CFAP43 p.Pro246=
c.738G>A · rs139043615 · VCV774472
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.34%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP -3.8 |
| Overall | ||
| CADD | 1.652 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.34%
South Asian · 1,213/90,266 alleles
Filtering AF
1.28%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.26%
Overall
0.271%
4,363/1,610,692 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.34% | 74 |
| Admixed American | 0.29% | 344 |
| Remaining individualsnot grpmax-eligible | 0.266% | 376 |
| Middle Eastern | 0.265% | 378 |
| European (non-Finnish) | 0.23% | 435 |
| African / African-American | 0.0548% | 1,826 |
| Finnishnot grpmax-eligible | 0.0469% | 2,132 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0442% | 2,264 |
| East Asian | 0.00446% | 22,409 |
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
- CFAP43
- Protein
- p.Pro246=
- Coding
- c.738G>A
- MANE Select
- NM_025145
- dbSNP
- rs139043615
- Type
- single nucleotide variant
- Location
- chr10:104207822 (GRCh38)
- Gene constraint
- LOEUF 0.78 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.27 · 1 PDB
Similar variants
- CFAP43 p.Pro246Leu Uncertain significance ★ ⚠ same residue
- CFAP43 p.Arg894Ter Pathogenic/Likely pathogenic ★★ same type
- CFAP43 p.Thr1075Lys Uncertain significance ★★ ⚠ same type
- CFAP43 c.2142-4A>G Benign ★★ same type
- CFAP43 p.Glu1540Gly Benign/Likely benign ★★ same type
- CFAP43 p.Leu1542Val Benign/Likely benign ★★ same type
- CFAP43 p.Leu616Phe Benign ★★ same type
- CFAP43 p.Leu802= Benign ★★ 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/cfap43-p-pro246 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown