CCDC50 p.Lys15=
c.45G>A · rs981589224 · VCV1211264
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0185%, 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 1.2 | GERP -2.1, phastCons 1 |
| Overall | ||
| CADD | 10.53 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0185%
Admixed American · 11/59,582 alleles
Filtering AF
0.0103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.008%
Overall
0.000683%
11/1,609,784 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.Lys15=
- Coding
- c.45G>A
- MANE Select
- NM_178335
- dbSNP
- rs981589224
- Type
- single nucleotide variant
- Location
- chr3:191329719 (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-lys15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown