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Aliases for FANCL Gene

Aliases for FANCL Gene

  • Fanconi Anemia Complementation Group L 2 3 5
  • Fanconi Anemia-Associated Polypeptide Of 43 KDa 3 4
  • RING-Type E3 Ubiquitin Transferase FANCL 3 4
  • Fanconi Anemia Group L Protein 3 4
  • PHD Finger Protein 9 2 3
  • FAAP43 3 4
  • PHF9 3 4
  • E3 Ubiquitin-Protein Ligase FANCL 3
  • EC 4
  • POG 3

External Ids for FANCL Gene

Previous HGNC Symbols for FANCL Gene

  • PHF9

Previous GeneCards Identifiers for FANCL Gene

  • GC00U912964
  • GC02M058360
  • GC02M058298

Summaries for FANCL Gene

Entrez Gene Summary for FANCL Gene

  • The Fanconi anemia complementation group (FANC) currently includes FANCA, FANCB, FANCC, FANCD1 (also called BRCA2), FANCD2, FANCE, FANCF, FANCG, FANCI, FANCJ (also called BRIP1), FANCL, FANCM and FANCN (also called PALB2). The previously defined group FANCH is the same as FANCA. Fanconi anemia is a genetically heterogeneous recessive disorder characterized by cytogenetic instability, hypersensitivity to DNA crosslinking agents, increased chromosomal breakage, and defective DNA repair. The members of the Fanconi anemia complementation group do not share sequence similarity; they are related by their assembly into a common nuclear protein complex. This gene encodes the protein for complementation group L. Alternative splicing results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

GeneCards Summary for FANCL Gene

FANCL (Fanconi Anemia Complementation Group L) is a Protein Coding gene. Diseases associated with FANCL include Fanconi Anemia, Complementation Group L and Fanconi Anemia, Complementation Group A. Among its related pathways are DNA damage_Role of Brca1 and Brca2 in DNA repair and Fanconi anemia pathway. GO annotations related to this gene include ligase activity and ubiquitin protein ligase binding.

UniProtKB/Swiss-Prot for FANCL Gene

  • Ubiquitin ligase protein that mediates monoubiquitination of FANCD2 in the presence of UBE2T, a key step in the DNA damage pathway (PubMed:12973351, PubMed:16916645, PubMed:17938197, PubMed:19111657, PubMed:24389026). Also mediates monoubiquitination of FANCI (PubMed:19589784). May stimulate the ubiquitin release from UBE2W. May be required for proper primordial germ cell proliferation in the embryonic stage, whereas it is probably not needed for spermatogonial proliferation after birth.

Gene Wiki entry for FANCL Gene

Additional gene information for FANCL Gene

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

Genomics for FANCL Gene

Regulatory Elements for FANCL Gene

Enhancers for FANCL 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
GH02H057759 2.2 Ensembl ENCODE 10.2 +481.6 481620 1.3 ELF3 PKNOX1 RB1 SIN3A BATF ZSCAN9 RAD21 ZNF121 ZNF143 ZNF207 FANCL ACTG1P22 LOC105377628
GH02H058107 1.4 FANTOM5 Ensembl ENCODE 9.7 +133.1 133128 2.8 GTF2F1 TBP PKNOX1 JUN SIN3A BRCA1 POLR2A FOS MAFK CHD2 VRK2 FANCL GC02P058072 ENSG00000273063
GH02H058041 1.2 Ensembl ENCODE 10.6 +199.2 199188 1.7 FOXA2 ARID4B FEZF1 SLC30A9 FOS RUNX3 JUNB ZNF491 MAFF SMARCA4 FANCL LOC105374726 GC02M057920
GH02H058447 1.1 Ensembl ENCODE 10.7 -206.6 -206569 1.1 ELF3 CTCF SAP130 CEBPG ZNF644 RAD21 YY1 TEAD3 SMC3 ZNF143 FANCL VRK2 GC02P058461 LINC01122
GH02H058038 1.1 Ensembl ENCODE 10.6 +202.6 202565 1.3 HDAC1 HDGF BMI1 ZBTB40 CHAMP1 TCF12 GATA2 ETV6 IKZF2 SMARCA5 FANCL LOC105374726 GC02M057920
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around FANCL on UCSC Golden Path with GeneCards custom track

Promoters for FANCL Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000117513 681 1600 PKNOX1 MLX ARID4B SIN3A DMAP1 YY1 SLC30A9 CBX5 ZNF143 SP3

Genomic Locations for FANCL Gene

Genomic Locations for FANCL Gene
82,439 bases
Minus strand

Genomic View for FANCL Gene

Genes around FANCL on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for FANCL Gene

Proteins for FANCL Gene

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

    Protein Symbol:
    Recommended name:
    E3 ubiquitin-protein ligase FANCL
    Protein Accession:
    Secondary Accessions:
    • Q6GU60

    Protein attributes for FANCL Gene

    375 amino acids
    Molecular mass:
    42905 Da
    Quaternary structure:
    • Interacts with GGN (By similarity). Belongs to the multisubunit FA complex composed of FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9 and FANCM (PubMed:12973351, PubMed:15502827, PubMed:16116422, PubMed:22343915). The complex is not found in FA patients. In complex with FANCF, FANCA and FANCG, but not with FANCC, nor FANCE, interacts with HES1; this interaction may be essential for the stability and nuclear localization of FA core complex proteins (PubMed:18550849). Interacts with FANCI (PubMed:21775430). Directly interacts (via the RING-type zinc finger) with UBE2T and UBE2W (PubMed:16916645, PubMed:17938197, PubMed:19111657, PubMed:21775430, PubMed:24389026).

    Three dimensional structures from OCA and Proteopedia for FANCL Gene

    Alternative splice isoforms for FANCL Gene


neXtProt entry for FANCL Gene

Post-translational modifications for FANCL Gene

  • The RING-type zinc finger domain is monoubiquitinated in the presence of UBE2T and UBE2W.
  • Ubiquitination at isoforms=249 and isoforms=2369
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for FANCL Gene

Domains & Families for FANCL Gene

Gene Families for FANCL Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for FANCL Gene

Graphical View of Domain Structure for InterPro Entry



  • The UBC-RWD region (URD) region mediates interaction with FANCI and FANCD2.
  • The UBC-RWD region (URD) region mediates interaction with FANCI and FANCD2.
genes like me logo Genes that share domains with FANCL: view

Function for FANCL Gene

Molecular function for FANCL Gene

UniProtKB/Swiss-Prot CatalyticActivity:
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.
UniProtKB/Swiss-Prot Function:
Ubiquitin ligase protein that mediates monoubiquitination of FANCD2 in the presence of UBE2T, a key step in the DNA damage pathway (PubMed:12973351, PubMed:16916645, PubMed:17938197, PubMed:19111657, PubMed:24389026). Also mediates monoubiquitination of FANCI (PubMed:19589784). May stimulate the ubiquitin release from UBE2W. May be required for proper primordial germ cell proliferation in the embryonic stage, whereas it is probably not needed for spermatogonial proliferation after birth.

Enzyme Numbers (IUBMB) for FANCL Gene

Phenotypes From GWAS Catalog for FANCL Gene

Gene Ontology (GO) - Molecular Function for FANCL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004842 ubiquitin-protein transferase activity ISS --
GO:0005515 protein binding IPI 24389026
GO:0016740 transferase activity IEA --
GO:0031625 ubiquitin protein ligase binding IPI 16916645
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with FANCL: view
genes like me logo Genes that share phenotypes with FANCL: view

Human Phenotype Ontology for FANCL Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for FANCL Gene

MGI Knock Outs for FANCL:

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for FANCL Gene

Localization for FANCL Gene

Subcellular locations from UniProtKB/Swiss-Prot for FANCL Gene

Cytoplasm. Nucleus.

Subcellular locations from

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 FANCL gene
Compartment Confidence
nucleus 5
cytoskeleton 2
cytosol 2
golgi apparatus 2
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for FANCL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005635 nuclear envelope IEA --
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
GO:0016604 nuclear body IDA --
genes like me logo Genes that share ontologies with FANCL: view

Pathways & Interactions for FANCL Gene

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

Pathways by source for FANCL Gene

1 BioSystems pathway for FANCL Gene
2 Reactome pathways for FANCL Gene

UniProtKB/Swiss-Prot Q9NW38-FANCL_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for FANCL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006281 DNA repair IEA,IMP 16916645
GO:0006513 protein monoubiquitination IDA 16916645
GO:0006974 cellular response to DNA damage stimulus IMP 16916645
GO:0007276 gamete generation IEA --
GO:0016567 protein ubiquitination IEA --
genes like me logo Genes that share ontologies with FANCL: view

No data available for SIGNOR curated interactions for FANCL Gene

Drugs & Compounds for FANCL Gene

(4) Drugs for FANCL Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Adenosine monophosphate Approved Nutra 0
ATP Nutra Agonist 0

(1) Additional Compounds for FANCL Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
genes like me logo Genes that share compounds with FANCL: view

Transcripts for FANCL Gene

Unigene Clusters for FANCL Gene

Fanconi anemia, complementation group L:
Representative Sequences:

Clone Products

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

No ASD Table

Relevant External Links for FANCL Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for FANCL Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for FANCL Gene

This gene is overexpressed in Plasma (55.3) and Bone marrow stromal cell (13.7).

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

Protein tissue co-expression partners for FANCL Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of FANCL Gene:


SOURCE GeneReport for Unigene cluster for FANCL Gene:


Evidence on tissue expression from TISSUES for FANCL Gene

  • Nervous system(4.7)
  • Eye(4)
  • Bone(2.2)

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

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • neck
  • nose
  • outer ear
  • pituitary gland
  • skull
  • breast
  • esophagus
  • heart
  • lung
  • rib
  • rib cage
  • intestine
  • kidney
  • large intestine
  • liver
  • stomach
  • anus
  • ovary
  • pelvis
  • penis
  • prostate
  • rectum
  • testicle
  • ureter
  • uterus
  • vagina
  • vulva
  • arm
  • digit
  • finger
  • forearm
  • hand
  • radius
  • upper limb
  • blood
  • blood vessel
  • bone marrow
  • coagulation system
  • hair
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with FANCL: view

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

Orthologs for FANCL Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for FANCL Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia FANCL 33 34
  • 99.29 (n)
(Canis familiaris)
Mammalia FANCL 33 34
  • 91.27 (n)
(Bos Taurus)
Mammalia FANCL 33 34
  • 90.44 (n)
(Mus musculus)
Mammalia Fancl 16 34 33
  • 83.42 (n)
(Monodelphis domestica)
Mammalia FANCL 34
  • 83 (a)
(Rattus norvegicus)
Mammalia Fancl 33
  • 82.53 (n)
(Ornithorhynchus anatinus)
Mammalia FANCL 34
  • 78 (a)
(Gallus gallus)
Aves FANCL 34 33
  • 73.01 (n)
(Anolis carolinensis)
Reptilia FANCL 34
  • 64 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia fancl 33
  • 68.94 (n)
(Danio rerio)
Actinopterygii fancl 33 34
  • 63.72 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2422 33
fruit fly
(Drosophila melanogaster)
Insecta Fancl 34
  • 22 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G65740 33
  • 45.82 (n)
(Oryza sativa)
Liliopsida Os03g0726900 33
  • 47.99 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 34 (a)
Species where no ortholog for FANCL was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for FANCL Gene

Gene Tree for FANCL (if available)
Gene Tree for FANCL (if available)

Paralogs for FANCL Gene

No data available for Paralogs for FANCL Gene

Variants for FANCL Gene

Sequence variations from dbSNP and Humsavar for FANCL Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs759217526 Pathogenic 58,159,793(+) TAAGG(-/TAAT)TAATT nc-transcript-variant, reference, utr-variant-3-prime, frameshift-variant
rs869320684 Pathogenic 58,226,733(-) AGATG(-/C)TTTTG intron-variant, nc-transcript-variant, reference, frameshift-variant
rs869320685 Pathogenic 58,204,171(-) ATGCT(-/T)CTGGT nc-transcript-variant, reference, frameshift-variant
rs878855046 Pathogenic 58,204,163(-) GAAGA(-/TGCTTCTGGTAGA)GAGCA nc-transcript-variant, reference, frameshift-variant
rs140088149 Likely benign 58,161,579(+) ACTTG(A/T)TCAGG nc-transcript-variant, downstream-variant-500B, reference, missense, utr-variant-3-prime

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

Variant ID Type Subtype PubMed ID
nsv817995 CNV loss 17921354
nsv582098 CNV loss 21841781
nsv582086 CNV gain 21841781
nsv525988 CNV gain 19592680
nsv458052 CNV loss 19166990
nsv457985 CNV gain 19166990
esv3590957 CNV loss 21293372
esv3590956 CNV loss 21293372
esv2662829 CNV deletion 23128226

Variation tolerance for FANCL Gene

Residual Variation Intolerance Score: 87.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.61; 45.20% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for FANCL Gene

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

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

Disorders for FANCL Gene

MalaCards: The human disease database

(8) MalaCards diseases for FANCL Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
fanconi anemia, complementation group l
  • fanconi anemia complementation group l
fanconi anemia, complementation group a
  • fanconi's anemia
fancl-related fanconi anemia
fanconi anemia, complementation group b
  • fanconi anemia complementation group b
clear cell ependymoma
  • cellular ependymoma
- elite association - COSMIC cancer census association via MalaCards
Search FANCL in MalaCards View complete list of genes associated with diseases


  • Fanconi anemia complementation group L (FANCL) [MIM:614083]: A disorder affecting all bone marrow elements and resulting in anemia, leukopenia and thrombopenia. It is associated with cardiac, renal and limb malformations, dermal pigmentary changes, and a predisposition to the development of malignancies. At the cellular level it is associated with hypersensitivity to DNA-damaging agents, chromosomal instability (increased chromosome breakage) and defective DNA repair. {ECO:0000269 PubMed:12973351}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for FANCL

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

No data available for Genatlas for FANCL Gene

Publications for FANCL Gene

  1. Mechanistic insight into site-restricted monoubiquitination of FANCD2 by Ube2t, FANCL, and FANCI. (PMID: 19111657) Alpi AF … Patel KJ (Molecular cell 2008) 3 4 22 60
  2. UBE2T is the E2 in the Fanconi anemia pathway and undergoes negative autoregulation. (PMID: 16916645) Machida YJ … Dutta A (Molecular cell 2006) 3 4 22 60
  3. Structure of the human FANCL RING-Ube2T complex reveals determinants of cognate E3-E2 selection. (PMID: 24389026) Hodson C … Walden H (Structure (London, England : 1993) 2014) 3 4 60
  4. FAAP20: a novel ubiquitin-binding FA nuclear core-complex protein required for functional integrity of the FA-BRCA DNA repair pathway. (PMID: 22343915) Ali AM … Meetei AR (Blood 2012) 3 4 60
  5. Structural analysis of human FANCL, the E3 ligase in the Fanconi anemia pathway. (PMID: 21775430) Hodson C … Walden H (The Journal of biological chemistry 2011) 3 4 60

Products for FANCL Gene

Sources for FANCL Gene

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