CUX1 (Homeobox protein cut-like 1) variants and mutations

CUX1 (also known as Homeobox protein cut-like 1) is a human protein-coding gene encoding a homeobox protein cut-like 1 protein. It regulates transcription and chromatin-associated processes involved in cell differentiation, proliferation, and neuronal development. Haploinsufficiency can cause neurodevelopmental impairment, while somatic loss is common in myeloid malignancies and often marks adverse-risk disease. This analysis covers 2,015 CUX1 variants and mutations. Of these, 74% have computational variant effect predictions. Disease context includes global developmental delay with or without impaired intellectual development, cancer, and myelodysplastic syndrome. Example CUX1 variants include M1V, M1L, and M1R.

Variant analysis overview

Gene: CUX1
Protein: Homeobox protein cut-like 1
UniProt accession: P39880
Organism: Homo sapiens
Variants analyzed: 2015
Variant scope: all variants
Completed: 2026-08-20

Variant and mutation evidence

Variant composition: 1,921 unspecified-consequence records; 66 missense variants; 6 frameshift variants; 15 synonymous variants; 4 stop-gained variants; 1 in-frame insertions; 2 substitution
Prediction scores: 1,500 variants have prediction scores (74% of the analyzed set).

Clinical, disease, and population context

Disease context: 25 disease associations are represented. Top associations: global developmental delay with or without impaired intellectual development, cancer, myelodysplastic syndrome, hereditary disease, acute lymphoblastic leukemia, leukemia, breast carcinoma, atrial fibrillation, neurodevelopmental disorder, chronic myelogenous leukemia, BCR-ABL1 positive, preeclampsia, alcohol drinking.

Protein structure and variant hotspots

Protein features: 10 post-translational modification sites.
PTM context: 10 variants overlap post-translational modification sites.
Experimental data: 82 protein positions have experimental scores. Source: CUX1 Homeobox domain domainome 1.0, CUX1 CUT domain domainome 1.0.

Data sources

Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.

Notable CUX1 variants

Examples include M1V, M1L, M1R, M1T, M1K, M1I, L2*, L2S. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.

CUX1 analysis run — CUX1 (2,015 variants) — completed 2026-08-20