CFAP57 p.Pro564=
c.1692C>T · rs143175489 · VCV2638740
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.283%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -3.4 |
| Overall | ||
| CADD | 6.608 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.283%
East Asian · 127/44,870 alleles
Filtering AF
0.243%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.228%
Overall
0.0256%
413/1,614,142 alleles · rare
exomes 370/1,461,882 · genomes 43/152,260 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.283% | 353 |
| Remaining individualsnot grpmax-eligible | 0.0304% | 3,290 |
| African / African-American | 0.0213% | 4,689 |
| European (non-Finnish) | 0.0201% | 4,979 |
| Middle Eastern | 0.0165% | 6,060 |
| Finnishnot grpmax-eligible | 0.00781% | 12,807 |
| Admixed American | 0.005% | 20,006 |
| South Asian | 0.00439% | 22,769 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
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
- CFAP57
- Protein
- p.Pro564=
- Coding
- c.1692C>T
- MANE Select
- NM_001378189
- dbSNP
- rs143175489
- Type
- single nucleotide variant
- Location
- chr1:43206869 (GRCh38)
- Gene constraint
- LOEUF 0.92 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.57 · 1 PDB
Similar variants
- CFAP57 p.Gln125Arg Likely benign ★★ ⚠ same type
- CFAP57 p.Ile322Met Likely benign ★★ same type
- CFAP57 p.Ser614= Likely benign ★★ same type
- CFAP57 p.Arg411Ter Likely pathogenic ★ same type
- CFAP57 p.Arg958Ter Pathogenic ★ same type
- CFAP57 c.1929+122A>C Uncertain significance ★ same type
- CFAP57 c.1929+139C>A Uncertain significance ★ same type
- CFAP57 c.1929+154A>T 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/cfap57-p-pro564 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown