria. Pseudogenes of this gene have been identified on chromosomes 7, 11, 16, and 19. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

GeneCards Summary for SLC25A1 Gene

SLC25A1 (Solute Carrier Family 25 Member 1) is a Protein Coding gene. Diseases associated with SLC25A1 include Combined D-2- And L-2-Hydroxyglutaric Aciduria and Presynaptic Congenital Myasthenic Syndromes. Among its related pathways are Metabolism and Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha). GO annotations related to this gene include citrate transmembrane transporter activity.

UniProtKB/Swiss-Prot for SLC25A1 Gene

  • Involved in citrate-H(+)/malate exchange. Important for the bioenergetics of hepatic cells as it provides a carbon source for fatty acid and sterol biosyntheses, and NAD(+) for the glycolytic pathway.

Gene Wiki entry for SLC25A1 Gene

Additional gene information for SLC25A1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC25A1 Gene

Genomics for SLC25A1 Gene

Regulatory Elements for SLC25A1 Gene

Enhancers for SLC25A1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH22H019169 1.7 Ensembl ENCODE dbSUPER 42.3 +4.2 4171 11 HDGF PKNOX1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 SLC25A1 CLTCL1 GSC2 ESS2 TSSK2 TSSK1A DGCR2 ENSG00000223461 UFD1 RPL7AP70
GH22H019217 1.3 Ensembl ENCODE 39.1 -39.7 -39674 1 ATF1 ARNT FEZF1 ZNF2 TCF12 ZNF121 GATA2 ATF7 ZC3H11A REST DGCR8 LINC01311 SLC25A1 TRMT2A ENSG00000273300 ZDHHC8 RPL7AP70 CLTCL1 RPL8P5 DGCR11
GH22H019285 1.3 Ensembl ENCODE dbSUPER 38.9 -108.3 -108256 3 TBP MXI1 MAX FEZF1 CEBPG PYGO2 RFX5 ZNF776 ZBTB48 FOS SLC25A1 DGCR8 TRMT2A LINC01311 CLTCL1 ENSG00000273300 RPL8P5 E2F6P1 ZDHHC8 GC22M019285
GH22H019270 1.1 ENCODE dbSUPER 29.3 -93.6 -93622 3 FOXA2 ARID4B FEZF1 RARA RFX5 YY1 ZNF121 ZSCAN5C SCRT2 ATF7 SLC25A1 CLTCL1 GC22M019285 KRT18P62
GH22H019184 0.7 ENCODE 42 -6.3 -6330 1 KLF1 RB1 MAX KLF4 HDAC8 ZIC2 SREBF1 ZFP69B ZNF692 POLR2A SLC25A1 CLTCL1 ESS2 PIR41749
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SLC25A1 on UCSC Golden Path with GeneCards custom track

Promoters for SLC25A1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000143726 363 1801 HDGF MLX ARNT ARID4B SIN3A FEZF1 DMAP1 YY1 ZNF143 SP3

Genomic Location for SLC25A1 Gene

Chromosome:
22
Start:
19,175,575 bp from pter
End:
19,178,863 bp from pter
Size:
3,289 bases
Orientation:
Minus strand

Genomic View for SLC25A1 Gene

Genes around SLC25A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC25A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC25A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC25A1 Gene

Proteins for SLC25A1 Gene

  • Protein details for SLC25A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P53007-TXTP_HUMAN
    Recommended name:
    Tricarboxylate transport protein, mitochondrial
    Protein Accession:
    P53007
    Secondary Accessions:
    • A8K8E8
    • Q9BSK6

    Protein attributes for SLC25A1 Gene

    Size:
    311 amino acids
    Molecular mass:
    34013 Da
    Quaternary structure:
    No Data Available

neXtProt entry for SLC25A1 Gene

Post-translational modifications for SLC25A1 Gene

  • Ubiquitination at Lys160, Lys178, and isoforms=255
  • Modification sites at PhosphoSitePlus

Other Protein References for SLC25A1 Gene

No data available for DME Specific Peptides for SLC25A1 Gene

Domains & Families for SLC25A1 Gene

Gene Families for SLC25A1 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted intracellular proteins
  • Transporters

Protein Domains for SLC25A1 Gene

Graphical View of Domain Structure for InterPro Entry

P53007

UniProtKB/Swiss-Prot:

TXTP_HUMAN :
  • Belongs to the mitochondrial carrier (TC 2.A.29) family.
Family:
  • Belongs to the mitochondrial carrier (TC 2.A.29) family.
genes like me logo Genes that share domains with SLC25A1: view

Function for SLC25A1 Gene

Molecular function for SLC25A1 Gene

GENATLAS Biochemistry:
solute carrier family 25 mitochondrial,member A1,citrate transporter,disrupted by ADU breakpoint
UniProtKB/Swiss-Prot Function:
Involved in citrate-H(+)/malate exchange. Important for the bioenergetics of hepatic cells as it provides a carbon source for fatty acid and sterol biosyntheses, and NAD(+) for the glycolytic pathway.

Phenotypes From GWAS Catalog for SLC25A1 Gene

Gene Ontology (GO) - Molecular Function for SLC25A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015137 citrate transmembrane transporter activity TAS 8666394
GO:0015142 tricarboxylic acid transmembrane transporter activity TAS --
genes like me logo Genes that share ontologies with SLC25A1: view
genes like me logo Genes that share phenotypes with SLC25A1: view

Human Phenotype Ontology for SLC25A1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for SLC25A1

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SLC25A1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for SLC25A1 Gene

Localization for SLC25A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC25A1 Gene

Mitochondrion inner membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SLC25A1 gene
Compartment Confidence
extracellular 5
mitochondrion 5
nucleus 5
plasma membrane 2
peroxisome 1
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for SLC25A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 21630459
GO:0005739 mitochondrion IEA --
GO:0005743 mitochondrial inner membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IBA,IEA --
genes like me logo Genes that share ontologies with SLC25A1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SLC25A1 Gene

Pathways & Interactions for SLC25A1 Gene

genes like me logo Genes that share pathways with SLC25A1: view

Gene Ontology (GO) - Biological Process for SLC25A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006094 gluconeogenesis TAS --
GO:0006810 transport IEA --
GO:0006839 mitochondrial transport IBA --
GO:0006843 mitochondrial citrate transport IBA --
GO:0035674 tricarboxylic acid transmembrane transport IEA --
genes like me logo Genes that share ontologies with SLC25A1: view

No data available for SIGNOR curated interactions for SLC25A1 Gene

Drugs & Compounds for SLC25A1 Gene

(3) Drugs for SLC25A1 Gene - From: DrugBank, DGIdb, IUPHAR, and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Sodium Citrate Approved Pharma Transporter, substrate 0
1,2,3-benzenetricarboxylic acid Pharma Inhibition, Inhibitor 0
NAD Pharma Full agonist, Agonist 0
genes like me logo Genes that share compounds with SLC25A1: view

Transcripts for SLC25A1 Gene

Unigene Clusters for SLC25A1 Gene

Solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SLC25A1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for SLC25A1 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c · 2d ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b
SP1: - - - - -
SP2: -
SP3: -
SP4: -
SP5: -
SP6: - - - - -
SP7: - - - - - -
SP8: -
SP9:
SP10: - - - -

Relevant External Links for SLC25A1 Gene

GeneLoc Exon Structure for
SLC25A1
ECgene alternative splicing isoforms for
SLC25A1

Expression for SLC25A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC25A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SLC25A1 Gene

This gene is overexpressed in Nasal epithelium (31.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SLC25A1 Gene



Protein tissue co-expression partners for SLC25A1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SLC25A1 Gene:

SLC25A1

SOURCE GeneReport for Unigene cluster for SLC25A1 Gene:

Hs.111024

Evidence on tissue expression from TISSUES for SLC25A1 Gene

  • Nervous system(4.7)
  • Liver(4.5)
  • Kidney(4.3)
  • Pancreas(2.6)
  • Eye(2)
  • Intestine(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC25A1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • immune
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • epiglottis
  • eye
  • eyelid
  • face
  • head
  • jaw
  • larynx
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • pharynx
  • skull
  • tongue
  • vocal cord
Thorax:
  • bronchus
  • chest wall
  • diaphragm
  • esophagus
  • lung
  • rib
  • rib cage
  • sternum
  • trachea
Abdomen:
  • stomach
Limb:
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
General:
  • blood
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal cord
  • white blood cell
genes like me logo Genes that share expression patterns with SLC25A1: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for SLC25A1 Gene

Orthologs for SLC25A1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SLC25A1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SLC25A1 34
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SLC25A1 34
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Slc25a1 34
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SLC25A1 34
  • 91 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SLC25A1 34
  • 91 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SLC25A1 34
  • 62 (a)
OneToOne
chicken
(Gallus gallus)
Aves SLC25A1 34
  • 85 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SLC25A1 34
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia MGC76218 33
African clawed frog
(Xenopus laevis)
Amphibia slc25a1-prov 33
zebrafish
(Danio rerio)
Actinopterygii SLC25A1 (3 of 3) 34
  • 83 (a)
OneToMany
slc25a1b 33 34
  • 72.92 (n)
slc25a1a 34
  • 66 (a)
OneToMany
zgc63578 33
fruit fly
(Drosophila melanogaster)
Insecta CG6782 35
  • 66 (a)
sea 34
  • 61 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea K11H3.3 35 34
  • 65 (a)
Y37B11A.3 34
  • 29 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CTP1 34 36 33
  • 46.32 (n)
OneToOne
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E18723g 33
  • 45.91 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3482 34
  • 68 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8914 33
Species where no ortholog for SLC25A1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SLC25A1 Gene

ENSEMBL:
Gene Tree for SLC25A1 (if available)
TreeFam:
Gene Tree for SLC25A1 (if available)

Paralogs for SLC25A1 Gene

(6) SIMAP similar genes for SLC25A1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with SLC25A1: view

No data available for Paralogs for SLC25A1 Gene

Variants for SLC25A1 Gene

Sequence variations from dbSNP and Humsavar for SLC25A1 Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type
rs431905509 Pathogenic, Combined D-2- and L-2-hydroxyglutaric aciduria (D2L2AD) [MIM:615182], Combined D-2- and L-2-hydroxyglutaric aciduria (D2L2AD) [MIM:615182] 19,176,222(-) TCCCC(C/G/T)GCCTG nc-transcript-variant, reference, missense
rs781925968 Combined D-2- and L-2-hydroxyglutaric aciduria (D2L2AD) [MIM:615182] 19,176,899(+) GGTTC(A/C/G)AGCCC nc-transcript-variant, reference, missense
rs782335811 Combined D-2- and L-2-hydroxyglutaric aciduria (D2L2AD) [MIM:615182] 19,176,872(+) AGGTC(A/G)TGACG nc-transcript-variant, reference, missense
VAR_069490 Combined D-2- and L-2-hydroxyglutaric aciduria (D2L2AD) [MIM:615182]
VAR_069491 Combined D-2- and L-2-hydroxyglutaric aciduria (D2L2AD) [MIM:615182]

Structural Variations from Database of Genomic Variants (DGV) for SLC25A1 Gene

Variant ID Type Subtype PubMed ID
esv3575418 CNV gain 25503493
nsv588213 CNV gain 21841781
nsv588216 CNV gain 21841781
nsv834122 CNV loss 17160897

Variation tolerance for SLC25A1 Gene

Residual Variation Intolerance Score: 34.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.50; 10.83% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SLC25A1 Gene

Human Gene Mutation Database (HGMD)
SLC25A1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLC25A1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC25A1 Gene

Disorders for SLC25A1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for SLC25A1 Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
combined d-2- and l-2-hydroxyglutaric aciduria
  • d,l-2-hydroxyglutaric aciduria
presynaptic congenital myasthenic syndromes
  • congenital myasthenic syndromes, presynaptic
l-2-hydroxyglutaric aciduria
  • combined d-2- and l-2-hydroxyglutaric aciduria
2-hydroxyglutaric aciduria
  • combined d-2- and l-2-hydroxyglutaric aciduria
velocardiofacial syndrome
  • cayler cardiofacial syndrome
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

TXTP_HUMAN
  • Combined D-2- and L-2-hydroxyglutaric aciduria (D2L2AD) [MIM:615182]: An autosomal recessive neurometabolic disorder characterized by neonatal-onset encephalopathy with severe muscular weakness, intractable seizures, respiratory distress, and lack of psychomotor development resulting in early death. Brain imaging shows abnormalities including enlarged ventricles, delayed myelination, and germinal layer cysts. {ECO:0000269 PubMed:23561848, ECO:0000269 PubMed:27306203}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SLC25A1

Genetic Association Database (GAD)
SLC25A1
Human Genome Epidemiology (HuGE) Navigator
SLC25A1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SLC25A1
genes like me logo Genes that share disorders with SLC25A1: view

No data available for Genatlas for SLC25A1 Gene

Publications for SLC25A1 Gene

  1. Cloning, genomic organization, and chromosomal localization of human citrate transport protein to the DiGeorge/velocardiofacial syndrome minimal critical region. (PMID: 8660975) Goldmuntz E … Budarf ML (Genomics 1996) 3 4 22 60
  2. Localization of the human mitochondrial citrate transporter protein gene to chromosome 22Q11 in the DiGeorge syndrome critical region. (PMID: 8666394) Heisterkamp N … Groffen J (Genomics 1995) 2 3 4 60
  3. Deficiency in SLC25A1, encoding the mitochondrial citrate carrier, causes combined D-2- and L-2-hydroxyglutaric aciduria. (PMID: 23561848) Nota B … Salomons GS (American journal of human genetics 2013) 3 4 60
  4. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 45 60
  5. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. (PMID: 19240061) Trynka G … Wijmenga C (Gut 2009) 3 45 60

Products for SLC25A1 Gene

Sources for SLC25A1 Gene

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