FPR1 p.Ser63=
c.189T>C · rs148014099 · VCV1113428
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0181%, nfe)
Conditions
1
gingival disorder
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 0.14 | GERP -3.1, phastCons 0.001 |
| Overall | ||
| CADD | 4.526 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0181%
European (non-Finnish) · 213/1,180,040 alleles
Filtering AF
0.016%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0152%
Overall
0.0138%
222/1,614,036 alleles · ultra-rare
exomes 216/1,461,888 · genomes 6/152,148 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0181% | 5,540 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,926 |
| South Asian | 0.0022% | 45,540 |
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
- FPR1
- Protein
- p.Ser63=
- Coding
- c.189T>C
- MANE Select
- NM_002029
- dbSNP
- rs148014099
- Type
- single nucleotide variant
- Location
- chr19:51746806 (GRCh38)
- Gene constraint
- LOEUF 1.921 · pLI 0.13 (gnomAD)
- Structure
- AlphaFold pLDDT 84.17 · 5 PDB
- Residue 63
- an α-helix
Similar variants
- FPR1 p.Ala225Val Uncertain significance ★★ ⚠ same condition
- FPR1 p.Ala315Thr Uncertain significance ★★ ⚠ same condition
- FPR1 p.Ile146Val Uncertain significance ★★ ⚠ same condition
- FPR1 p.Ile147Thr Uncertain significance ★★ ⚠ same condition
- FPR1 p.Ile216Val Uncertain significance ★★ ⚠ same condition
- FPR1 p.Ile228Phe Uncertain significance ★★ ⚠ same condition
- FPR1 p.Met197Ile Uncertain significance ★★ ⚠ same condition
- FPR1 p.Met275Thr 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/fpr1-p-ser63 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown