USF3

Chr 3

upstream transcription factor family member 3

Also known as: KIAA2018

This gene encodes a transcriptional regulator containing a helix-loop-helix domain that negatively regulates epithelial-mesenchymal transition, the process by which epithelial cells lose polarity and become migratory mesenchymal cells. Mutations cause neurodevelopmental disorders with intellectual disability and developmental delay, following an autosomal dominant inheritance pattern. The gene is highly constrained against loss-of-function variants in the population, indicating that such variants are likely to be pathogenic.

OMIMResearchSummary from RefSeq, UniProt
LOFmechanismLOEUF 0.19
Clinical SummaryUSF3
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

LoF intolerant — likely haploinsufficient
LoF Constraint
0.19LOEUF
pLI 1.000
Z-score 6.94
OE 0.10 (0.060.19)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
0.79Z-score
OE missense 0.93 (0.890.98)
1063 obs / 1138.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.10 (0.060.19)
00.351.4
Missense OE0.93 (0.890.98)
00.61.4
Synonymous OE0.95
01.21.6
LoF obs/exp: 7 / 69.3Missense obs/exp: 1063 / 1138.3Syn Z: 0.78
DN
0.2798th %ile
GOF
0.2099th %ile
LOF
0.77top 10%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.19

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

USF3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC