FANCE

Chr 6AR

FA complementation group E

Also known as: FACE, FAE

NCBI Gene: 2178ENSG00000112039UniProt: Q9HB96OMIM: 613976

The FANCE protein functions as part of the Fanconi anemia complex in DNA cross-link repair and is required for nuclear accumulation of FANCC, providing a critical bridge between the FA complex and FANCD2. Mutations cause Fanconi anemia complementation group E, an autosomal recessive disorder characterized by cytogenetic instability, hypersensitivity to DNA crosslinking agents, increased chromosomal breakage, and defective DNA repair. The gene is highly intolerant to loss-of-function variants (pLI nearly 1.0), reflecting the critical nature of this DNA repair pathway.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.892 OMIM phenotypes
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
67 unique Pathogenic / Likely Pathogenic· 186 VUS of 500 total submissions
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Clinical Trials
3 active or recruiting trials — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →
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GeneReview available — FANCE
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.89LOEUF
pLI 0.000
Z-score 1.96
OE 0.56 (0.36–0.89)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.13Z-score
OE missense 0.98 (0.88–1.09)
238 obs / 243.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.56 (0.36–0.89)
0≤0.351.4
Missense OE0.98 (0.88–1.09)
0≤0.61.4
Synonymous OE0.99
0≤1.21.6
LoF obs/exp: 13 / 23.2Missense obs/exp: 238 / 243.7Syn Z: 0.12

ClinVar Variant Classifications

500 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic26
Likely Pathogenic41
VUS186
Likely Benign217
Benign9
Conflicting8
26
Pathogenic
41
Likely Pathogenic
186
VUS
217
Likely Benign
9
Benign
8
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
24
0
2
0
26
Likely Pathogenic
39
0
2
0
41
VUS
3
159
21
3
186
Likely Benign
0
2
82
133
217
Benign
0
1
8
0
9
Conflicting
—8
Total66162115136487

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.

3D Protein StructureAlphaFold
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
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
2025
Integrated analysis of FANCE expression and its regulatory role in the immune microenvironment of oral squamous cell carcinoma.
Lin B et al.·Oncol Lett
2025Open Access
Fance deficiency impaired DNA damage repair of prospermatogonia and altered the repair dynamics of spermatocytes.
Yin H et al.·Reprod Biol Endocrinol
2024Open Access
Reduced FANCE Confers Genomic Instability and Malignant Behavior by Regulating Cell Cycle Progression in Endometrial Cancer.
Zheng C et al.·J Cancer
2023Open 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
2023Open Access
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients