FANCF

FA complementation group F, the group of FA complementation groups|FA core complex

Basic information

Region (hg38): 11:22622533-22625823

Links

ENSG00000183161 ∙ NCBI:2188 ∙ OMIM:613897 ∙ HGNC:3587 ∙ Uniprot:Q9NPI8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Fanconi anemia complementation group F (Definitive), mode of inheritance: AR
• Fanconi anemia complementation group F (Strong), mode of inheritance: AR
• Fanconi anemia (Supportive), mode of inheritance: AR
• Fanconi anemia complementation group F (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Fanconia anemia, complementation group F	AR	Allergy/Immunology/Infectious; Cardiovascular; Hematologic; Oncologic	Specific treatments can help manifestations (eg, oral androgens for blood counts; G-CSF for neutrophil count); HSCT can be curative, but solid tumor risk may remain; Surveillance for complications such as bone marrow failure is recommended; Fanconi anemia can involve congenital cardiac (and other) anomalies, and awareness may allow early management	Audiologic/Otolaryngologic; Allergy/Immunology/Infectious; Cardiovascular; Dermatologic; Gastrointestinal; Hematologic; Musculoskeletal; Neurologic; Oncologic; Ophthalmologic; Renal	10615118; 20301575

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FANCF gene.

• Fanconi anemia (17 variants)
• Fanconi anemia complementation group F (8 variants)
• not specified (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FANCF gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			8	98	4	110
missense			211	4	1	216
nonsense	4	9	3			16
start loss	2	2				4
frameshift	13	14	1			28
inframe indel			4			4
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			35	3	10	48
Total	19	25	262	105	15

Highest pathogenic variant AF is 0.000125

Variants in FANCF

This is a list of pathogenic ClinVar variants found in the FANCF region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-22622563-C-T		Fanconi anemia complementation group F	Benign (Jan 12, 2018)
11-22622612-T-C		Fanconi anemia complementation group F	Uncertain significance (Jan 13, 2018)
11-22622615-T-C		Fanconi anemia complementation group F	Uncertain significance (Jan 13, 2018)
11-22622802-A-G		Fanconi anemia complementation group F	Uncertain significance (Jan 12, 2018)
11-22622807-A-G		not specified • Fanconi anemia complementation group F	Uncertain significance (Jan 13, 2018)
11-22622990-C-T		Fanconi anemia complementation group F	Uncertain significance (Jan 12, 2018)
11-22623054-C-G		Fanconi anemia complementation group F	Uncertain significance (Jan 12, 2018)
11-22623056-C-T		Fanconi anemia complementation group F	Uncertain significance (Jan 13, 2018)
11-22623057-G-A		Fanconi anemia complementation group F	Benign (Jan 12, 2018)
11-22623151-A-T		Fanconi anemia complementation group F	Uncertain significance (Jan 12, 2018)
11-22623161-A-C		Fanconi anemia complementation group F	Uncertain significance (Jan 13, 2018)
11-22623174-T-C		Fanconi anemia complementation group F	Uncertain significance (Jan 13, 2018)
11-22623177-C-G		Fanconi anemia complementation group F	Uncertain significance (Jan 13, 2018)
11-22623202-C-T		Fanconi anemia complementation group F	Likely benign (Jan 12, 2018)
11-22623246-T-C		Fanconi anemia complementation group F	Uncertain significance (Jan 13, 2018)
11-22623266-T-C		Fanconi anemia complementation group F	Uncertain significance (Jan 12, 2018)
11-22623347-A-AT		Fanconi anemia	Uncertain significance (Jun 14, 2016)
11-22623496-G-T		Fanconi anemia complementation group F	Uncertain significance (Jan 12, 2018)
11-22623567-A-T		Fanconi anemia complementation group F	Uncertain significance (Jan 13, 2018)
11-22623592-T-C		Fanconi anemia complementation group F	Uncertain significance (Jan 13, 2018)
11-22623829-C-T		Fanconi anemia complementation group F	Uncertain significance (Jan 12, 2018)
11-22623867-G-A		Fanconi anemia complementation group F	Benign (Jan 13, 2018)
11-22623904-T-C		Fanconi anemia complementation group F	Uncertain significance (Jan 13, 2018)
11-22623948-A-C		Fanconi anemia complementation group F	Benign (Apr 27, 2017)
11-22623977-C-A		Fanconi anemia complementation group F	Likely benign (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FANCF	protein_coding	protein_coding	ENST00000327470	1	3309

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.459	0.455	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.83	257	187	1.38	0.00000982	2383
Missense in Polyphen		70	53.471	1.3091		722
Synonymous	-3.08	120	84.1	1.43	0.00000439	838
Loss of Function	1.16	0	1.57	0.00	6.91e-8	13

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA repair protein that may operate in a postreplication repair or a cell cycle checkpoint function. May be implicated in interstrand DNA cross-link repair and in the maintenance of normal chromosome stability (By similarity). {ECO:0000250}.
• Disease: DISEASE: Fanconi anemia complementation group F (FANCF) [MIM:603467]: A disorder affecting all bone marrow elements and resulting in anemia, leukopenia and thrombopenia. It is associated with cardiac, renal and limb malformations, dermal pigmentary changes, and a predisposition to the development of malignancies. At the cellular level it is associated with hypersensitivity to DNA-damaging agents, chromosomal instability (increased chromosome breakage) and defective DNA repair. {ECO:0000269|PubMed:10615118}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Fanconi anemia pathway - Homo sapiens (human);Fanconi Anemia Pathway;DNA Repair;role of brca1 brca2 and atr in cancer susceptibility;brca1 dependent ub ligase activity;Fanconi anemia pathway;BARD1 signaling events (Consensus)

Recessive Scores

• pRec: 0.292

Intolerance Scores

• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.09

Haploinsufficiency Scores

• pHI: 0.0822
• hipred: Y
• hipred_score: 0.581
• ghis: 0.406

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.965

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Fancf
• Phenotype: neoplasm; endocrine/exocrine gland phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: ovarian follicle development;cellular response to DNA damage stimulus;spermatogenesis;biological_process;protein ubiquitination;interstrand cross-link repair
• Cellular component: nucleoplasm;Fanconi anaemia nuclear complex
• Molecular function: molecular_function;protein binding;ubiquitin protein ligase activity