Is FPR3 p.Ile167Val (c.499A>G) pathogenic?

FPR3 p.Ile167Val (c.499A>G) is classified Likely benign in FPR3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-08). AlphaMissense: likely benign (0.0823); Very rare (popmax 0.00223%, eas).

How common is FPR3 p.Ile167Val (c.499A>G) in the general population?

FPR3 p.Ile167Val (c.499A>G) is very rare (popmax 0.00223%, eas) (gnomAD).

What do computational predictors say about FPR3 p.Ile167Val (c.499A>G)?

AlphaMissense predicts likely benign (score 0.0823) — an in-silico prediction, not a clinical call.

FPR3 p.Ile167Val

c.499A>G · VCV3851524

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0823 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0823	likely benign
REVEL	0.096	moderately benign-leaning
SaProt	LLR -6.08	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Pangolin	Δ0.38	gain · loss 0.00 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP -1.8	GERP -1.1
Regional constraint	o/e 0.78	unconstrained · MANE · 1,058 bp · p 3.9e-06 · regional, not allelic
Overall
CADD	0.062	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 0.00223% East Asian · 1/44,892 alleles

Filtering AF 0.000183% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00012%

Overall 0.000558% 9/1,614,074 alleles · very rare exomes 8/1,461,872 · genomes 1/152,202 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,892
African / African-American	0.00133%	74,922
South Asian	0.0011%	91,090
European (non-Finnish)	0.000508%	196,672

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: FPR3
Protein: p.Ile167Val
Coding: c.499A>G
MANE Select: NM_002030
Type: single nucleotide variant
Location: chr19:51824247 (GRCh38)
Gene constraint: LOEUF 1.906 · pLI 0.15 (gnomAD)
Structure: AlphaFold pLDDT 83.62

Full FPR3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

FPR3 p.Ala198Gly Uncertain significance ★ ⚠ same type
FPR3 p.Ala244Val Uncertain significance ★ ⚠ same type
FPR3 p.Ala86Thr Uncertain significance ★ ⚠ same type
FPR3 p.Arg123His Uncertain significance ★ ⚠ same type
FPR3 p.Arg241Cys Uncertain significance ★ ⚠ same type
FPR3 p.Arg57His Uncertain significance ★ ⚠ same type
FPR3 p.Asn274Tyr Uncertain significance ★ ⚠ same type
FPR3 p.Cys124Ser 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/fpr3-p-ile167val (accessed [today's date]).

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