CNOT3 p.Phe673del
c.2014TTC[1] · VCV3347417
Pathogenic
No assertion criteria
Classification
Pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
Conditions
1
CNOT3-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.6 | GERP 1, phastCons 1 |
Variant & gene context
- Gene
- CNOT3
- Protein
- p.Phe673del
- Coding
- c.2014TTC[1]
- MANE Select
- NM_014516
- Type
- Microsatellite
- Location
- chr19:54152974 (GRCh38)
- Gene constraint
- LOEUF 0.057 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 68.53 · 6 PDB
- Residue 673
- the 'repressor domain' region; a UniProt-annotated variant site (in iddsadf); an α-helix
Disease context
CNOT3-related disorder
Similar variants
- CNOT3 p.Glu710Lys Uncertain significance ★★ ⚠ same condition
- CNOT3 c.703+1G>A Likely pathogenic ★ same condition
- CNOT3 p.Ala475fs Likely pathogenic ★ same condition
- CNOT3 p.Arg57Gly Likely pathogenic ★ same condition
- CNOT3 p.Gln61Ter Likely pathogenic ★ same condition
- CNOT3 p.Gly406Ter Likely pathogenic ★ same condition
- CNOT3 p.Pro578fs Likely pathogenic ★ same condition
- CNOT3 p.Tyr648Ter Likely pathogenic ★ same condition
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/cnot3-p-phe673del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown