FANCE

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

Basic information

Region (hg38): 6:35452338-35467104

Previous symbols: [ "FACE" ]

Links

ENSG00000112039

∙ NCBI:2178 ∙ OMIM:613976 ∙ HGNC:3586 ∙ Uniprot:Q9HB96 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Fanconi anemia, complementation group E	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	11001585; 17924555; 20301575; 22778927

ClinVar

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

Fanconi_anemia_complementation_group_E (708 variants)
not_provided (64 variants)
Inborn_genetic_diseases (51 variants)
not_specified (40 variants)
Fanconi_anemia (39 variants)
FANCE-related_disorder (21 variants)
Ovarian_cancer (7 variants)
Hereditary_cancer-predisposing_syndrome (1 variants)
Carcinoma_of_colon (1 variants)
Microcephaly (1 variants)
See_cases (1 variants)
Carcinoma_of_pancreas (1 variants)
Hereditary_breast_ovarian_cancer_syndrome (1 variants)
Exstrophy-epispadias_complex (1 variants)
Malignant_tumor_of_breast (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FANCE gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021922.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous	1 clinvar	1 clinvar	5 clinvar	195 clinvar		202
missense	1 clinvar	3 clinvar	299 clinvar	18 clinvar	4 clinvar	325
nonsense	11 clinvar	9 clinvar	3 clinvar			23
start loss		2	2			4
frameshift	16 clinvar	26 clinvar	4 clinvar			46
splice donor/acceptor (+/-2bp)	1 clinvar	17 clinvar				18
Total	30	58	313	213	4

Highest pathogenic variant AF is 0.000107213

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FANCE	protein_coding	protein_coding	ENST00000229769	10	14743

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000153	0.963	125686	0	62	125748	0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.129	238	244	0.977	0.0000136	3378
Missense in Polyphen		79	72.37	1.0916		1067
Synonymous	0.117	105	107	0.986	0.00000583	1158
Loss of Function	1.96	13	23.2	0.561	0.00000129	292

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000486	0.000485
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000301	0.000299
Middle Eastern	0.0000544	0.0000544
South Asian	0.000425	0.000425
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: As part of the Fanconi anemia (FA) complex functions in DNA cross-links repair. Required for the nuclear accumulation of FANCC and provides a critical bridge between the FA complex and FANCD2. {ECO:0000269|PubMed:12093742, ECO:0000269|PubMed:17296736}.;
Disease: DISEASE: Fanconi anemia complementation group E (FANCE) [MIM:600901]: 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:11001585, ECO:0000269|PubMed:17924555}. 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: 0.476

Intolerance Scores

loftool: 0.818
rvis_EVS: -0.31
rvis_percentile_EVS: 32.06

Haploinsufficiency Scores

pHI: 0.0289
hipred: Y
hipred_score: 0.658
ghis: 0.528

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.624

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Fance
Phenotype

Gene ontology

Biological process: interstrand cross-link repair
Cellular component: nucleus;nucleoplasm;Fanconi anaemia nuclear complex
Molecular function: molecular_function