CNOT1 p.Pro2004=
c.6012T>C · VCV3632288
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -4.9, phastCons 0.99 |
| Overall | ||
| CADD | 8.43 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CNOT1
- Protein
- p.Pro2004=
- Coding
- c.6012T>C
- MANE Select
- NM_016284
- Type
- single nucleotide variant
- Location
- chr16:58532279 (GRCh38)
- Gene constraint
- LOEUF 0.064 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 75.22 · 21 PDB
- Residue 2004
- a UniProt-annotated variant site (in vibos)
Similar variants
- CNOT1 c.434-2A>G Pathogenic ★★ same type
- CNOT1 p.Arg26Ter Pathogenic/Likely pathogenic ★★ same type
- CNOT1 p.Arg535Cys Pathogenic ★★ same type
- CNOT1 c.310-3C>G Uncertain significance ★★ same type
- CNOT1 c.5895+4T>C Uncertain significance ★★ same type
- CNOT1 p.Ala1368Val Uncertain significance ★★ ⚠ same type
- CNOT1 p.Ala1503Thr Uncertain significance ★★ ⚠ same type
- CNOT1 p.Ala1604Gly Uncertain significance ★★ ⚠ 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-pro2004 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown