Is FPR3 p.Val35Asp (c.104T>A) pathogenic?

FPR3 p.Val35Asp (c.104T>A) is classified Uncertain significance in FPR3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-02). AlphaMissense: likely pathogenic (0.7793); Ultra-rare (popmax 0.0133%, amr).

How common is FPR3 p.Val35Asp (c.104T>A) in the general population?

FPR3 p.Val35Asp (c.104T>A) is ultra-rare (popmax 0.0133%, amr) (gnomAD).

What do computational predictors say about FPR3 p.Val35Asp (c.104T>A)?

AlphaMissense predicts likely pathogenic (score 0.7793) — an in-silico prediction, not a clinical call.

FPR3 p.Val35Asp

c.104T>A · rs1169936513 · VCV3096665

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7793 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0133%, amr)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.7793	likely pathogenic
REVEL	0.291	indeterminate
SaProt	LLR -13.14	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5	GERP 1.7, phastCons 0.81
Regional constraint	o/e 0.78	unconstrained · MANE · 1,058 bp · p 3.9e-06 · regional, not allelic
Overall
CADD	24.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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 0.0133% Admixed American · 8/59,964 alleles

Filtering AF 0.00662% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00483%

Overall 0.000496% 8/1,613,794 alleles · ultra-rare exomes 6/1,461,834 · genomes 2/151,960 · 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: FPR3
Protein: p.Val35Asp
Coding: c.104T>A
MANE Select: NM_002030
dbSNP: rs1169936513
Type: single nucleotide variant
Location: chr19:51823852 (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-val35asp (accessed [today's date]).

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