Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	55120
Gene name	FA complementation group L
Gene symbol	FANCL
Synonyms (NCBI Gene)	FAAP43PHF9POG
Chromosome	2
Chromosome location	2p16.1
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 p

Show/Hide all (9)

SNP ID	Visualize variation	Clinical significance	Consequence
rs144729980	C>G,T	Likely-pathogenic	Splice donor variant, intron variant
rs753105795	G>A,C	Pathogenic	Coding sequence variant, missense variant, stop gained, non coding transcript variant, intron variant
rs761039364	G>-,GG	Pathogenic	5 prime UTR variant, frameshift variant, coding sequence variant, non coding transcript variant
rs779544327	TT>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant, intron variant
rs869320684	G>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant, intron variant
rs869320685	A>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant, intron variant
rs878855046	ACCAGAAGCATCT>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant, intron variant
rs1205006300	C>A	Likely-pathogenic	Splice donor variant, intron variant
rs1558741321	C>A	Likely-pathogenic	Non coding transcript variant, stop gained, coding sequence variant, genic downstream transcript variant

Show/Hide all (8)

miRTarBase ID	miRNA	Experiments	Reference
MIRT727691	hsa-miR-30a-5p	HITS-CLIP	22473208
MIRT727690	hsa-miR-30b-5p	HITS-CLIP	22473208
MIRT727688	hsa-miR-30c-5p	HITS-CLIP	22473208
MIRT727689	hsa-miR-30d-5p	HITS-CLIP	22473208
MIRT727687	hsa-miR-30e-5p	HITS-CLIP	22473208
MIRT2530840	hsa-miR-3161	CLIP-seq
MIRT2530841	hsa-miR-4775	CLIP-seq
MIRT2530842	hsa-miR-590-3p	CLIP-seq

Show/Hide all (34)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	IDA	22343915
GO:0004842	Function	Ubiquitin-protein transferase activity	IDA	16916645, 19111657
GO:0004842	Function	Ubiquitin-protein transferase activity	IEA
GO:0004842	Function	Ubiquitin-protein transferase activity	ISS
GO:0005515	Function	Protein binding	IPI	24389026, 25416956, 32296183, 35512704
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005635	Component	Nuclear envelope	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006281	Process	DNA repair	IBA
GO:0006281	Process	DNA repair	IEA
GO:0006281	Process	DNA repair	IMP	16916645
GO:0006513	Process	Protein monoubiquitination	IBA
GO:0006513	Process	Protein monoubiquitination	IDA	16916645, 24389026
GO:0006974	Process	DNA damage response	IEA
GO:0006974	Process	DNA damage response	IMP	16916645
GO:0007276	Process	Gamete generation	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0016567	Process	Protein ubiquitination	IEA
GO:0016604	Component	Nuclear body	IDA
GO:0016740	Function	Transferase activity	IEA
GO:0031625	Function	Ubiquitin protein ligase binding	IPI	16916645, 17938197, 19111657
GO:0036297	Process	Interstrand cross-link repair	IEA
GO:0036297	Process	Interstrand cross-link repair	NAS	19965384
GO:0042127	Process	Regulation of cell population proliferation	IEA
GO:0043240	Component	Fanconi anaemia nuclear complex	IDA	20347428, 22343915
GO:0043240	Component	Fanconi anaemia nuclear complex	IEA
GO:0043240	Component	Fanconi anaemia nuclear complex	NAS	22343915
GO:0046872	Function	Metal ion binding	IEA
GO:0061630	Function	Ubiquitin protein ligase activity	IBA
GO:0061630	Function	Ubiquitin protein ligase activity	IDA	19589784
GO:0061630	Function	Ubiquitin protein ligase activity	IEA

MIM	HGNC	e!Ensembl
608111	20748	ENSG00000115392

Q9NW38

Protein name

E3 ubiquitin-protein ligase FANCL (EC 2.3.2.27) (Fanconi anemia group L protein) (Fanconi anemia-associated polypeptide of 43 kDa) (FAAP43) (RING-type E3 ubiquitin transferase FANCL)

Protein function

Ubiquitin ligase protein that mediates monoubiquitination of FANCD2 in the presence of UBE2T, a key step in the DNA damage pathway (PubMed:12973351, PubMed:16916645, PubMed:17938197, PubMed:19111657, PubMed:24389026). Also mediates monoubiquitin

PDB

3ZQS , 4CCG , 7KZP , 7KZQ , 7KZR , 7KZS , 7KZT , 7KZV

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF09765	FANCL_d1	5 → 93	FANCL UBC-like domain 1	Domain
PF18890	FANCL_d2	108 → 197	FANCL UBC-like domain 2	Domain
PF18891	FANCL_d3	199 → 295	FANCL UBC-like domain 3	Domain
PF11793	FANCL_C	303 → 371	FANCL C-terminal domain	Domain

Sequence

MAVTEASLLRQCPLLLPQNRSKTVYEGFISAQGRDFHLRIVLPEDLQLKNARLLCSWQLR
TILSGYHRIVQQRMQHSPDLMSFMMELKMLLEVALKNRQELYALPPPPQFYSSLIEEIGT
LGWDKLVYADTCFSTIKLKAEDASGREHLITLKLKAKYPAESPDYFVDFPVPFCASWTPQ
SSLISIYSQFLAAIESLKAFWDVMDEIDEKTWVLEPEKPPRSATARRIALGNNVSINIEV
DPRHPTMLPECFFLGADHVVKPLGIKLSRNIHLWDPENSVLQNLKDVLEIDFPARAILEK
SDFTMDCGICYAYQLDGTIPDQVCDNSQCGQPFHQICLYEWLRGLLTSRQSFNIIFGECP
YCSKPITLKMSGRKH

Sequence length

375

Interactions

View interactions

	KEGG		Reactome
	Fanconi anemia pathway Ubiquitin mediated proteolysis		Fanconi Anemia Pathway

874

Show/Hide Causal Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
FANCL-related disorder	Likely pathogenic	rs2466610093	RCV003406179
Fanconi anemia	Likely pathogenic; Pathogenic	rs750871999, rs768814501, rs1558735946, rs1490932431, rs1191111879, rs772037896, rs1196510455, rs2104783888, rs2105148069, rs1423411761, rs1693048371, rs779587713, rs1204245665, rs1386476396, rs2467657340 View all (57 more)	RCV005408836 RCV001377977 RCV001384023 RCV001390762 RCV003635972 RCV003635974 RCV001919910 RCV002009693 RCV001889720 RCV001983048 RCV002256968 RCV002282910 RCV002612477 RCV002647442 RCV003117124 RCV002676578 RCV002790386 RCV002814331 RCV001388973 RCV001857678 RCV002862042 RCV002871725 RCV002970673 RCV003005679 RCV003042113 RCV000232991 RCV003636035 RCV003636036 RCV005100166 RCV003523190 RCV003779033 RCV003636037 RCV003636038 RCV003523967 RCV003524285 RCV003635910 RCV003522183 RCV003525005 RCV003525080 RCV003525171 RCV003525191 RCV003523738 RCV003522703 RCV003522639 RCV003524799 RCV003637280 RCV003637234 RCV003637348 RCV003637794 RCV003637863 RCV003637901 RCV003635544 RCV003635435 RCV003635618 RCV003635738 RCV003635604 RCV003635803 RCV003636561 RCV003636821 RCV003636848 RCV003858041 RCV003842829 RCV005101929 RCV000544104 RCV000630868 RCV000690372 RCV000697873 RCV000686056 RCV000705984 RCV000694144 RCV000686799 RCV001044015 RCV001069191 RCV001862686 RCV001381353 RCV001202568 RCV001205714 RCV001231987
Fanconi anemia complementation group A	Pathogenic	rs2104799592	RCV002227888
Fanconi anemia complementation group L	Likely pathogenic; Pathogenic	rs750871999, rs768814501, rs1490932431, rs2104799800, rs772037896, rs1693048371, rs2467657643, rs779587713, rs2467657340, rs869320684, rs869320685, rs771742741, rs2104795249, rs2466546655, rs1364312021 View all (33 more)	RCV002504517 RCV003462954 RCV004570975 RCV001806294 RCV005032201 RCV003464431 RCV002283914 RCV003459763 RCV003465815 RCV000191022 RCV000191023 RCV005027986 RCV003461551 RCV003461552 RCV003461554 RCV003461555 RCV003468185 RCV003461556 RCV003461557 RCV003461558 RCV003461559 RCV003468186 RCV003468188 RCV003461560 RCV003461561 RCV003461562 RCV003461563 RCV003468189 RCV003461564 RCV003468190 RCV004574067 RCV000387483 RCV004574072 RCV004574283 RCV004573265 RCV004573356 RCV004576594 RCV004576595 RCV004576596 RCV004576597 RCV004576598 RCV003470721 RCV003459665 RCV001729683 RCV001000101 RCV001000102 RCV005029685 RCV001195068 RCV002480759
Squamous cell lung carcinoma	Likely pathogenic	rs2467653249	RCV005931541
VACTERL association, X-linked, with or without hydrocephalus	Likely pathogenic; Pathogenic	rs869320685	RCV001195065
VATER association	Pathogenic	rs869320684	RCV001195063

Show/Hide Unknown Diseases (20)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Benign; Uncertain significance	rs75902380, rs1060501896	RCV005923756 RCV005899471
Cervical cancer	Benign	rs75902380	RCV005923757
Cholangiocarcinoma	Benign	rs75902380, rs79588315	RCV005923760 RCV005891432
Chronic lymphocytic leukemia/small lymphocytic lymphoma	Benign	rs79588315	RCV005891433
Colon adenocarcinoma	Likely benign	rs1021979267	RCV005931470
Familial cancer of breast	Benign	rs12624152, rs79588315	RCV005920143 RCV005891421
Familial pancreatic carcinoma	Benign	rs79588315	RCV005891427
Hepatocellular carcinoma	Benign	rs79588315	RCV005891423
Lymphoma	Benign	rs79588315	RCV005891429
Malignant lymphoma, large B-cell, diffuse	Benign	rs79588315	RCV005891428
Mesothelioma	Benign	rs79588315	RCV005891422
Nonpapillary renal cell carcinoma	Benign	rs79588315	RCV005891424
Ovarian cancer	Benign	rs79588315	RCV005891425
Premature ovarian insufficiency	Conflicting classifications of pathogenicity	rs747253294	RCV000766177
Sarcoma	Benign; Likely benign	rs75902380, rs757560351	RCV005923758 RCV005934679
See cases	Uncertain significance	rs563513081	RCV002252132
Thymoma	Benign	rs79588315	RCV005891431
Uterine carcinosarcoma	Benign	rs75902380, rs79588315	RCV005923759 RCV005891430
Uterine corpus endometrial carcinoma	Benign	rs75902380	RCV005923761
Uveal melanoma	Benign	rs79588315	RCV005891426

Show/Hide Text Mining Associations (21)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adenomatous Polyposis Coli	Associate	39519399
Anemia Hemolytic	Associate	30942098, 36894310
Bone Marrow Failure Disorders	Associate	37327301
Bronchopulmonary Dysplasia	Associate	32091150
Carcinogenesis	Associate	32420600
Colorectal Neoplasms	Associate	35567913, 36356413
Esophageal Neoplasms	Associate	21279724
Esophageal Squamous Cell Carcinoma	Associate	21279724
Fanconi Anemia	Associate	15256425, 16720839, 17106252, 19129235, 19405097, 21279724, 23613520, 23783032, 26119737, 27986371, 28535027, 28678401, 31513304, 31525021, 32420600, 33727708 View all (1 more)
Genetic Diseases Inborn	Associate	30122582
Hereditary Breast and Ovarian Cancer Syndrome	Associate	30306255
Leukemia Myeloid Acute	Associate	33893150
Lung Neoplasms	Associate	26385482
Microsatellite Instability	Associate	36356413
Neoplasms	Associate	17106252, 30665374, 30942098, 32420600, 37327301, 40421962
Neoplastic Syndromes Hereditary	Associate	28050010
Obesity	Associate	24885863, 29220676
Pancytopenia	Associate	37327301
Precursor T Cell Lymphoblastic Leukemia Lymphoma	Associate	18607065
Recombinant chromosome 8 syndrome	Associate	30293905, 36627197
Squamous Cell Carcinoma of Head and Neck	Associate	28678401

FANCL (FA complementation group L)