CNOT3 p.Ser396=
c.1188C>T · rs370903869 · VCV1973023
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0851%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.025 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -6.5 | GERP -1.3 |
| Overall | ||
| CADD | 0.514 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0851%
African / African-American · 63/73,998 alleles
Filtering AF
0.0683%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0621%
Overall
0.02%
313/1,566,244 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0851% | 1,175 |
| Middle Eastern | 0.0345% | 2,902 |
| Admixed American | 0.0266% | 3,761 |
| European (non-Finnish) | 0.0189% | 5,294 |
| Remaining individualsnot grpmax-eligible | 0.0116% | 8,630 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00759% | 13,170 |
| East Asian | 0.00678% | 14,756 |
| South Asian | 0.00241% | 41,447 |
| Finnishnot grpmax-eligible | 0.00163% | 61,168 |
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
- CNOT3
- Protein
- p.Ser396=
- Coding
- c.1188C>T
- MANE Select
- NM_014516
- dbSNP
- rs370903869
- Type
- single nucleotide variant
- Location
- chr19:54148441 (GRCh38)
- Gene constraint
- LOEUF 0.057 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 68.53 · 6 PDB
- Residue 396
- the 'disordered' region
Similar variants
- CNOT3 p.Ser396Asn Likely benign ★★ ⚠ same residue
- CNOT3 c.1904+2T>C Pathogenic/Likely pathogenic ★★ same type
- CNOT3 p.Arg697Ter Pathogenic ★★ same type
- CNOT3 p.Arg81Ser Likely pathogenic ★★ same type
- CNOT3 p.Arg96Ter Pathogenic/Likely pathogenic ★★ same type
- CNOT3 p.Thr86= Likely pathogenic ★★ same type
- CNOT3 c.1905-7C>G Uncertain significance ★★ same type
- CNOT3 c.483+6T>G 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/cnot3-p-ser396 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown