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

    Gene ID: 55120, updated on 26-Jul-2021

    Summary

    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
    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
    NEW
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    Genomic context

    See FANCL in Genome Data Viewer
    Location:
    2p16.1
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (58159243..58241681, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (58386378..58468515, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene VRK serine/threonine kinase 2 Neighboring gene formin-2-like Neighboring gene VRK2 intron CAGE-defined low expression enhancer 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

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
    GeneReviews: Not available
    Biological insights from 108 schizophrenia-associated genetic loci.
    GeneReviews: Not available
    Fanconi anemia, complementation group L Compare labs
    Genetic determinants of common epilepsies: a meta-analysis of genome-wide association studies.
    GeneReviews: Not available
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    GeneReviews: Not available

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    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
    PubMed 
    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 repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in DNA repair IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cellular response to DNA damage stimulus 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 IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein monoubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    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 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    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
    PubMed 

    General protein information

    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_060532.2
    XP_005264452.1
    XP_011531241.1
    XP_011531242.1
    XP_011531243.1
    XP_011531244.1
    XP_011531246.1
    XP_011531247.1
    XP_016859904.1
    XP_016859905.1

    NCBI Reference Sequences (RefSeq)

    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_001114636.1NP_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)
      AK001197, AK225147, BC041627, DB032206
      Consensus CDS
      CCDS46294.1
      UniProtKB/Swiss-Prot
      Q9NW38
      Related
      ENSP00000385021.3, ENST00000402135.7
      Conserved Domains (3) summary
      cd16490
      Location:312367
      RING-CH-C4HC3_FANCL; RING-CH finger (C4HC3-type) [structural motif]
      pfam09765
      Location:23300
      WD-3; WD-repeat region
      pfam11793
      Location:308376
      FANCL_C; FANCL C-terminal domain
    2. NM_001374615.1NP_001361544.1  E3 ubiquitin-protein ligase FANCL isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC007250
      Conserved Domains (2) summary
      pfam09765
      Location:23310
      WD-3; WD-repeat region
      pfam11793
      Location:318386
      FANCL_C; FANCL C-terminal domain
    3. NM_018062.4NP_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
      Q9NW38
      Related
      ENSP00000233741.5, ENST00000233741.9
      Conserved Domains (3) summary
      cd16490
      Location:307362
      RING-CH-C4HC3_FANCL; RING-CH finger (C4HC3-type) [structural motif]
      pfam09765
      Location:23295
      WD-3; WD-repeat region
      pfam11793
      Location:303371
      FANCL_C; FANCL C-terminal domain

    RNA

    1. NR_156742.1 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
    2. NR_164659.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC007250

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

      Range
      58159243..58241681 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017004416.1XP_016859905.1  E3 ubiquitin-protein ligase FANCL isoform X10

      Related
      ENSP00000384046.1, ENST00000403676.5
    2. XM_011532940.3XP_011531242.1  E3 ubiquitin-protein ligase FANCL isoform X2

      Conserved Domains (2) summary
      pfam09765
      Location:15310
      WD-3; WD-repeat region
      pfam11793
      Location:318379
      FANCL_C; FANCL C-terminal domain
    3. XM_011532942.3XP_011531244.1  E3 ubiquitin-protein ligase FANCL isoform X5

      Conserved Domains (2) summary
      pfam09765
      Location:15300
      WD-3; WD-repeat region
      pfam11793
      Location:308369
      FANCL_C; FANCL C-terminal domain
    4. XM_011532941.2XP_011531243.1  E3 ubiquitin-protein ligase FANCL isoform X3

      Conserved Domains (2) summary
      pfam09765
      Location:15315
      WD-3; WD-repeat region
      pfam11793
      Location:323391
      FANCL_C; FANCL C-terminal domain
    5. XM_011532939.3XP_011531241.1  E3 ubiquitin-protein ligase FANCL isoform X1

      Conserved Domains (2) summary
      pfam09765
      Location:15315
      WD-3; WD-repeat region
      pfam11793
      Location:323384
      FANCL_C; FANCL C-terminal domain
    6. XM_011532945.2XP_011531247.1  E3 ubiquitin-protein ligase FANCL isoform X9

      Conserved Domains (2) summary
      pfam09765
      Location:8183
      WD-3; WD-repeat region
      pfam11793
      Location:191252
      FANCL_C; FANCL C-terminal domain
    7. XM_011532944.2XP_011531246.1  E3 ubiquitin-protein ligase FANCL isoform X8

      Conserved Domains (2) summary
      pfam09765
      Location:8198
      WD-3; WD-repeat region
      pfam11793
      Location:206267
      FANCL_C; FANCL C-terminal domain
    8. XM_005264395.4XP_005264452.1  E3 ubiquitin-protein ligase FANCL isoform X6

      Conserved Domains (2) summary
      pfam09765
      Location:15295
      WD-3; WD-repeat region
      pfam11793
      Location:303364
      FANCL_C; FANCL C-terminal domain
    9. XM_017004415.2XP_016859904.1  E3 ubiquitin-protein ligase FANCL isoform X7

    RNA

    1. XR_002959309.1 RNA Sequence

    2. XR_001738803.2 RNA Sequence

    3. XR_939692.2 RNA Sequence

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