CFAP53 p.Glu269=
c.807G>A · rs374506948 · VCV738571
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0587%, afr)
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 0.41 | GERP -0.27, phastCons 0.035 |
| Overall | ||
| CADD | 7.048 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0587%
African / African-American · 44/74,912 alleles
Filtering AF
0.0449%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0401%
Overall
0.00297%
48/1,613,964 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0587% | 1,703 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,827 |
| Admixed American | 0.00167% | 59,982 |
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
- CFAP53
- Protein
- p.Glu269=
- Coding
- c.807G>A
- MANE Select
- NM_145020
- dbSNP
- rs374506948
- Type
- single nucleotide variant
- Location
- chr18:50250947 (GRCh38)
- Gene constraint
- LOEUF 1.282 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 86.17 · 2 PDB
- Residue 269
- the trichohyalin-plectin-homology domain; a UniProt-annotated variant site (in htx6; uncertain significance; no overt effects on the structure or function of respiratory cilia)
Similar variants
- CFAP53 p.Ala185Thr Uncertain significance ★★ ⚠ same type
- CFAP53 p.Ala385Ser Uncertain significance ★★ ⚠ same type
- CFAP53 p.Arg158Gly Uncertain significance ★★ ⚠ same type
- CFAP53 p.Arg257Cys Uncertain significance ★★ ⚠ same type
- CFAP53 p.Arg470His Uncertain significance ★★ ⚠ same type
- CFAP53 p.Arg505His Uncertain significance ★★ ⚠ same type
- CFAP53 p.Arg505Leu Uncertain significance ★★ ⚠ same type
- CFAP53 p.Arg505Ser 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/cfap53-p-glu269 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown