Is FPR1 p.Thr199= (c.597G>A) pathogenic?

FPR1 p.Thr199= (c.597G>A) is classified Likely benign in FPR1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-15). Ultra-rare (popmax 0.0165%, mid); Associated with gingival disorder.

What condition is associated with FPR1 p.Thr199= (c.597G>A)?

FPR1 p.Thr199= (c.597G>A) is associated with gingival disorder (ClinVar).

How common is FPR1 p.Thr199= (c.597G>A) in the general population?

FPR1 p.Thr199= (c.597G>A) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

FPR1 p.Thr199=

c.597G>A · VCV4743253

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

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 -9.2	GERP -3.7
Overall
CADD	0.328	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% Middle Eastern · 1/6,062 alleles

Filtering AF 0.00298% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00195%

Overall 0.00186% 30/1,614,168 alleles · ultra-rare exomes 23/1,461,880 · genomes 7/152,288 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,062
East Asian	0.00891%	11,218
South Asian	0.00659%	15,180
African / African-American	0.00267%	37,515
Admixed American	0.00167%	60,030
Remaining individualsnot grpmax-eligible	0.0016%	62,508
European (non-Finnish)	0.00127%	78,669

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.Thr199=
Coding: c.597G>A
MANE Select: NM_002029
Type: single nucleotide variant
Location: chr19:51746398 (GRCh38)
Gene constraint: LOEUF 1.921 · pLI 0.13 (gnomAD)
Structure: AlphaFold pLDDT 84.17 · 5 PDB
Residue 199: 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.Thr199Met Uncertain significance ★ ⚠ same residue
FPR1 p.Thr199Ser Uncertain significance ★ ⚠ same residue
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

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-thr199 (accessed [today's date]).

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