Is FPR1 p.Ile116= (c.348C>T) pathogenic?

FPR1 p.Ile116= (c.348C>T) is classified Benign in FPR1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-02-03). Common (popmax 30.8%, afr) — too common for a highly-penetrant pathogenic allele; Associated with gingival disorder.

What condition is associated with FPR1 p.Ile116= (c.348C>T)?

FPR1 p.Ile116= (c.348C>T) is associated with gingival disorder (ClinVar).

FPR1 p.Ile116=

Q: How common is FPR1 p.Ile116= (c.348C>T) in the general population?

FPR1 p.Ile116= (c.348C>T) is common (popmax 30.8%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.348C>T · rs5030879 · VCV456366

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 30.8%, afr) — too common for a highly-penetrant pathogenic allele

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 -5.8	GERP -3.7
Overall
CADD	0.412	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 30.8% African / African-American · 23,036/74,904 alleles

Filtering AF 30.4% ClinGen BA1/BS1 input FAF95, joint · FAF99 30.3%

Overall 2.05% 33,021/1,614,018 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	30.8%	3
Middle Eastern	4.16%	24
Remaining individualsnot grpmax-eligible	2.72%	37
Admixed American	2.52%	40
South Asian	1.89%	53
Ashkenazi Jewishnot grpmax-eligible	1.11%	90
European (non-Finnish)	0.374%	268
Amishnot grpmax-eligible	0.11%	912
East Asian	0.0713%	1,402
Finnishnot grpmax-eligible	0.0406%	2,463

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.Ile116=
Coding: c.348C>T
MANE Select: NM_002029
dbSNP: rs5030879
Type: single nucleotide variant
Location: chr19:51746647 (GRCh38)
Gene constraint: LOEUF 1.921 · pLI 0.13 (gnomAD)
Structure: AlphaFold pLDDT 84.17 · 5 PDB
Residue 116: a disulfide bond; 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.Ile116Phe 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
FPR1 p.Met197Ile 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-ile116 (accessed [today's date]).

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