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    FANCL FA complementation group L [ Homo sapiens (human) ]

    Gene ID: 55120, updated on 10-Dec-2024

    Summary

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    Official Symbol
    FANCLprovided by HGNC
    Official Full Name
    FA complementation group Lprovided by HGNC
    Primary source
    HGNC:HGNC:20748
    See related
    Ensembl:ENSG00000115392 MIM:608111; AllianceGenome:HGNC:20748
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    POG; PHF9; FAAP43
    Summary
    This gene encodes a ubiquitin ligase that is a member of the Fanconi anemia complementation group (FANC). Members of this group are related by their assembly into a common nuclear protein complex rather than by sequence similarity. This gene encodes the protein for complementation group L that mediates monoubiquitination of FANCD2 as well as FANCI. Fanconi anemia is a genetically heterogeneous recessive disorder characterized by cytogenetic instability, hypersensitivity to DNA crosslinking agents, increased chromosomal breakage, and defective DNA repair. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2018]
    Expression
    Ubiquitous expression in adrenal (RPKM 16.9), testis (RPKM 12.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See FANCL in Genome Data Viewer
    Location:
    2p16.1
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (58159243..58241380, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (58164077..58246209, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (58386382..58468460, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124907770 Neighboring gene VRK serine/threonine kinase 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:58206217-58206824 Neighboring gene MPRA-validated peak3709 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15792 Neighboring gene formin-2-like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:58273209-58273764 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:58273765-58274320 Neighboring gene Sharpr-MPRA regulatory region 1372 Neighboring gene VRK2 intron CAGE-defined low expression enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:58343433-58343934 Neighboring gene NANOG hESC enhancer GRCh37_chr2:58345900-58346401 Neighboring gene MPRA-validated peak3710 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:58434313-58435228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11507 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15794 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:58478751-58479291 Neighboring gene eukaryotic translation initiation factor 3 subunit F pseudogene 3 Neighboring gene long intergenic non-protein coding RNA 1795

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Autosomal recessive systemic microangiopathy associated with FANCL Fanconi anaemia. Cousyn L, et al. J Neurol Neurosurg Psychiatry, 2023 Dec 14. PMID 37451692
    2. Altered expression of FANCL confers mitomycin C sensitivity in Calu-6 lung cancer cells. Zhang J, et al. Cancer Biol Ther, 2006 Dec. PMID 17106252
    3. FAVL impairment of the Fanconi anemia pathway promotes the development of human bladder cancer. Panneerselvam J, et al. Cell Cycle, 2012 Aug 1. PMID 22828653, Free PMC Article
    4. The PI3K/Akt1 pathway enhances steady-state levels of FANCL. Dao KH, et al. Mol Biol Cell, 2013 Aug. PMID 23783032, Free PMC Article
    5. A founder variant in the South Asian population leads to a high prevalence of FANCL Fanconi anemia cases in India. Donovan FX, et al. Hum Mutat, 2020 Jan. PMID 31513304, Free PMC Article

    See all (94) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Autosomal recessive systemic microangiopathy associated with FANCL Fanconi anaemia.
      Title: Autosomal recessive systemic microangiopathy associated with FANCL Fanconi anaemia.
    2. FANCL gene mutations in premature ovarian insufficiency.
      Title: FANCL gene mutations in premature ovarian insufficiency.
    3. Severe telomere shortening in Fanconi anemia complementation group L.
      Title: Severe telomere shortening in Fanconi anemia complementation group L.
    4. A founder variant in the South Asian population leads to a high prevalence of FANCL Fanconi anemia cases in India.
      Title: A founder variant in the South Asian population leads to a high prevalence of FANCL Fanconi anemia cases in India.
    5. Characterization of FANCL variants observed in patient cancer cells.
      Title: Characterization of FANCL variants observed in patient cancer cells.
    6. A novel homozygous mutation c.822_823insCTTTCAGG (p.Asp275LeufsX13) in the FANCL gene identified in a Chinese patient with Fanconi anemia.
      Title: Novel homozygous FANCL mutation and somatic heterozygous SETBP1 mutation in a Chinese girl with Fanconi Anemia.
    7. Using small interfering RNA (siRNA), knockdown of FANCF, FANCL, or FANCD2 inhibited function of the FA/BRCA pathway in A549, A549/DDP and SK-MES-1 cells, and potentiated sensitivity of the three cells to cisplatin.
      Title: RNA interferences targeting the Fanconi anemia/BRCA pathway upstream genes reverse cisplatin resistance in drug-resistant lung cancer cells.
    8. Loss-of-Function FANCL Mutations Associate with Severe Fanconi Anemia Overlapping the VACTERL Association
      Title: Loss-of-Function FANCL Mutations Associate with Severe Fanconi Anemia Overlapping the VACTERL Association.
    9. a signal transduction pathway involved in self-renewal and survival of hematopoietic stem cells also functions to stabilize FANCL and suggesting that FANCL participates directly in support of stem cell function.
      Title: The PI3K/Akt1 pathway enhances steady-state levels of FANCL.
    10. FAVL elevation can increase the tumorigenic potential of bladder cancer cells, including the invasive potential that confers the development of advanced bladder cancer.
      Title: FAVL impairment of the Fanconi anemia pathway promotes the development of human bladder cancer.
    Submit: New GeneRIF Correction See all GeneRIFs (25)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Fanconi anemia complementation group L
    MedGen: C3469528 OMIM: 614083 GeneReviews: Fanconi Anemia
    		Compare labs

    EBI GWAS Catalog

    Description
    Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
    EBI GWAS Catalog
    Biological insights from 108 schizophrenia-associated genetic loci.
    EBI GWAS Catalog
    Genetic determinants of common epilepsies: a meta-analysis of genome-wide association studies.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10335

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin protein ligase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ubiquitin protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin-protein transferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ubiquitin-protein transferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA damage response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA repair IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in gamete generation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in interstrand cross-link repair NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in protein monoubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein monoubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of Fanconi anaemia nuclear complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of Fanconi anaemia nuclear complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nuclear envelope IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase FANCL
    Names
    Fanconi anemia complementation group L
    PHD finger protein 9
    RING-type E3 ubiquitin transferase FANCL
    fanconi anemia group L protein
    fanconi anemia-associated polypeptide of 43 kDa
    NP_001108108.1
    NP_001361544.1
    NP_001397721.1
    NP_060532.2
    XP_005264452.1
    XP_011531241.1
    XP_011531242.1
    XP_011531244.1
    XP_011531246.1
    XP_011531247.1
    XP_016859905.1
    XP_047300808.1
    XP_047300809.1
    XP_047300810.1
    XP_047300811.1
    XP_047300812.1
    XP_054198691.1
    XP_054198692.1
    XP_054198693.1
    XP_054198694.1
    XP_054198695.1
    XP_054198696.1
    XP_054198697.1
    XP_054198698.1
    XP_054198699.1
    XP_054198700.1
    XP_054198701.1
    XP_054198702.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_007418.1 RefSeqGene

      Range
      5000..87137
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_501

    mRNA and Protein(s)

    1. NM_001114636.2 → NP_001108108.1  E3 ubiquitin-protein ligase FANCL isoform 1

      See identical proteins and their annotated locations for NP_001108108.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC007250
      Consensus CDS
      CCDS46294.1
      UniProtKB/TrEMBL
      A0A8Q3WMD8
      Related
      ENSP00000385021.3, ENST00000402135.8
      Conserved Domains (3) summary
      cd16490
      Location:312 → 367
      RING-CH-C4HC3_FANCL; RING-CH finger (C4HC3-type) [structural motif]
      pfam09765
      Location:23 → 300
      WD-3; WD-repeat region
      pfam11793
      Location:308 → 376
      FANCL_C; FANCL C-terminal domain

    2. NM_001374615.1 → NP_001361544.1  E3 ubiquitin-protein ligase FANCL isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC007250
      Consensus CDS
      CCDS92760.1
      UniProtKB/TrEMBL
      A0A8Q3WMD8, H7C1M0
      Related
      ENSP00000400969.3, ENST00000427708.7
      Conserved Domains (2) summary
      pfam09765
      Location:23 → 310
      WD-3; WD-repeat region
      pfam11793
      Location:318 → 386
      FANCL_C; FANCL C-terminal domain

    3. NM_001410792.1 → NP_001397721.1  E3 ubiquitin-protein ligase FANCL isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC007250
      Consensus CDS
      CCDS92759.1
      UniProtKB/TrEMBL
      A0A8Q3SIK5, A0A8Q3WMD8
      Related
      ENSP00000512562.1, ENST00000696326.1

    4. NM_018062.4 → NP_060532.2  E3 ubiquitin-protein ligase FANCL isoform 2

      See identical proteins and their annotated locations for NP_060532.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has an alternate splice site in the CDS, as compared to variant 1. The resulting isoform (2) lacks an internal segment and has identical N- and C-termini, as compared to isoform 1.
      Source sequence(s)
      AC007250
      Consensus CDS
      CCDS1860.1
      UniProtKB/Swiss-Prot
      Q6GU60, Q9NW38
      UniProtKB/TrEMBL
      A0A8Q3WMD8
      Related
      ENSP00000233741.5, ENST00000233741.9
      Conserved Domains (3) summary
      cd16490
      Location:307 → 362
      RING-CH-C4HC3_FANCL; RING-CH finger (C4HC3-type) [structural motif]
      pfam09765
      Location:23 → 295
      WD-3; WD-repeat region
      pfam11793
      Location:303 → 371
      FANCL_C; FANCL C-terminal domain

    RNA

    1. NR_156742.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks four consecutive internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC007250
      Related
      ENST00000403676.6

    2. NR_164659.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC007250
      Related
      ENST00000696545.1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      58159243..58241380 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047444854.1 → XP_047300810.1  E3 ubiquitin-protein ligase FANCL isoform X7

      UniProtKB/TrEMBL
      A0A8Q3SIK9, C9J512
      Related
      ENSP00000390991.2, ENST00000446381.6

    2. XM_047444856.1 → XP_047300812.1  E3 ubiquitin-protein ligase FANCL isoform X12

      UniProtKB/TrEMBL
      A0A8Q3WMH1
      Related
      ENSP00000512628.1, ENST00000696434.1

    3. XM_047444853.1 → XP_047300809.1  E3 ubiquitin-protein ligase FANCL isoform X6

      UniProtKB/TrEMBL
      A0A8Q3SIK9

    4. XM_017004416.2 → XP_016859905.1  E3 ubiquitin-protein ligase FANCL isoform X11

      UniProtKB/TrEMBL
      A0A8Q3WMH1

    5. XM_047444855.1 → XP_047300811.1  E3 ubiquitin-protein ligase FANCL isoform X9

      UniProtKB/TrEMBL
      A0A8Q3WMH1

    6. XM_011532945.3 → XP_011531247.1  E3 ubiquitin-protein ligase FANCL isoform X10

      UniProtKB/TrEMBL
      A0A8Q3WMH1
      Conserved Domains (2) summary
      pfam09765
      Location:8 → 183
      WD-3; WD-repeat region
      pfam11793
      Location:191 → 252
      FANCL_C; FANCL C-terminal domain

    7. XM_011532944.3 → XP_011531246.1  E3 ubiquitin-protein ligase FANCL isoform X8

      UniProtKB/TrEMBL
      A0A8Q3WMH1
      Conserved Domains (2) summary
      pfam09765
      Location:8 → 198
      WD-3; WD-repeat region
      pfam11793
      Location:206 → 267
      FANCL_C; FANCL C-terminal domain

    8. XM_005264395.5 → XP_005264452.1  E3 ubiquitin-protein ligase FANCL isoform X4

      UniProtKB/TrEMBL
      A0A8Q3WMD8
      Conserved Domains (2) summary
      pfam09765
      Location:15 → 295
      WD-3; WD-repeat region
      pfam11793
      Location:303 → 364
      FANCL_C; FANCL C-terminal domain

    9. XM_011532940.4 → XP_011531242.1  E3 ubiquitin-protein ligase FANCL isoform X2

      UniProtKB/TrEMBL
      A0A8Q3WMD8
      Conserved Domains (2) summary
      pfam09765
      Location:15 → 310
      WD-3; WD-repeat region
      pfam11793
      Location:318 → 379
      FANCL_C; FANCL C-terminal domain

    10. XM_011532942.4 → XP_011531244.1  E3 ubiquitin-protein ligase FANCL isoform X3

      UniProtKB/TrEMBL
      A0A8Q3WMD8
      Conserved Domains (2) summary
      pfam09765
      Location:15 → 300
      WD-3; WD-repeat region
      pfam11793
      Location:308 → 369
      FANCL_C; FANCL C-terminal domain

    11. XM_011532939.4 → XP_011531241.1  E3 ubiquitin-protein ligase FANCL isoform X1

      UniProtKB/TrEMBL
      A0A8Q3WMD8
      Conserved Domains (2) summary
      pfam09765
      Location:15 → 315
      WD-3; WD-repeat region
      pfam11793
      Location:323 → 384
      FANCL_C; FANCL C-terminal domain

    12. XM_047444852.1 → XP_047300808.1  E3 ubiquitin-protein ligase FANCL isoform X5

      UniProtKB/TrEMBL
      A0A8Q3SIQ9, A0A8Q3SIR9
      Related
      ENSP00000512723.1, ENST00000696565.1

    RNA

    1. XR_007077528.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      58164077..58246209 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054342722.1 → XP_054198697.1  E3 ubiquitin-protein ligase FANCL isoform X7

      UniProtKB/TrEMBL
      A0A8Q3SIK9, C9J512

    2. XM_054342727.1 → XP_054198702.1  E3 ubiquitin-protein ligase FANCL isoform X12

      UniProtKB/TrEMBL
      A0A8Q3WMH1

    3. XM_054342721.1 → XP_054198696.1  E3 ubiquitin-protein ligase FANCL isoform X6

      UniProtKB/TrEMBL
      A0A8Q3SIK9

    4. XM_054342726.1 → XP_054198701.1  E3 ubiquitin-protein ligase FANCL isoform X11

      UniProtKB/TrEMBL
      A0A8Q3WMH1

    5. XM_054342724.1 → XP_054198699.1  E3 ubiquitin-protein ligase FANCL isoform X9

      UniProtKB/TrEMBL
      A0A8Q3WMH1

    6. XM_054342725.1 → XP_054198700.1  E3 ubiquitin-protein ligase FANCL isoform X10

      UniProtKB/TrEMBL
      A0A8Q3WMH1

    7. XM_054342723.1 → XP_054198698.1  E3 ubiquitin-protein ligase FANCL isoform X8

      UniProtKB/TrEMBL
      A0A8Q3WMH1

    8. XM_054342719.1 → XP_054198694.1  E3 ubiquitin-protein ligase FANCL isoform X4

      UniProtKB/TrEMBL
      A0A8Q3WMD8

    9. XM_054342717.1 → XP_054198692.1  E3 ubiquitin-protein ligase FANCL isoform X2

      UniProtKB/TrEMBL
      A0A8Q3WMD8

    10. XM_054342718.1 → XP_054198693.1  E3 ubiquitin-protein ligase FANCL isoform X3

      UniProtKB/TrEMBL
      A0A8Q3WMD8

    11. XM_054342716.1 → XP_054198691.1  E3 ubiquitin-protein ligase FANCL isoform X1

      UniProtKB/TrEMBL
      A0A8Q3WMD8

    12. XM_054342720.1 → XP_054198695.1  E3 ubiquitin-protein ligase FANCL isoform X5

      UniProtKB/TrEMBL
      A0A8Q3SIQ9, A0A8Q3SIR9

    RNA

    1. XR_008486423.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NW38.2 GenPept UniProtKB/Swiss-Prot:Q9NW38

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