CFAP53 p.Arg145=
c.433A>C · rs748125320 · VCV262552
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.5e-05%, nfe)
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 5 | GERP 0.81, phastCons 1 |
| Overall | ||
| CADD | 12.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.5e-05%
European (non-Finnish) · 1/1,177,044 alleles
Overall
6.9e-05%
1/1,449,006 alleles · very rare
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.Arg145=
- Coding
- c.433A>C
- MANE Select
- NM_145020
- dbSNP
- rs748125320
- Type
- single nucleotide variant
- Location
- chr18:50261104 (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 145
- 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-arg145 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown