CNOT10 p.Asn183=
c.549C>T · VCV3494464
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.186%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.76 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.082 | GERP 1.1, phastCons 0.91 |
| Overall | ||
| CADD | 7.727 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.186%
Middle Eastern · 11/5,914 alleles
Filtering AF
0.104%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0806%
Overall
0.00796%
127/1,595,142 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.186% | 538 |
| Ashkenazi Jewishnot grpmax-eligible | 0.147% | 679 |
| South Asian | 0.0357% | 2,800 |
| Remaining individualsnot grpmax-eligible | 0.00972% | 10,290 |
| European (non-Finnish) | 0.00298% | 33,578 |
| Admixed American | 0.00186% | 53,888 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CNOT10
- Protein
- p.Asn183=
- Coding
- c.549C>T
- MANE Select
- NM_015442
- Type
- single nucleotide variant
- Location
- chr3:32713345 (GRCh38)
- Gene constraint
- LOEUF 0.405 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.87 · 2 PDB
- Residue 183
- the 'disordered' region
Similar variants
- CNOT10 p.Ala11Gly Uncertain significance ★ ⚠ same type
- CNOT10 p.Ala225Val Uncertain significance ★ ⚠ same type
- CNOT10 p.Ala250Val Uncertain significance ★ ⚠ same type
- CNOT10 p.Ala279Thr Uncertain significance ★ ⚠ same type
- CNOT10 p.Ala2Thr Uncertain significance ★ ⚠ same type
- CNOT10 p.Ala305Val Uncertain significance ★ ⚠ same type
- CNOT10 p.Ala319Ser Uncertain significance ★ ⚠ same type
- CNOT10 p.Ala669Val 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/cnot10-p-asn183 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown