CCDC50 p.Asp253Glu
c.759C>A · rs758591090 · VCV498661
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.11 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.23 | GERP -1.8, phastCons 0.009 |
| Regional constraint | o/e 0.96 | unconstrained · MANE · 62 kb · p 0.39 · regional, not allelic |
| Overall | ||
| CADD | 21.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CCDC50
- Protein
- p.Asp253Glu
- Coding
- c.759C>A
- MANE Select
- NM_178335
- dbSNP
- rs758591090
- Type
- single nucleotide variant
- Location
- chr3:191375372 (GRCh38)
- Gene constraint
- LOEUF 0.933 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.90 · 1 PDB
- Residue 253
- the 'disordered' region
Similar variants
- 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
- CCDC50 p.Arg309Gly 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-asp253glu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown