Is F2RL3 p.Ser31Arg (c.93C>A) pathogenic?

F2RL3 p.Ser31Arg (c.93C>A) is classified Uncertain significance in F2RL3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-19). AlphaMissense: likely benign (0.2278); Very rare (popmax 0.00134%, afr).

How common is F2RL3 p.Ser31Arg (c.93C>A) in the general population?

F2RL3 p.Ser31Arg (c.93C>A) is very rare (popmax 0.00134%, afr) (gnomAD).

What do computational predictors say about F2RL3 p.Ser31Arg (c.93C>A)?

AlphaMissense predicts likely benign (score 0.2278) — an in-silico prediction, not a clinical call.

F2RL3 p.Ser31Arg

c.93C>A · VCV3511278

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2278 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2278	likely benign
REVEL	0.041	moderately benign-leaning
SaProt	LLR -7.70	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 -0.97
Regional constraint	o/e 1.02	unconstrained · MANE · 1,428 bp · p 0.56 · regional, not allelic
Overall
CADD	14.69	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 0.00134% African / African-American · 1/74,644 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000188% 3/1,594,560 alleles · very rare exomes 2/1,442,366 · genomes 1/152,194 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00134%	74,644
European (non-Finnish)	0.000171%	585,974

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: F2RL3
Protein: p.Ser31Arg
Coding: c.93C>A
MANE Select: NM_003950
Type: single nucleotide variant
Location: chr19:16889282 (GRCh38)
Gene constraint: LOEUF 1.746 · pLI 0.06 (gnomAD)
Structure: AlphaFold pLDDT 80.67 · 3 PDB
Residue 31: the 'disordered' region

Full F2RL3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

F2RL3 p.Ala120Thr Benign ★★ same type
F2RL3 p.Leu257= Benign ★★ same type
F2RL3 p.Tyr322= Benign ★★ same type
F2RL3 p.Ala128Val Uncertain significance ★ ⚠ same type
F2RL3 p.Ala186Gly Uncertain significance ★ ⚠ same type
F2RL3 p.Ala199Ser Uncertain significance ★ ⚠ same type
F2RL3 p.Ala200Val Uncertain significance ★ ⚠ same type
F2RL3 p.Ala208Ser 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/f2rl3-p-ser31arg (accessed [today's date]).

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