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

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

    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; 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
    NEW
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    Genomic context

    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

    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

    BioGRID CRISPR Screen Phenotypes (115 hits/1321 screens)

    Associated conditions

    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

    Pathways from PubChem

    Interactions

    General gene information

    Clone Names

    • FLJ10335

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding  
    enables protein binding PubMed 
    enables ubiquitin protein ligase activity  
    enables ubiquitin protein ligase activity PubMed 
    enables ubiquitin protein ligase binding PubMed 
    enables ubiquitin-protein transferase activity PubMed 
    enables ubiquitin-protein transferase activity  
    Process Evidence Code Pubs
    involved_in DNA damage response PubMed 
    involved_in DNA repair  
    involved_in DNA repair PubMed 
    involved_in gamete generation  
    involved_in interstrand cross-link repair PubMed 
    involved_in protein monoubiquitination  
    involved_in protein monoubiquitination PubMed 
    involved_in regulation of cell population proliferation  
    Component Evidence Code Pubs
    part_of Fanconi anaemia nuclear complex PubMed 
    part_of Fanconi anaemia nuclear complex PubMed 
    located_in chromatin PubMed 
    located_in cytosol  
    located_in intracellular membrane-bounded organelle  
    located_in nuclear body  
    located_in nuclear envelope  
    located_in nucleoplasm  
    is_active_in nucleus  

    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_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)

    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

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