CCDC38 p.Pro95=
c.285G>A · VCV4649509
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0228%, eas)
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 -0.26 | GERP -3.7 |
| Overall | ||
| CADD | 1.845 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0228%
East Asian · 10/43,790 alleles
Filtering AF
0.0123%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00937%
Overall
0.00184%
29/1,576,592 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0228% | 4,379 |
| Remaining individualsnot grpmax-eligible | 0.00329% | 30,407 |
| European (non-Finnish) | 0.00145% | 68,877 |
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
- CCDC38
- Protein
- p.Pro95=
- Coding
- c.285G>A
- MANE Select
- NM_182496
- Type
- single nucleotide variant
- Location
- chr12:95917148 (GRCh38)
- Gene constraint
- LOEUF 0.955 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.84
Similar variants
- CCDC38 p.Pro95Leu Likely benign ★ same residue
- CCDC38 p.Ala125Ser Uncertain significance ★ ⚠ same type
- CCDC38 p.Ala175Ser Uncertain significance ★ ⚠ same type
- CCDC38 p.Ala175Thr Uncertain significance ★ ⚠ same type
- CCDC38 p.Ala407Val Uncertain significance ★ ⚠ same type
- CCDC38 p.Ala425Val Uncertain significance ★ ⚠ same type
- CCDC38 p.Ala76Pro Uncertain significance ★ ⚠ same type
- CCDC38 p.Arg107Met 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/ccdc38-p-pro95 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown