Aliases for SFXN1 Gene

Aliases for SFXN1 Gene

  • Sideroflexin 1 2 3 5
  • Sideroflexin-1 3 4
  • Tricarboxylate Carrier Protein 3
  • SLC56A1 3
  • TCC 3

External Ids for SFXN1 Gene

Previous GeneCards Identifiers for SFXN1 Gene

  • GC05U990169
  • GC05P175644
  • GC05P174840
  • GC05P174886
  • GC05P174838
  • GC05P170004

Summaries for SFXN1 Gene

GeneCards Summary for SFXN1 Gene

SFXN1 (Sideroflexin 1) is a Protein Coding gene. Diseases associated with SFXN1 include Aceruloplasminemia. Gene Ontology (GO) annotations related to this gene include cation transmembrane transporter activity and ion transmembrane transporter activity. An important paralog of this gene is SFXN3.

UniProtKB/Swiss-Prot Summary for SFXN1 Gene

  • Mitochondrial serine transporter that mediates transport of serine into mitochondria, an important step of the one-carbon metabolism pathway (PubMed:30442778). Mitochondrial serine is converted to glycine and formate, which then exits to the cytosol where it is used to generate the charged folates that serve as one-carbon donors (PubMed:30442778). Transports both D-serine and L-serine (PubMed:30442778). Also able to transport other amino-acids, such as alanine (PubMed:30442778). May be indirectly involved in the transport of a component required for iron utilization into or out of the mitochondria (By similarity).

Gene Wiki entry for SFXN1 Gene

Additional gene information for SFXN1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SFXN1 Gene

Genomics for SFXN1 Gene

GeneHancer (GH) Regulatory Elements for SFXN1 Gene

Promoters and enhancers for SFXN1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J175477 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 757.3 +1.9 1866 3.9 FOXA1 RBPJ POLR2A NR2F6 HLF L3MBTL2 RAD21 MNT RELA ZNF148 SFXN1 lnc-HRH2-5 ENSG00000251414 ENSG00000270839 lnc-DRD1-2
GH05J175516 Enhancer 1.2 Ensembl ENCODE dbSUPER 11.4 +40.6 40636 2.2 SMARCE1 HLF DACH1 TEAD4 CBFA2T2 SMARCA4 POLR2A TRIM24 MTA1 EGR1 SFXN1 RF00017-5126 HSALNG0046810
GH05J175521 Enhancer 0.8 Ensembl ENCODE dbSUPER 14.3 +45.1 45139 6 HLF MNT CTBP1 ZNF184 ZNF687 SFXN1 RF00017-5126 HSALNG0046810
GH05J175494 Enhancer 0.8 Ensembl ENCODE 12.1 +17.5 17488 1.1 TCF7L2 MNT CEBPG CREB1 TARDBP CTBP1 CEBPB E4F1 PKNOX1 ZNF592 FAF2 SFXN1 ENSG00000250909 ENSG00000270839 lnc-DRD1-2 RF00017-5126
GH05J175434 Enhancer 0.4 Ensembl 10.4 -41.5 -41461 2.4 CEBPG CEBPB ZNF558 NANOG SFXN1 DRD1 piR-43325-078
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SFXN1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SFXN1 gene promoter:
  • AREB6
  • E4BP4
  • GCNF
  • GCNF-1
  • GCNF-2
  • HNF-1A
  • PPAR-gamma1
  • PPAR-gamma2
  • TBP
  • TFIID

Genomic Locations for SFXN1 Gene

Genomic Locations for SFXN1 Gene
chr5:175,477,062-175,529,742
(GRCh38/hg38)
Size:
52,681 bases
Orientation:
Plus strand
chr5:174,904,065-174,956,745
(GRCh37/hg19)
Size:
52,681 bases
Orientation:
Plus strand

Genomic View for SFXN1 Gene

Genes around SFXN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SFXN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SFXN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SFXN1 Gene

Proteins for SFXN1 Gene

  • Protein details for SFXN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H9B4-SFXN1_HUMAN
    Recommended name:
    Sideroflexin-1
    Protein Accession:
    Q9H9B4
    Secondary Accessions:
    • B3KPW3
    • D3DQN2
    • Q9HA53

    Protein attributes for SFXN1 Gene

    Size:
    322 amino acids
    Molecular mass:
    35619 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH20517.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB14003.1; Type=Miscellaneous discrepancy; Note=Cloning artifact.; Evidence={ECO:0000305}; Sequence=BAB14318.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

neXtProt entry for SFXN1 Gene

Post-translational modifications for SFXN1 Gene

  • Ubiquitination at Lys72 and Lys170
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SFXN1 Gene

Domains & Families for SFXN1 Gene

Gene Families for SFXN1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for SFXN1 Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SFXN1 Gene

GenScript: Design optimal peptide antigens:
  • Tricarboxylate carrier protein (SFXN1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9H9B4

UniProtKB/Swiss-Prot:

SFXN1_HUMAN :
  • Belongs to the sideroflexin family.
Family:
  • Belongs to the sideroflexin family.
genes like me logo Genes that share domains with SFXN1: view

Function for SFXN1 Gene

Molecular function for SFXN1 Gene

UniProtKB/Swiss-Prot Function:
Mitochondrial serine transporter that mediates transport of serine into mitochondria, an important step of the one-carbon metabolism pathway (PubMed:30442778). Mitochondrial serine is converted to glycine and formate, which then exits to the cytosol where it is used to generate the charged folates that serve as one-carbon donors (PubMed:30442778). Transports both D-serine and L-serine (PubMed:30442778). Also able to transport other amino-acids, such as alanine (PubMed:30442778). May be indirectly involved in the transport of a component required for iron utilization into or out of the mitochondria (By similarity).
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=170 uM for serine {ECO:0000269 PubMed:30442778}; KM=371 uM for alanine {ECO:0000269 PubMed:30442778};

Phenotypes From GWAS Catalog for SFXN1 Gene

Gene Ontology (GO) - Molecular Function for SFXN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015075 ion transmembrane transporter activity IEA --
GO:0015194 L-serine transmembrane transporter activity IDA 30442778
GO:0042945 D-serine transmembrane transporter activity IDA 30442778
genes like me logo Genes that share ontologies with SFXN1: view
genes like me logo Genes that share phenotypes with SFXN1: view

Animal Models for SFXN1 Gene

MGI Knock Outs for SFXN1:
  • Sfxn1 Sfxn1<tm1b(EUCOMM)Wtsi>

Animal Model Products

  • Taconic Biosciences Mouse Models for SFXN1

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SFXN1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SFXN1 Gene

Localization for SFXN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SFXN1 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 SFXN1 gene
Compartment Confidence
mitochondrion 5
peroxisome 2
cytosol 2
nucleus 0
golgi apparatus 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SFXN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IDA --
GO:0005743 mitochondrial inner membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0031305 integral component of mitochondrial inner membrane IDA 30442778
genes like me logo Genes that share ontologies with SFXN1: view

Pathways & Interactions for SFXN1 Gene

PathCards logo

SuperPathways for SFXN1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SFXN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006730 one-carbon metabolic process IDA,IEA 30442778
GO:0006811 ion transport IEA --
GO:0006826 iron ion transport IEA --
GO:0006865 amino acid transport IEA --
GO:0015825 L-serine transport IDA 30442778
genes like me logo Genes that share ontologies with SFXN1: view

No data available for Pathways by source and SIGNOR curated interactions for SFXN1 Gene

Drugs & Compounds for SFXN1 Gene

(1) Drugs for SFXN1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Iron Approved, Experimental Pharma 1452
genes like me logo Genes that share compounds with SFXN1: view

Transcripts for SFXN1 Gene

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SFXN1

Alternative Splicing Database (ASD) splice patterns (SP) for SFXN1 Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c · 3d ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12a · 12b
SP1: - - - - -
SP2: - - - -
SP3: - - - - - -
SP4: - -
SP5: -
SP6: -
SP7: -

Relevant External Links for SFXN1 Gene

GeneLoc Exon Structure for
SFXN1
ECgene alternative splicing isoforms for
SFXN1

Expression for SFXN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SFXN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SFXN1 Gene

This gene is overexpressed in Nasal epithelium (22.0) and Bone (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SFXN1 Gene



Protein tissue co-expression partners for SFXN1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SFXN1 Gene:

SFXN1

SOURCE GeneReport for Unigene cluster for SFXN1 Gene:

Hs.369440

mRNA Expression by UniProt/SwissProt for SFXN1 Gene:

Q9H9B4-SFXN1_HUMAN
Tissue specificity: Highly expressed in tissues with high one-carbon metabolism activity, such as blood, liver and kidney.

Evidence on tissue expression from TISSUES for SFXN1 Gene

  • Nervous system(4.5)
  • Liver(4.4)
  • Lung(4.2)
genes like me logo Genes that share expression patterns with SFXN1: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SFXN1 Gene

Orthologs for SFXN1 Gene

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

Orthologs for SFXN1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SFXN1 33 32
  • 99.69 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SFXN1 33
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SFXN1 33 32
  • 91.93 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SFXN1 33
  • 90 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SFXN1 33 32
  • 89.86 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sfxn1 32
  • 85.09 (n)
mouse
(Mus musculus)
Mammalia Sfxn1 17 33 32
  • 84.58 (n)
chicken
(Gallus gallus)
Aves SFXN1 33 32
  • 81.37 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SFXN1 33
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sfxn1 32
  • 78.99 (n)
African clawed frog
(Xenopus laevis)
Amphibia xm278-prov 32
zebrafish
(Danio rerio)
Actinopterygii sfxn1 33 32
  • 75.05 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004519 32
  • 60.02 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG11739 33 32
  • 55.38 (n)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea sfxn-1.5 33 32
  • 58.01 (n)
ManyToMany
sfxn-1.4 33
  • 51 (a)
ManyToMany
sfxn-1.1 33
  • 48 (a)
ManyToMany
sfxn-1.2 33
  • 48 (a)
ManyToMany
sfxn-1.3 33
  • 47 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes FSF1 33
  • 37 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10377 33
  • 64 (a)
OneToMany
Species where no ortholog for SFXN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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)
  • 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 SFXN1 Gene

ENSEMBL:
Gene Tree for SFXN1 (if available)
TreeFam:
Gene Tree for SFXN1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SFXN1: view image

Paralogs for SFXN1 Gene

Paralogs for SFXN1 Gene

(3) SIMAP similar genes for SFXN1 Gene using alignment to 6 proteins:

  • SFXN1_HUMAN
  • D6RAE9_HUMAN
  • D6RDG7_HUMAN
  • D6RFI0_HUMAN
  • H0Y9J5_HUMAN
  • S4R2X2_HUMAN
genes like me logo Genes that share paralogs with SFXN1: view

Variants for SFXN1 Gene

Sequence variations from dbSNP and Humsavar for SFXN1 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000008053 -- 175,486,528(+) A/G intron_variant
rs1000037758 -- 175,515,440(+) A/C genic_downstream_transcript_variant, intron_variant
rs1000095326 -- 175,507,736(+) C/T intron_variant
rs1000127874 -- 175,478,886(+) C/T intron_variant
rs1000130445 -- 175,529,992(+) T/C downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SFXN1 Gene

Variant ID Type Subtype PubMed ID
esv3607650 CNV gain 21293372
nsv469707 CNV loss 16826518
nsv472628 CNV novel sequence insertion 20440878

Variation tolerance for SFXN1 Gene

Residual Variation Intolerance Score: 66.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.64; 31.45% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SFXN1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SFXN1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SFXN1 Gene

Disorders for SFXN1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SFXN1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
aceruloplasminemia
  • hemosiderosis, systemic, due to aceruloplasminemia
- elite association - COSMIC cancer census association via MalaCards
Search SFXN1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SFXN1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SFXN1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SFXN1 Gene

Publications for SFXN1 Gene

  1. SFXN1 is a mitochondrial serine transporter required for one-carbon metabolism. (PMID: 30442778) Kory N … Sabatini DM (Science (New York, N.Y.) 2018) 3 4 56
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 43 56
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 56
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 56
  5. Loss of ER retention motif of AGR2 can impact mTORC signaling and promote cancer metastasis. (PMID: 30575818) Tiemann K … Kani K (Oncogene 2019) 3 56

Products for SFXN1 Gene

Sources for SFXN1 Gene