FOXL3

Chr 7

forkhead box L3

NCBI Gene: 116033993 ENSG00000248767 UniProt: A0A1W2PRP0

The protein is a transcriptional regulator that binds DNA and controls gene expression by RNA polymerase II, with predicted roles in cell differentiation and anatomical structure development. Currently, no human diseases have been definitively associated with FOXL3 mutations in the medical literature. The inheritance pattern for FOXL3-related conditions has not been established due to limited clinical data.

ResearchSummary from RefSeq, UniProt

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in anatomical structure morphogenesis; cell differentiation; and regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

DNmechanism

Clinical Summary— FOXL3

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ClinVar Variants

4 VUS of 4 total submissions

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Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

This gene — mechanism propensity

0.6550th %ile

GOF

0.5661th %ile

LOF

0.49top 25%

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

4 submitted variants in ClinVar

ClinVar

Classification Summary

VUS4

VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	4	4
Likely Benign	0	0
Benign	0	0
Total	4	4

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

17 pathogenic / likely-pathogenic (of 24) ClinVar copy-number / structural variants overlap FOXL3 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →