CCNL2 p.Ser327=
c.981G>A · rs367995434 · VCV3060913
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0628%, afr)
Conditions
1
CCNL2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.265 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -14 | GERP -3.4 |
| Overall | ||
| CADD | 0.118 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0628%
African / African-American · 47/74,884 alleles
Filtering AF
0.0484%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0433%
Overall
0.00515%
83/1,611,870 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0628% | 1,593 |
| East Asian | 0.029% | 3,445 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,785 |
| South Asian | 0.00439% | 22,754 |
| Admixed American | 0.00334% | 29,964 |
| European (non-Finnish) | 0.00119% | 84,166 |
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
- CCNL2
- Protein
- p.Ser327=
- Coding
- c.981G>A
- MANE Select
- NM_030937
- dbSNP
- rs367995434
- Type
- single nucleotide variant
- Location
- chr1:1390255 (GRCh38)
- Gene constraint
- LOEUF 0.665 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.06 · 4 PDB
- Residue 327
- the 'disordered' region
Disease context
CCNL2-related disorder
Similar variants
- CCNL2 c.*4G>A Benign same condition
- CCNL2 p.Arg40= Likely benign same condition
- CCNL2 p.Ser25Cys Likely benign ⚠ same condition
- CCNL2 p.Ser330= Likely benign same condition
- CCNL2 p.Ser67= Likely benign same condition
- CCNL2 c.473+10_473+13del Likely benign same condition
- CCNL2 c.474-6del Likely benign same condition
- CCNL2 p.Arg476Trp 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/ccnl2-p-ser327 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown