CCDC18 p.Cys430=
c.1290C>T · rs189830464 · VCV716047
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.742%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.037 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.22 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -0.14 | GERP -1.5, phastCons 0.003 |
| Overall | ||
| CADD | 6.004 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.742%
African / African-American · 557/75,026 alleles
Filtering AF
0.691%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.671%
Overall
0.037%
597/1,613,730 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.742% | 135 |
| Remaining individualsnot grpmax-eligible | 0.04% | 2,500 |
| Admixed American | 0.0183% | 5,456 |
| Middle Eastern | 0.0165% | 6,060 |
| European (non-Finnish) | 0.000254% | 393,233 |
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
- CCDC18
- Protein
- p.Cys430=
- Coding
- c.1290C>T
- MANE Select
- NM_001378204
- dbSNP
- rs189830464
- Type
- single nucleotide variant
- Location
- chr1:93210882 (GRCh38)
- Gene constraint
- LOEUF 0.901 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.83
Similar variants
- CCDC18 p.Leu817= Benign ★★ same type
- CCDC18 p.Pro108= Benign ★★ same type
- CCDC18 p.Ala1077Val Uncertain significance ★ ⚠ same type
- CCDC18 p.Ala1209Gly Uncertain significance ★ ⚠ same type
- CCDC18 p.Ala1209Pro Uncertain significance ★ ⚠ same type
- CCDC18 p.Ala1287Thr Uncertain significance ★ ⚠ same type
- CCDC18 p.Ala241Thr Uncertain significance ★ ⚠ same type
- CCDC18 p.Ala373Ser 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/ccdc18-p-cys430 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown