CCNJ p.Ser213=
c.639G>A · VCV4222143
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.216%, afr)
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 · G>T here scores Δ0.52 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -1.3, phastCons 1 |
| Overall | ||
| CADD | 10.45 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.216%
African / African-American · 162/75,004 alleles
Filtering AF
0.189%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.178%
Overall
0.0144%
232/1,613,998 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.216% | 463 |
| South Asian | 0.0318% | 3,141 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,209 |
| Admixed American | 0.0133% | 7,501 |
| European (non-Finnish) | 0.00178% | 56,186 |
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
- CCNJ
- Protein
- p.Ser213=
- Coding
- c.639G>A
- MANE Select
- NM_001134375
- Type
- single nucleotide variant
- Location
- chr10:96057146 (GRCh38)
- Gene constraint
- LOEUF 0.497 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 73.34
Similar variants
- CCNJ p.Ala158Gly Uncertain significance ★ ⚠ same type
- CCNJ p.Ala232Val Uncertain significance ★ ⚠ same type
- CCNJ p.Ala60Thr Uncertain significance ★ ⚠ same type
- CCNJ p.Arg218His Uncertain significance ★ ⚠ same type
- CCNJ p.Arg218Pro Uncertain significance ★ ⚠ same type
- CCNJ p.Arg229Cys Uncertain significance ★ ⚠ same type
- CCNJ p.Arg281Gln Uncertain significance ★ ⚠ same type
- CCNJ p.Arg281Trp 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/ccnj-p-ser213 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown