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

Gene ID: 55120, updated on 3-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (58159243..58241380, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (58164077..58246209, complement)
105.20220307 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 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: 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

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Related articles in PubMed

  1. FANCL gene mutations in premature ovarian insufficiency. Yang Y, et al. Hum Mutat, 2020 May. PMID 32048394
  2. 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
  3. Loss-of-Function FANCL Mutations Associate with Severe Fanconi Anemia Overlapping the VACTERL Association. Vetro A, et al. Hum Mutat, 2015 May. PMID 25754594
  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. 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

See all (92) 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

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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)

Genotypes

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 
part_of 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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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
    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_2023_10

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
    C9J512
    Related
    ENSP00000390991.2, ENST00000446381.6

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

    Related
    ENSP00000512628.1, ENST00000696434.1

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

  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

  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
    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
    C9J512

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

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

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

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

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

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

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

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

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

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

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

    UniProtKB/TrEMBL
    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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