CFAP20DC p.Cys136Phe
c.407G>T · rs371916517 · VCV3143364
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00848%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.627 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.4, phastCons 1 |
| Regional constraint | o/e 1.04 | unconstrained · MANE · 307 kb · p 0.24 · regional, not allelic |
| Overall | ||
| CADD | 28.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00848%
European (non-Finnish) · 100/1,179,666 alleles
Filtering AF
0.00708%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0066%
Overall
0.00645%
104/1,613,386 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00848% | 11,797 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| African / African-American | 0.00133% | 74,968 |
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.Cys136Phe
- Coding
- c.407G>T
- MANE Select
- NM_001394063
- dbSNP
- rs371916517
- Type
- single nucleotide variant
- Location
- chr3:58913851 (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.Glu462Gln Uncertain significance ★ same type
- CFAP20DC p.His346Pro 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-cys136phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown