CCNL2 p.Arg40=
c.120G>A · rs374471834 · VCV3058762
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.679%, sas)
Conditions
1
CCNL2-related disorder
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 0.76 | GERP -3.4, phastCons 1 |
| Overall | ||
| CADD | 11.92 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.679%
South Asian · 616/90,746 alleles
Filtering AF
0.634%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.617%
Overall
0.0552%
888/1,610,138 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.679% | 147 |
| Middle Eastern | 0.0826% | 1,210 |
| Remaining individualsnot grpmax-eligible | 0.0513% | 1,949 |
| Admixed American | 0.0234% | 4,276 |
| European (non-Finnish) | 0.0183% | 5,458 |
| African / African-American | 0.00404% | 24,775 |
| East Asian | 0.00225% | 44,496 |
| Finnishnot grpmax-eligible | 0.00159% | 63,060 |
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.Arg40=
- Coding
- c.120G>A
- MANE Select
- NM_030937
- dbSNP
- rs374471834
- Type
- single nucleotide variant
- Location
- chr1:1399187 (GRCh38)
- Gene constraint
- LOEUF 0.665 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.06 · 4 PDB
Disease context
CCNL2-related disorder
Similar variants
- CCNL2 c.*4G>A Benign same condition
- CCNL2 p.Ser25Cys Likely benign same condition
- CCNL2 p.Ser327= 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-arg40 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown