CFAP57 p.Ala592=
c.1776G>A · VCV4970469
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0147%, afr)
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 -0.83 | GERP -3.7 |
| Overall | ||
| CADD | 0.93 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0147%
African / African-American · 11/74,920 alleles
Filtering AF
0.00815%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00633%
Overall
0.0018%
29/1,614,032 alleles · ultra-rare
exomes 22/1,461,826 · genomes 7/152,206 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0147% | 6,811 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,623 |
| Admixed American | 0.005% | 20,003 |
| South Asian | 0.00329% | 30,359 |
| East Asian | 0.00223% | 44,896 |
| European (non-Finnish) | 0.000593% | 168,577 |
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.Ala592=
- Coding
- c.1776G>A
- MANE Select
- NM_001378189
- Type
- single nucleotide variant
- Location
- chr1:43209763 (GRCh38)
- Gene constraint
- LOEUF 0.92 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.57 · 1 PDB
- Residue 592
- a UniProt-annotated variant site (found in a patient with primary ciliary dyskinesia; uncertain significance; loss of location to ciliary axoneme; reduced beat frequency)
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-ala592 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown