CFAP52 p.Thr421=
c.1263C>T · rs187332485 · VCV720040
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.202%, sas)
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 -15 | GERP -3 |
| Overall | ||
| CADD | 0.411 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.202%
South Asian · 184/91,070 alleles
Filtering AF
0.178%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.169%
Overall
0.0126%
204/1,614,176 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.202% | 495 |
| East Asian | 0.00669% | 14,959 |
| Admixed American | 0.005% | 20,006 |
| African / African-American | 0.00266% | 37,531 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,510 |
| European (non-Finnish) | 0.000932% | 107,275 |
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.Thr421=
- Coding
- c.1263C>T
- MANE Select
- NM_145054
- dbSNP
- rs187332485
- Type
- single nucleotide variant
- Location
- chr17:9632976 (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-thr421 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown