FANCE
Chr 6ARFA complementation group E
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
Primary Disease Associations & Inheritance
Fanconi anemia, complementation group EMIM #600901
AR
Fanconi anemia, complementation group EMIM #600901
AR
UniProtFanconi anemia complementation group E
587
ClinVar variants
63
Pathogenic / LP
0.00
pLI score
3
Active trials
Clinical Summary— FANCE
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Gene-Disease Validity (ClinGen)
Fanconi anemia complementation group E · ARDefinitive
Definitive — sufficient evidence for diagnostic panels
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Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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ClinVar Variants
63 Pathogenic / Likely Pathogenic· 228 VUS of 587 total submissions
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Clinical Trials
3 active or recruiting trials — potential therapeutic options may be available
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.89LOEUF
pLI 0.000
Z-score 1.96
OE 0.56 (0.36–0.89)
Typical tolerance to LoF variation
Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.13Z-score
OE missense 0.98 (0.88–1.09)
238 obs / 243.7 exp
Mild missense constraint
Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.56 (0.36–0.89)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.98 (0.88–1.09)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.99
0≤1.21.6
LoF obs/exp: 13 / 23.2Missense obs/exp: 238 / 243.7Syn Z: 0.12
ClinVar Variant Classifications
587 submitted variants in ClinVar
Classification Summary
Pathogenic23
Likely Pathogenic40
VUS228
Likely Benign262
Benign10
Conflicting24
23
Pathogenic
40
Likely Pathogenic
228
VUS
262
Likely Benign
10
Benign
24
Conflicting
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 12 | 0 | 11 | 0 | 23 |
Likely Pathogenic | 31 | 1 | 8 | 0 | 40 |
VUS | 3 | 187 | 35 | 3 | 228 |
Likely Benign | 0 | 4 | 102 | 156 | 262 |
Benign | 0 | 2 | 8 | 0 | 10 |
Conflicting | — | 24 | |||
| Total | 46 | 194 | 164 | 159 | 587 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
FANCE · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
Gene2Phenotype Curations
FANCE-related Fanconi anemia
definitiveGene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org
OMIM — Genotype-Phenotype Relationships
2 OMIM entries
FANCE GENE; FANCE
MIM #613976 · *
Autosomal recessive
FANCONI ANEMIA, COMPLEMENTATION GROUP E; FANCE
MIM #600901 · #
Autosomal recessive
External Resources
Links to major genomics databases and tools
Variant Interpretation
Population Databases
Gene Resources
Expert Curation
ClinGen
Expert-curated gene-disease validity
GenCC
Gene Curation Coalition — multi-curator classifications
Orphanet
Rare disease encyclopedia and gene-disease associations
PanelApp
Gene panels for rare disease diagnostics (Genomics England)
LOVD
Leiden Open Variation Database — variant listings
GeneReviews
Expert-authored summaries of heritable conditions (NCBI)
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Open GeneReview ↗GeneReview available — FANCE
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
Molecular Characterization of KRAS Wild-type Tumors in Patients with Pancreatic Adenocarcinoma.
Philip PA et al.·Clin Cancer Res
2022Cohort
Multigene panel testing beyond BRCA1/2 in breast/ovarian cancer Spanish families and clinical actionability of findings.
Bonache S et al.·J Cancer Res Clin Oncol
2018
Biomarkers and immunotherapy in endometrial cancer: mechanisms and clinical applications.
Zhao L et al.·Front Immunol
2025Review
Pathogenic variants reveal candidate genes for prostate cancer germline testing for men of African ancestry.
Gheybi K et al.·Nat Commun
2025
Prevalence of germline variants in Brazilian pancreatic carcinoma patients.
Rodrigues LM et al.·Sci Rep
2024Cohort
Germline analysis of an international cohort of pediatric diffuse midline glioma patients.
Mateos MK et al.·Neuro Oncol
2025Cohort
Fanconi Anemia Complementation Group E, a DNA Repair-Related Gene, Is a Potential Marker of Poor Prognosis in Hepatocellular Carcinoma.
Takahashi J et al.·Oncology
2022
Neonatally Lethal Fanconi Anemia due to an Amish Founder FANCE Gene Variant; Evidence for Genotype-Phenotype Correlation.
Scott EM et al.·Am J Med Genet A
2025Case report
Heterozygous Germline Fanconi Anemia-Related Gene Mutations Increase Susceptibility to Germ Cell Tumors.
Wang J et al.·JCO Precis Oncol
2025
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Integrated analysis of FANCE expression and its regulatory role in the immune microenvironment of oral squamous cell carcinoma.
Lin B et al.·Oncol Lett
2025🔓 Open Access
Fance deficiency impaired DNA damage repair of prospermatogonia and altered the repair dynamics of spermatocytes.
Yin H et al.·Reprod Biol Endocrinol
2024🔓 Open Access
Reduced FANCE Confers Genomic Instability and Malignant Behavior by Regulating Cell Cycle Progression in Endometrial Cancer.
Zheng C et al.·J Cancer
2023🔓 Open Access
Fance deficiency inhibits primordial germ cell proliferation associated with transcription-replication conflicts accumulate and DNA repair defects.
Zhou Z et al.·J Ovarian Res
2023🔓 Open Access
Top 5 resultsSearch Europe PMC ↗
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
Triple Negative Breast CancerBreast Cancer
Serial Circulating Tumor DNA (ctDNA) Monitoring During Adjuvant Capecitabine in Early Triple-negative Breast Cancer
RECRUITINGNCT04768426Phase PHASE2Stanford UniversityStarted 2021-02-03
Capecitabine
Polycythemia VeraEssential ThrombocythaemiaMyelofibrosis
Prevalence Of Germline Gene Mutations In Patients With Myeloproliferative Neoplasms With Family History
NOT YET RECRUITINGNCT06923670Phase NAFondazione Policlinico Universitario Agostino Gemelli IRCCSStarted 2025-05-21
NGS testingNGS analysis for mutations in genes involved in familial predisposition to hematological malignancies
Advanced Solid TumorsEwing SarcomaHepatocellular Carcinoma (HCC)
A Phase 1/1B Study of ST-01156, a Small Molecule RBM39 Degrader, in Patients With Advanced Solid Malignancies
RECRUITINGNCT07197554Phase PHASE1SEED Therapeutics, Inc.Started 2025-12-01
ST-01156
External Resources
Links to major genomics databases and tools
Variant Interpretation
Population Databases
Gene Resources
Expert Curation
ClinGen
Expert-curated gene-disease validity
GenCC
Gene Curation Coalition — multi-curator classifications
Orphanet
Rare disease encyclopedia and gene-disease associations
PanelApp
Gene panels for rare disease diagnostics (Genomics England)
LOVD
Leiden Open Variation Database — variant listings
GeneReviews
Expert-authored summaries of heritable conditions (NCBI)