Is FPR1 p.Thr9Met (c.26C>T) pathogenic?

FPR1 p.Thr9Met (c.26C>T) is classified Likely benign in FPR1 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-29). AlphaMissense: likely benign (0.104); Rare (popmax 0.57%, afr); Associated with gingival disorder.

What condition is associated with FPR1 p.Thr9Met (c.26C>T)?

FPR1 p.Thr9Met (c.26C>T) is associated with gingival disorder (ClinVar).

How common is FPR1 p.Thr9Met (c.26C>T) in the general population?

FPR1 p.Thr9Met (c.26C>T) is rare (popmax 0.57%, afr) (gnomAD).

What do computational predictors say about FPR1 p.Thr9Met (c.26C>T)?

AlphaMissense predicts likely benign (score 0.104) — an in-silico prediction, not a clinical call.

FPR1 p.Thr9Met

c.26C>T · rs148095693 · VCV456364

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.104 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.57%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

gingival disorder

Computational evidence

Protein change
AlphaMissense	0.104	likely benign
REVEL	0.013	strongly benign-leaning
SaProt	LLR -7.82	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.71 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.16	GERP -3.4
Regional constraint	o/e 0.90	unconstrained · MANE · 1,049 bp · p 0.031 · regional, not allelic
Overall
CADD	1.193	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.57% African / African-American · 427/74,960 alleles

Filtering AF 0.525% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.507%

Overall 0.0754% 1,216/1,612,534 alleles · rare exomes 894/1,460,340 · genomes 322/152,194 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.57%	176
Middle Eastern	0.566%	177
Admixed American	0.227%	441
Remaining individualsnot grpmax-eligible	0.152%	657
South Asian	0.0472%	2,117
European (non-Finnish)	0.0406%	2,461
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,564
East Asian	0.00223%	44,824

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.Thr9Met
Coding: c.26C>T
MANE Select: NM_002029
dbSNP: rs148095693
Type: single nucleotide variant
Location: chr19:51746969 (GRCh38)
Gene constraint: LOEUF 1.921 · pLI 0.13 (gnomAD)
Structure: AlphaFold pLDDT 84.17 · 5 PDB

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.Thr9= Likely benign ★ 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-thr9met (accessed [today's date]).

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