CCNL2 p.Ser330=
c.990T>C · rs1273411297 · VCV3053233
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00416%, nfe)
Conditions
1
CCNL2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.071 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -13 | GERP -3.4 |
| Overall | ||
| CADD | 0.455 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00416%
European (non-Finnish) · 49/1,176,820 alleles
Filtering AF
0.00319%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00287%
Overall
0.00343%
50/1,457,836 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00416% | 24,017 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,270 |
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.Ser330=
- Coding
- c.990T>C
- MANE Select
- NM_030937
- dbSNP
- rs1273411297
- Type
- single nucleotide variant
- Location
- chr1:1390246 (GRCh38)
- Gene constraint
- LOEUF 0.665 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.06 · 4 PDB
- Residue 330
- a modified residue (phosphoserine); 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.Ser327= 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-ser330 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown