FANCE

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

Basic information

Region (hg38): 6:35452337-35467104

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 (538 variants)
• not provided (61 variants)
• not specified (45 variants)
• Fanconi anemia (40 variants)
• Inborn genetic diseases (22 variants)
• Ovarian cancer (7 variants)
• FANCE-related condition (4 variants)
• Carcinoma of colon (1 variants)
• Carcinoma of pancreas (1 variants)
• Exstrophy-epispadias complex (1 variants)
• See cases (1 variants)
• Hereditary breast ovarian cancer syndrome (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.

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			4	112	2	118
missense		1	234	5	4	244
nonsense	7	5	3			15
start loss		1	1			2
frameshift	6	19				25
inframe indel			6	1		7
splice donor/acceptor (+/-2bp)	1	13				14
splice region		1	11	20	1	33
non coding			17	60	14	91
Total	14	39	265	178	20

Highest pathogenic variant AF is 0.0000394

Variants in FANCE

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

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

Position	Type	Phenotype	Significance	ClinVar
6-35452349-C-T		Fanconi anemia complementation group E	Uncertain significance (Jan 12, 2018)
6-35452364-G-A		Fanconi anemia complementation group E	Uncertain significance (Jan 12, 2018)
6-35452379-C-T		Fanconi anemia complementation group E	Uncertain significance (Jan 13, 2018)
6-35452384-G-C		Fanconi anemia complementation group E	Uncertain significance (Jan 13, 2018)
6-35452414-A-G		Fanconi anemia complementation group E	Uncertain significance (Jan 12, 2018)
6-35452420-T-A		Fanconi anemia complementation group E	Uncertain significance (Apr 27, 2017)
6-35452441-C-T		Fanconi anemia complementation group E	Uncertain significance (Jan 12, 2018)
6-35452446-C-T		Fanconi anemia complementation group E	Uncertain significance (Apr 19, 2022)
6-35452490-C-T		Fanconi anemia complementation group E	Benign/Likely benign (Jul 07, 2023)
6-35452514-A-T		Fanconi anemia complementation group E	Uncertain significance (Jan 13, 2018)
6-35452527-G-C		Fanconi anemia complementation group E	Uncertain significance (Jan 12, 2018)
6-35452542-C-T		FANCE-related disorder	Likely benign (Mar 21, 2019)
6-35452542-CGGCATGGCGACACCG-C		Fanconi anemia complementation group E	Uncertain significance (May 26, 2021)
6-35452543-G-C		not specified	Uncertain significance (Oct 27, 2017)
6-35452545-CATGGCG-C		Fanconi anemia	Likely pathogenic (May 18, 2022)
6-35452547-T-C		Fanconi anemia • Fanconi anemia complementation group E	Conflicting classifications of pathogenicity (Jan 29, 2024)
6-35452547-TGGCGACACCG-T		Fanconi anemia complementation group E	Pathogenic (Dec 15, 2023)
6-35452549-G-C		Fanconi anemia complementation group E	Uncertain significance (Aug 31, 2021)
6-35452550-C-T		Fanconi anemia complementation group E	Uncertain significance (Jul 30, 2022)
6-35452553-C-T		Fanconi anemia complementation group E	Uncertain significance (May 31, 2022)
6-35452554-A-C			Uncertain significance (Feb 07, 2011)
6-35452556-C-T		Inborn genetic diseases	Uncertain significance (Jul 26, 2021)
6-35452557-G-A		Fanconi anemia	Likely benign (Aug 24, 2021)
6-35452559-A-T		Fanconi anemia complementation group E	Uncertain significance (Jan 29, 2019)
6-35452560-C-T		Fanconi anemia complementation group E	Likely benign (Jan 09, 2024)

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

Gene ontology

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