CCDC50 p.Lys303del
c.908_910del · VCV4685034
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000254%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.9 | GERP -1.5, phastCons 1 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000254%
European (non-Finnish) · 3/1,179,796 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000205%
3/1,461,396 alleles · very rare
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
- CCDC50
- Protein
- p.Lys303del
- Coding
- c.908_910del
- MANE Select
- NM_178335
- Type
- Deletion
- Location
- chr3:191375519 (GRCh38)
- Gene constraint
- LOEUF 0.933 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.90 · 1 PDB
- Residue 303
- the 'disordered' region
Similar variants
- CCDC50 p.Lys303Arg Benign ★★ same residue
- CCDC50 c.*7_*14del Likely benign ★★ same type
- CCDC50 p.Asp452fs Pathogenic ★ same type
- CCDC50 c.1093-5_1093-3del Uncertain significance ★ same type
- CCDC50 c.1429+6_1429+7del Uncertain significance ★ same type
- CCDC50 c.331-5del Likely benign ★ same type
- CCDC50 c.49+231_49+233del Benign ★ same type
- CCDC50 c.49+232_49+233del Benign ★ 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/ccdc50-p-lys303del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown