Is FPR1 p.Cys253Phe (c.758G>T) pathogenic?

FPR1 p.Cys253Phe (c.758G>T) is classified Uncertain significance in FPR1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-19). AlphaMissense: likely pathogenic (0.5671); Absent from gnomAD v4.1; Associated with gingival disorder.

What condition is associated with FPR1 p.Cys253Phe (c.758G>T)?

FPR1 p.Cys253Phe (c.758G>T) is associated with gingival disorder (ClinVar).

How common is FPR1 p.Cys253Phe (c.758G>T) in the general population?

FPR1 p.Cys253Phe (c.758G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about FPR1 p.Cys253Phe (c.758G>T)?

AlphaMissense predicts likely pathogenic (score 0.5671) — an in-silico prediction, not a clinical call.

FPR1 p.Cys253Phe

c.758G>T · rs2122321483 · VCV1501594

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.5671 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

gingival disorder

Computational evidence

Protein change
AlphaMissense	0.5671	likely pathogenic
REVEL	0.478	indeterminate
SaProt	LLR -8.89	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2	GERP 1.7, phastCons 0.99
Regional constraint	o/e 0.90	unconstrained · MANE · 1,049 bp · p 0.031 · regional, not allelic
Overall
CADD	23.9	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: FPR1
Protein: p.Cys253Phe
Coding: c.758G>T
MANE Select: NM_002029
dbSNP: rs2122321483
Type: single nucleotide variant
Location: chr19:51746237 (GRCh38)
Gene constraint: LOEUF 1.921 · pLI 0.13 (gnomAD)
Structure: AlphaFold pLDDT 84.17 · 5 PDB
Residue 253: 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-cys253phe (accessed [today's date]).

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