CUX1 p.Phe585fs
c.1754del · VCV3381623
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen); NMD-escape possible for C-terminal truncations |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 3.1 | GERP 1, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CUX1
- Protein
- p.Phe585fs
- Coding
- c.1754del
- MANE Select
- NM_181552 · reported on NM_001913
- Type
- Deletion
- Location
- chr7:102280109 (GRCh38)
- Gene constraint
- LOEUF 0.277 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.84 · 3 PDB
- Residue 585
- a DNA-binding region
Similar variants
- CUX1 p.Ser585= Likely benign ★ same residue
- CUX1 p.Ser526fs Pathogenic/Likely pathogenic ★★ same type
- CUX1 c.3655+190_*301del Pathogenic ★ same type
- CUX1 p.Ala1415fs Likely pathogenic ★ same type
- CUX1 p.Ala957fs Likely pathogenic ★ same type
- CUX1 p.Gln789fs Likely pathogenic ★ same type
- CUX1 p.Glu353fs Likely pathogenic ★ same type
- CUX1 p.Gly439fs Likely pathogenic ★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cux1-p-phe585fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown