CCDC18 p.Arg1108=
c.3324G>A · rs61729705 · VCV3053338
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.68%, eas)
Conditions
1
CCDC18-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.009 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.13 | GERP -1.1, phastCons 0.7 |
| Overall | ||
| CADD | 6.291 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.68%
East Asian · 1,195/44,666 alleles
Filtering AF
2.55%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.5%
Overall
0.0805%
1,296/1,610,440 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 2.68% | 37 |
| Remaining individualsnot grpmax-eligible | 0.0995% | 1,006 |
| Middle Eastern | 0.0496% | 2,015 |
| South Asian | 0.0199% | 5,020 |
| Admixed American | 0.00508% | 19,703 |
| European (non-Finnish) | 0.00127% | 78,587 |
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.Arg1108=
- Coding
- c.3324G>A
- MANE Select
- NM_001378204
- dbSNP
- rs61729705
- Type
- single nucleotide variant
- Location
- chr1:93254596 (GRCh38)
- Gene constraint
- LOEUF 0.901 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.83
Disease context
CCDC18-related disorder
Similar variants
- CCDC18 p.Arg1108Ser Benign same residue
- CCDC18 c.2982-6T>C Likely benign same condition
- CCDC18 c.569+9A>G Benign same condition
- CCDC18 p.Ala153= Likely benign same condition
- CCDC18 p.Arg1281= Benign same condition
- CCDC18 p.Arg429Cys Benign same condition
- CCDC18 p.Asn314= Benign same condition
- CCDC18 p.Asn326Thr Benign ⚠ same condition
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-arg1108 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown