CFAP20DC p.Lys367Arg
c.1100A>G · rs145324023 · VCV3143368
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.179%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.046 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>A here scores Δ0.23 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 4.3 | GERP 0.23, phastCons 1 |
| Regional constraint | o/e 1.04 | unconstrained · MANE · 307 kb · p 0.24 · regional, not allelic |
| Overall | ||
| CADD | 17.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.179%
African / African-American · 134/75,044 alleles
Filtering AF
0.154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.145%
Overall
0.01%
162/1,613,744 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.179% | 560 |
| Admixed American | 0.0233% | 4,287 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,463 |
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.Lys367Arg
- Coding
- c.1100A>G
- MANE Select
- NM_001394063
- dbSNP
- rs145324023
- Type
- single nucleotide variant
- Location
- chr3:58867852 (GRCh38)
- Gene constraint
- LOEUF 0.894 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 53.59
- Residue 367
- the 'disordered' region
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-lys367arg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown