CCDC50 p.Ser209=
c.627G>A · rs199687225 · VCV2179413
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0317%, 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 -0.12 | GERP -3.1 |
| Overall | ||
| CADD | 5.672 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0317%
Admixed American · 19/59,958 alleles
Filtering AF
0.0207%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0172%
Overall
0.00415%
67/1,613,714 alleles · ultra-rare
exomes 45/1,461,542 · genomes 22/152,172 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0317% | 3,156 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,248 |
| Finnishnot grpmax-eligible | 0.00937% | 10,670 |
| South Asian | 0.00439% | 22,767 |
| African / African-American | 0.00267% | 37,478 |
| European (non-Finnish) | 0.0022% | 45,377 |
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.Ser209=
- Coding
- c.627G>A
- MANE Select
- NM_178335
- dbSNP
- rs199687225
- Type
- single nucleotide variant
- Location
- chr3:191375240 (GRCh38)
- Gene constraint
- LOEUF 0.933 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.90 · 1 PDB
Similar variants
- CCDC50 p.Ser209Leu Benign/Likely benign ★★ same residue
- CCDC50 p.Ala453Val Uncertain significance ★★ ⚠ same type
- CCDC50 p.Arg138Pro Uncertain significance ★★ ⚠ same type
- CCDC50 p.Arg227Gln Uncertain significance ★★ same type
- CCDC50 p.Arg227Trp Uncertain significance ★★ same type
- CCDC50 p.Arg270Ter Uncertain significance ★★ same type
- CCDC50 p.Arg274Ter Uncertain significance ★★ same type
- CCDC50 p.Arg305Thr 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/ccdc50-p-ser209 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown