Is FPR1 p.Thr286= (c.858A>G) pathogenic?

FPR1 p.Thr286= (c.858A>G) is classified Likely benign in FPR1 (ClinVar, Single submitter, 2 submitters; last evaluated 2025-10-27). Ultra-rare (popmax 0.0459%, nfe); Associated with gingival disorder.

What condition is associated with FPR1 p.Thr286= (c.858A>G)?

FPR1 p.Thr286= (c.858A>G) is associated with gingival disorder (ClinVar).

How common is FPR1 p.Thr286= (c.858A>G) in the general population?

FPR1 p.Thr286= (c.858A>G) is ultra-rare (popmax 0.0459%, nfe) (gnomAD).

FPR1 p.Thr286=

c.858A>G · rs371692364 · VCV1147556

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0459%, nfe)

Conditions

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 -6.4	GERP -3.7
Overall
CADD	0.092	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0459% European (non-Finnish) · 542/1,180,054 alleles

Filtering AF 0.0427% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0415%

Overall 0.037% 598/1,614,102 alleles · ultra-rare exomes 574/1,461,894 · genomes 24/152,208 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.0468%	2,135
European (non-Finnish)grpmax	0.0459%	2,177
Remaining individualsnot grpmax-eligible	0.0208%	4,807
Admixed American	0.01%	9,999
African / African-American	0.00934%	10,705

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Thr286=
Coding: c.858A>G
MANE Select: NM_002029
dbSNP: rs371692364
Type: single nucleotide variant
Location: chr19:51746137 (GRCh38)
Gene constraint: LOEUF 1.921 · pLI 0.13 (gnomAD)
Structure: AlphaFold pLDDT 84.17 · 5 PDB
Residue 286: an α-helix

Full FPR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

gingival disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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-thr286 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown