CCNB3 p.Ser248=
c.744G>A · rs375491454 · VCV2660543
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.03%, sas)
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 -3 |
| Overall | ||
| CADD | 0.21 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.03%
South Asian · 17/56,673 alleles
Filtering AF
0.0191%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0157%
Overall
0.00521%
63/1,209,632 alleles · ultra-rare
exomes 59/1,098,060 · genomes 4/111,572 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.03% | 3,334 |
| Remaining individualsnot grpmax-eligible | 0.0105% | 9,522 |
| African / African-American | 0.007% | 14,292 |
| Admixed American | 0.00438% | 22,855 |
| European (non-Finnish) | 0.0038% | 26,327 |
| East Asian | 0.00296% | 33,736 |
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
- CCNB3
- Protein
- p.Ser248=
- Coding
- c.744G>A
- MANE Select
- NM_033031
- dbSNP
- rs375491454
- Type
- single nucleotide variant
- Location
- chrX:50308913 (GRCh38)
- Structure
- AlphaFold pLDDT 42.25
Similar variants
- CCNB3 p.Ser248Leu Likely benign ★ same residue
- CCNB3 p.Ala702= Benign ★★ same type
- CCNB3 p.Gly1001Arg Benign ★★ same type
- CCNB3 p.Lys857Gln Likely benign ★★ same type
- CCNB3 p.Ser188Thr Benign ★★ same type
- CCNB3 p.Ala1208Thr Uncertain significance ★ ⚠ same type
- CCNB3 p.Ala312Pro Uncertain significance ★ ⚠ same type
- CCNB3 p.Ala437Ser 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/ccnb3-p-ser248 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown