CNOT3 p.Ser695fs
c.2081dup · VCV3907905
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 LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 17 of 18 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 1, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CNOT3
- Protein
- p.Ser695fs
- Coding
- c.2081dup
- MANE Select
- NM_014516
- Type
- Duplication
- Location
- chr19:54153757 (GRCh38)
- Gene constraint
- LOEUF 0.057 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 68.53 · 6 PDB
- Residue 695
- the 'repressor domain' region; a UniProt-annotated variant site (in iddsadf)
Similar variants
- CNOT3 p.Tyr648fs Pathogenic ★★ same type
- CNOT3 p.Ala345fs Pathogenic ★ same type
- CNOT3 p.Ala480fs Likely pathogenic ★ same type
- CNOT3 p.Glu26fs Pathogenic ★ same type
- CNOT3 p.Gly481fs Pathogenic ★ same type
- CNOT3 p.Pro390fs Pathogenic ★ same type
- CNOT3 p.Ser415fs Pathogenic ★ same type
- CNOT3 p.Ser459fs 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/cnot3-p-ser695fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown