Is FPR1 p.Ile208Phe (c.622A>T) pathogenic?

FPR1 p.Ile208Phe (c.622A>T) is classified Uncertain significance in FPR1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-08). AlphaMissense: likely benign (0.1474); Absent from gnomAD v4.1.

How common is FPR1 p.Ile208Phe (c.622A>T) in the general population?

FPR1 p.Ile208Phe (c.622A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about FPR1 p.Ile208Phe (c.622A>T)?

AlphaMissense predicts likely benign (score 0.1474) — an in-silico prediction, not a clinical call.

FPR1 p.Ile208Phe

c.622A>T · rs2513920001 · VCV2535491

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1474 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1474	likely benign
REVEL	0.067	moderately benign-leaning
SaProt	LLR -2.42	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1	GERP -3.7
Regional constraint	o/e 0.90	unconstrained · MANE · 1,049 bp · p 0.031 · regional, not allelic
Overall
CADD	8.197	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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.Ile208Phe
Coding: c.622A>T
MANE Select: NM_002029
dbSNP: rs2513920001
Type: single nucleotide variant
Location: chr19:51746373 (GRCh38)
Gene constraint: LOEUF 1.921 · pLI 0.13 (gnomAD)
Structure: AlphaFold pLDDT 84.17 · 5 PDB
Residue 208: an α-helix

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

Similar variants

FPR1 p.Ile208Thr Uncertain significance ★ ⚠ same residue
FPR1 p.Ile208= Likely benign ★ same residue
FPR1 p.Ala225Val Uncertain significance ★★ ⚠ same type
FPR1 p.Ala315Thr Uncertain significance ★★ ⚠ same type
FPR1 p.Ile146Val Uncertain significance ★★ ⚠ same type
FPR1 p.Ile147Thr Uncertain significance ★★ ⚠ same type
FPR1 p.Ile216Val Uncertain significance ★★ ⚠ same type
FPR1 p.Ile228Phe Uncertain significance ★★ ⚠ same type

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-ile208phe (accessed [today's date]).

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