CFAP52 p.Asp133=
c.399T>C · rs1597764518 · VCV750565
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 -1.3 | GERP -3.9, phastCons 0.001 |
| Overall | ||
| CADD | 4.136 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.5e-05%
European (non-Finnish) · 1/1,176,666 alleles
Overall
6.24e-05%
1/1,601,942 alleles · very rare
exomes 1/1,449,608 · genomes 0/152,334 · joint denominator
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
- CFAP52
- Protein
- p.Asp133=
- Coding
- c.399T>C
- MANE Select
- NM_145054
- dbSNP
- rs1597764518
- Type
- single nucleotide variant
- Location
- chr17:9586826 (GRCh38)
- Gene constraint
- LOEUF 1.022 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.59 · 2 PDB
Similar variants
- CFAP52 p.Ala147Thr Uncertain significance ★★ ⚠ same type
- CFAP52 p.Ala161Asp Uncertain significance ★★ ⚠ same type
- CFAP52 p.Arg106Gln Uncertain significance ★★ ⚠ same type
- CFAP52 p.Arg170Gln Uncertain significance ★★ ⚠ same type
- CFAP52 p.Arg594Cys Uncertain significance ★★ ⚠ same type
- CFAP52 p.Gly343Ser Uncertain significance ★★ ⚠ same type
- CFAP52 p.Gly534Ala Uncertain significance ★★ same type
- CFAP52 p.Met551Thr 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/cfap52-p-asp133 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown