CFAP20DC p.His346Pro
c.1037A>C · rs1247197893 · VCV3143367
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.17 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>A here scores Δ0.29 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 1.9 | GERP 0.17, phastCons 1 |
| Regional constraint | o/e 1.04 | unconstrained · MANE · 307 kb · p 0.24 · regional, not allelic |
| Overall | ||
| CADD | 23.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,179,338 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,612,590 alleles · very rare
exomes 1/1,460,414 · genomes 1/152,176 · joint denominator
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.His346Pro
- Coding
- c.1037A>C
- MANE Select
- NM_001394063
- dbSNP
- rs1247197893
- Type
- single nucleotide variant
- Location
- chr3:58867915 (GRCh38)
- Gene constraint
- LOEUF 0.894 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 53.59
- Residue 346
- 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-his346pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown