CCDC50 p.Glu317=
c.951G>A · VCV4751576
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, 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 -0.24, phastCons 1 |
| Overall | ||
| CADD | 3.213 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Admixed American · 10/59,886 alleles
Filtering AF
0.00901%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00683%
Overall
0.000684%
10/1,461,096 alleles · ultra-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.Glu317=
- Coding
- c.951G>A
- MANE Select
- NM_178335
- Type
- single nucleotide variant
- Location
- chr3:191375564 (GRCh38)
- Gene constraint
- LOEUF 0.933 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.90 · 1 PDB
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-glu317 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown