C2CD2L p.Leu340=
c.1020G>T · VCV3826271
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, amr)
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 4.5 | GERP -1.2, phastCons 1 |
| Overall | ||
| CADD | 15.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
Admixed American · 12/59,876 alleles
Filtering AF
0.0115%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.009%
Overall
0.000931%
15/1,611,932 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.02% | 4,990 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,310 |
| African / African-American | 0.00134% | 74,856 |
| European (non-Finnish) | 8.48e-05% | 1,179,601 |
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
- C2CD2L
- Protein
- p.Leu340=
- Coding
- c.1020G>T
- MANE Select
- NM_001290474
- Type
- single nucleotide variant
- Location
- chr11:119112328 (GRCh38)
- Gene constraint
- LOEUF 0.494 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 64.75 · 1 PDB
- Residue 340
- the c2 domain
Similar variants
- C2CD2L c.451-8G>A Benign ★★ same type
- C2CD2L p.Ala14Thr Uncertain significance ★ ⚠ same type
- C2CD2L p.Ala173Thr Uncertain significance ★ ⚠ same type
- C2CD2L p.Ala245Ser Uncertain significance ★ ⚠ same type
- C2CD2L p.Ala245Thr Uncertain significance ★ ⚠ same type
- C2CD2L p.Ala326Val Uncertain significance ★ ⚠ same type
- C2CD2L p.Ala512Val Uncertain significance ★ ⚠ same type
- C2CD2L p.Ala524Thr 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/c2cd2l-p-leu340 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown