CFAP52 p.Ser547=
c.1641G>A · rs143049274 · VCV1547099
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.06%, sas)
Conditions
1
situs inversus
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 -2.4 | GERP -3.6 |
| Overall | ||
| CADD | 0.866 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.06%
South Asian · 964/91,062 alleles
Filtering AF
1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.981%
Overall
0.0678%
1,095/1,613,942 alleles · low-frequency
exomes 1,018/1,461,666 · genomes 77/152,276 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.06% | 94 |
| Middle Eastern | 0.198% | 505 |
| Remaining individualsnot grpmax-eligible | 0.0896% | 1,116 |
| East Asian | 0.0357% | 2,804 |
| Admixed American | 0.0317% | 3,159 |
| African / African-American | 0.00933% | 10,720 |
| European (non-Finnish) | 0.00178% | 56,185 |
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.Ser547=
- Coding
- c.1641G>A
- MANE Select
- NM_145054
- dbSNP
- rs143049274
- Type
- single nucleotide variant
- Location
- chr17:9641789 (GRCh38)
- Gene constraint
- LOEUF 1.022 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.59 · 2 PDB
Similar variants
- CFAP52 p.Ser547Leu Uncertain significance ★ ⚠ same residue
- CFAP52 p.Ser547Thr Uncertain significance ★ ⚠ same residue
- CFAP52 p.Ala147Thr Uncertain significance ★★ ⚠ same condition
- CFAP52 p.Ala161Asp Uncertain significance ★★ ⚠ same condition
- CFAP52 p.Arg170Gln Uncertain significance ★★ ⚠ same condition
- CFAP52 p.Arg594Cys Uncertain significance ★★ ⚠ same condition
- CFAP52 p.Gly343Ser Uncertain significance ★★ ⚠ same condition
- CFAP52 p.Gly534Ala Uncertain significance ★★ same condition
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-ser547 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown