Is FPR2 p.Ile116Val (c.346A>G) pathogenic?

FPR2 p.Ile116Val (c.346A>G) is classified Uncertain significance in FPR2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-04). AlphaMissense: likely benign (0.2822); Very rare (popmax 0.00167%, amr).

How common is FPR2 p.Ile116Val (c.346A>G) in the general population?

FPR2 p.Ile116Val (c.346A>G) is very rare (popmax 0.00167%, amr) (gnomAD).

What do computational predictors say about FPR2 p.Ile116Val (c.346A>G)?

AlphaMissense predicts likely benign (score 0.2822) — an in-silico prediction, not a clinical call.

FPR2 p.Ile116Val

c.346A>G · VCV3279717

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2822 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.2822	likely benign
REVEL	0.335	indeterminate
SaProt	LLR -6.58	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.8	GERP 0.68, phastCons 1
Regional constraint	o/e 0.85	unconstrained · MANE · 1,052 bp · p 0.0023 · regional, not allelic
Overall
CADD	20.6	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

Grpmax group 0.00167% Admixed American · 1/60,014 alleles

Overall 6.2e-05% 1/1,613,986 alleles · very rare exomes 1/1,461,894 · genomes 0/152,092 · joint denominator

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: FPR2
Protein: p.Ile116Val
Coding: c.346A>G
MANE Select: NM_001005738
Type: single nucleotide variant
Location: chr19:51769004 (GRCh38)
Gene constraint: LOEUF 1.667 · pLI 0.08 (gnomAD)
Structure: AlphaFold pLDDT 84.87 · 13 PDB
Residue 116: an α-helix

Full FPR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

FPR2 p.Phe74Leu Benign/Likely benign ★★ ⚠ same type
FPR2 c.-15+1402C>T Uncertain significance ★ same type
FPR2 p.Ala245Val Uncertain significance ★ ⚠ same type
FPR2 p.Ala248Ser Uncertain significance ★ ⚠ same type
FPR2 p.Arg137Cys Uncertain significance ★ same type
FPR2 p.Arg57Cys Uncertain significance ★ ⚠ same type
FPR2 p.Arg57His Uncertain significance ★ ⚠ same type
FPR2 p.Cys296Trp 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/fpr2-p-ile116val (accessed [today's date]).

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