CCDC8 p.Ala20=
c.60T>C · rs149839442 · VCV781882
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.22%, mid)
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 -4.1 | GERP -2.7 |
| Overall | ||
| CADD | 2.68 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.22%
Middle Eastern · 74/6,062 alleles
Filtering AF
1.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.09%
Overall
0.907%
14,637/1,613,898 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.22% | 82 |
| European (non-Finnish) | 1.11% | 90 |
| Remaining individualsnot grpmax-eligible | 0.731% | 137 |
| South Asian | 0.473% | 211 |
| Admixed American | 0.435% | 230 |
| Ashkenazi Jewishnot grpmax-eligible | 0.199% | 502 |
| African / African-American | 0.199% | 503 |
| Finnishnot grpmax-eligible | 0.15% | 665 |
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
- CCDC8
- Protein
- p.Ala20=
- Coding
- c.60T>C
- MANE Select
- NM_032040
- dbSNP
- rs149839442
- Type
- single nucleotide variant
- Location
- chr19:46412751 (GRCh38)
- Gene constraint
- LOEUF 1.796 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 46.83 · 1 PDB
Similar variants
- CCDC8 p.Ala20Gly Uncertain significance ★ ⚠ same residue
- CCDC8 p.Ala217Thr Uncertain significance ★★ ⚠ same type
- CCDC8 p.Ala293Thr Uncertain significance ★★ ⚠ same type
- CCDC8 p.Ala393Val Uncertain significance ★★ ⚠ same type
- CCDC8 p.Ala527Val Uncertain significance ★★ ⚠ same type
- CCDC8 p.Arg15Gln Uncertain significance ★★ ⚠ same type
- CCDC8 p.Arg225Gly Uncertain significance ★★ ⚠ same type
- CCDC8 p.Arg277His 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/ccdc8-p-ala20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown