CCDC85A p.Pro256=
c.768C>T · rs374744627 · VCV2650954
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0467%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -2.9 |
| Overall | ||
| CADD | 0.658 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0467%
African / African-American · 35/74,896 alleles
Filtering AF
0.0345%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0303%
Overall
0.00762%
123/1,613,482 alleles · ultra-rare
exomes 97/1,461,592 · genomes 26/151,890 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0467% | 2,140 |
| Remaining individualsnot grpmax-eligible | 0.0416% | 2,403 |
| Admixed American | 0.0183% | 5,454 |
| South Asian | 0.00769% | 13,007 |
| European (non-Finnish) | 0.00373% | 26,813 |
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
- CCDC85A
- Protein
- p.Pro256=
- Coding
- c.768C>T
- MANE Select
- NM_001080433
- dbSNP
- rs374744627
- Type
- single nucleotide variant
- Location
- chr2:56192968 (GRCh38)
- Gene constraint
- LOEUF 1.058 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.16
- Residue 256
- the 'disordered' region
Similar variants
- CCDC85A p.Ala13Val Uncertain significance ★ ⚠ same type
- CCDC85A p.Ala142Ser Uncertain significance ★ ⚠ same type
- CCDC85A p.Ala178Val Uncertain significance ★ ⚠ same type
- CCDC85A p.Ala201Pro Uncertain significance ★ ⚠ same type
- CCDC85A p.Ala201Val Uncertain significance ★ ⚠ same type
- CCDC85A p.Ala21Ser Uncertain significance ★ ⚠ same type
- CCDC85A p.Ala21Val Uncertain significance ★ ⚠ same type
- CCDC85A p.Ala28Asp 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/ccdc85a-p-pro256 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown