CFAP20DC p.Val289Ala
c.866T>C · rs757759275 · VCV3143366
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00401%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.021 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.82 | GERP -5.3, phastCons 0.001 |
| Regional constraint | o/e 1.04 | unconstrained · MANE · 307 kb · p 0.24 · regional, not allelic |
| Overall | ||
| CADD | 7.452 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00401%
African / African-American · 3/74,806 alleles
Filtering AF
0.00307%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00275%
Overall
0.00329%
53/1,609,942 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00401% | 24,935 |
| European (non-Finnish) | 0.00399% | 25,072 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,149 |
| South Asian | 0.00111% | 89,970 |
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
- CFAP20DC
- Protein
- p.Val289Ala
- Coding
- c.866T>C
- MANE Select
- NM_001394063
- dbSNP
- rs757759275
- Type
- single nucleotide variant
- Location
- chr3:58869477 (GRCh38)
- Gene constraint
- LOEUF 0.894 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 53.59
Similar variants
- CFAP20DC p.Arg222His Benign ★★ same type
- CFAP20DC p.Gln418Glu Benign/Likely benign ★★ same type
- CFAP20DC p.Ile260= Benign ★★ same type
- CFAP20DC p.Arg201Ter Uncertain significance ★ same type
- CFAP20DC p.Arg295Ter Uncertain significance ★ same type
- CFAP20DC p.Arg362Thr Uncertain significance ★ same type
- CFAP20DC p.Cys136Phe Uncertain significance ★ same type
- CFAP20DC p.Glu462Gln 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/cfap20dc-p-val289ala (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown