CNOT1 p.Pro41fs
c.120_127del · VCV4281414
Likely pathogenic
Single submitter
Classification
Likely pathogenic
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 | predicted | premature termination codon in exon 3 of 49 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.3, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CNOT1
- Protein
- p.Pro41fs
- Coding
- c.120_127del
- MANE Select
- NM_016284
- Type
- Deletion
- Location
- chr16:58588882 (GRCh38)
- Gene constraint
- LOEUF 0.064 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 75.22 · 21 PDB
- Residue 41
- a UniProt-annotated variant site (in vibos)
Similar variants
- CNOT1 c.4434+195del Benign ★★ same type
- CNOT1 c.4434+1del Likely pathogenic ★ same type
- CNOT1 p.Glu1268fs Likely pathogenic ★ same type
- CNOT1 p.Gly307fs Likely pathogenic ★ same type
- CNOT1 p.Leu111fs Likely pathogenic ★ same type
- CNOT1 p.Leu184fs Likely pathogenic ★ same type
- CNOT1 p.Leu2016fs Likely pathogenic ★ same type
- CNOT1 p.Leu255fs 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/cnot1-p-pro41fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown