CCDC50 p.Arg263Pro
c.788G>C · rs534593003 · VCV3031138
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.112%, sas)
Conditions
1
CCDC50-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.033 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.45 | GERP -0.47 |
| Regional constraint | o/e 0.96 | unconstrained · MANE · 62 kb · p 0.39 · regional, not allelic |
| Overall | ||
| CADD | 6.218 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.112%
South Asian · 102/91,036 alleles
Filtering AF
0.0944%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0878%
Overall
0.00644%
104/1,613,724 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.112% | 893 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,245 |
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.Arg263Pro
- Coding
- c.788G>C
- MANE Select
- NM_178335
- dbSNP
- rs534593003
- Type
- single nucleotide variant
- Location
- chr3:191375401 (GRCh38)
- Gene constraint
- LOEUF 0.933 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.90 · 1 PDB
- Residue 263
- the 'disordered' region
Disease context
CCDC50-related disorder
Similar variants
- CCDC50 p.Glu412Lys Uncertain significance ★★ ⚠ same condition
- CCDC50 p.Gln57His Uncertain significance ★ ⚠ same condition
- CCDC50 c.448+5C>G Likely benign same condition
- CCDC50 p.Ile381= Likely benign same condition
- CCDC50 c.977-7_977-5dup Benign same condition
- CCDC50 p.Ala453Val Uncertain significance ★★ ⚠ same type
- CCDC50 p.Arg138Pro Uncertain significance ★★ ⚠ same type
- CCDC50 p.Arg227Gln 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-arg263pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown