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

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: mouse all
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Genomic context

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Autosomal recessive systemic microangiopathy associated with FANCL Fanconi anaemia.
Title: Autosomal recessive systemic microangiopathy associated with FANCL Fanconi anaemia.
FANCL gene mutations in premature ovarian insufficiency.
Title: FANCL gene mutations in premature ovarian insufficiency.
Severe telomere shortening in Fanconi anemia complementation group L.
Title: Severe telomere shortening in Fanconi anemia complementation group L.
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.
Characterization of FANCL variants observed in patient cancer cells.
Title: Characterization of FANCL variants observed in patient cancer cells.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic determinants of common epilepsies: a meta-analysis of genome-wide association studies. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-18292 (e-PCR)
- UniSTS:30989

SHGC-35879 (e-PCR)
- UniSTS:40461

D2S1547E (e-PCR)
- UniSTS:150632

RH78793 (e-PCR)
- UniSTS:2746

G44723 (e-PCR)
- UniSTS:95198

D2S2913 (e-PCR)
- UniSTS:238

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

EC 2.3.2.27

NP_001361544.1

EC 2.3.2.27

NP_001397721.1

EC 2.3.2.27

NP_060532.2

EC 2.3.2.27

XP_005264452.1

EC 2.3.2.27

XP_011531241.1

EC 2.3.2.27

XP_011531242.1

EC 2.3.2.27

XP_011531244.1

EC 2.3.2.27

XP_011531246.1

EC 2.3.2.27

XP_011531247.1

EC 2.3.2.27

XP_016859905.1

EC 2.3.2.27

XP_047300808.1

EC 2.3.2.27

XP_047300809.1

EC 2.3.2.27

XP_047300810.1

EC 2.3.2.27

XP_047300811.1

EC 2.3.2.27

XP_047300812.1

EC 2.3.2.27

XP_054198691.1

EC 2.3.2.27

XP_054198692.1

EC 2.3.2.27

XP_054198693.1

EC 2.3.2.27

XP_054198694.1

EC 2.3.2.27

XP_054198695.1

EC 2.3.2.27

XP_054198696.1

EC 2.3.2.27

XP_054198697.1

EC 2.3.2.27

XP_054198698.1

EC 2.3.2.27

XP_054198699.1

EC 2.3.2.27

XP_054198700.1

EC 2.3.2.27

XP_054198701.1

EC 2.3.2.27

XP_054198702.1

EC 2.3.2.27

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

NG_007418.1 RefSeqGene

Range

5000..87137

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_501

mRNA and Protein(s)

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
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
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
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

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
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

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

58159243..58241380 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

C9J512

Related

ENSP00000390991.2, ENST00000446381.6
XM_047444856.1 → XP_047300812.1 E3 ubiquitin-protein ligase FANCL isoform X12

Related

ENSP00000512628.1, ENST00000696434.1
XM_047444853.1 → XP_047300809.1 E3 ubiquitin-protein ligase FANCL isoform X6
XM_017004416.2 → XP_016859905.1 E3 ubiquitin-protein ligase FANCL isoform X11

UniProtKB/TrEMBL

A0A8Q3WMH1
XM_047444855.1 → XP_047300811.1 E3 ubiquitin-protein ligase FANCL isoform X9
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
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
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
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
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
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
XM_047444852.1 → XP_047300808.1 E3 ubiquitin-protein ligase FANCL isoform X5

UniProtKB/TrEMBL

A0A8Q3SIR9

Related

ENSP00000512723.1, ENST00000696565.1

RNA

XR_007077528.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

58164077..58246209 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

C9J512
XM_054342727.1 → XP_054198702.1 E3 ubiquitin-protein ligase FANCL isoform X12
XM_054342721.1 → XP_054198696.1 E3 ubiquitin-protein ligase FANCL isoform X6
XM_054342726.1 → XP_054198701.1 E3 ubiquitin-protein ligase FANCL isoform X11
XM_054342724.1 → XP_054198699.1 E3 ubiquitin-protein ligase FANCL isoform X9
XM_054342725.1 → XP_054198700.1 E3 ubiquitin-protein ligase FANCL isoform X10
XM_054342723.1 → XP_054198698.1 E3 ubiquitin-protein ligase FANCL isoform X8
XM_054342719.1 → XP_054198694.1 E3 ubiquitin-protein ligase FANCL isoform X4
XM_054342717.1 → XP_054198692.1 E3 ubiquitin-protein ligase FANCL isoform X2
XM_054342718.1 → XP_054198693.1 E3 ubiquitin-protein ligase FANCL isoform X3
XM_054342716.1 → XP_054198691.1 E3 ubiquitin-protein ligase FANCL isoform X1
XM_054342720.1 → XP_054198695.1 E3 ubiquitin-protein ligase FANCL isoform X5

UniProtKB/TrEMBL

A0A8Q3SIR9