CCDC9 p.Glu412=
c.1236G>A · rs2514849201 · VCV2650144
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, afr)
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 0.74 | GERP 2, phastCons 0.95 |
| Overall | ||
| CADD | 0.762 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,868 alleles
Overall
0.000137%
2/1,459,798 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00134% | 74,868 |
| European (non-Finnish) | 8.48e-05% | 1,179,021 |
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
- CCDC9
- Protein
- p.Glu412=
- Coding
- c.1236G>A
- MANE Select
- NM_015603
- dbSNP
- rs2514849201
- Type
- single nucleotide variant
- Location
- chr19:47271318 (GRCh38)
- Gene constraint
- LOEUF 1.119 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 59.06
- Residue 412
- the 'disordered' region
Similar variants
- CCDC9 p.Ala15Val Uncertain significance ★ ⚠ same type
- CCDC9 p.Ala175Thr Uncertain significance ★ ⚠ same type
- CCDC9 p.Ala322Val Uncertain significance ★ ⚠ same type
- CCDC9 p.Ala356Ser Uncertain significance ★ ⚠ same type
- CCDC9 p.Ala360Val Uncertain significance ★ ⚠ same type
- CCDC9 p.Ala405Val Uncertain significance ★ ⚠ same type
- CCDC9 p.Ala455Val Uncertain significance ★ ⚠ same type
- CCDC9 p.Ala525Ser 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/ccdc9-p-glu412 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown