Is FCER2 p.Arg267Pro (c.800G>C) pathogenic?

FCER2 p.Arg267Pro (c.800G>C) is classified Uncertain significance in FCER2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-05). AlphaMissense: likely pathogenic (0.7099); Ultra-rare (popmax 0.0603%, eas).

How common is FCER2 p.Arg267Pro (c.800G>C) in the general population?

FCER2 p.Arg267Pro (c.800G>C) is ultra-rare (popmax 0.0603%, eas) (gnomAD).

What do computational predictors say about FCER2 p.Arg267Pro (c.800G>C)?

AlphaMissense predicts likely pathogenic (score 0.7099) — an in-silico prediction, not a clinical call.

FCER2 p.Arg267Pro

c.800G>C · rs548023601 · VCV2518102

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7099 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0603%, eas)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.7099	likely pathogenic
REVEL	0.032	moderately benign-leaning
SaProt	LLR -11.40	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.079	GERP -2.1
Regional constraint	o/e 1.01	unconstrained · MANE · 11 kb · p 0.79 · regional, not allelic
Overall
CADD	16.07	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 0.0603% East Asian · 27/44,750 alleles

Filtering AF 0.0425% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0366%

Overall 0.00304% 49/1,610,356 alleles · ultra-rare exomes 42/1,458,056 · genomes 7/152,300 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0603%	1,657
South Asian	0.011%	9,060
Remaining individualsnot grpmax-eligible	0.00964%	10,369
Admixed American	0.00168%	59,518
European (non-Finnish)	0.000424%	235,767

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: FCER2
Protein: p.Arg267Pro
Coding: c.800G>C
MANE Select: NM_001220500
dbSNP: rs548023601
Type: single nucleotide variant
Location: chr19:7689359 (GRCh38)
Gene constraint: LOEUF 1.087 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.76 · 23 PDB
Residue 267: the c-type lectin domain

Full FCER2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

FCER2 p.Ala246Asp Uncertain significance ★ ⚠ same type
FCER2 p.Ala246Ser Uncertain significance ★ ⚠ same type
FCER2 p.Ala271Asp Uncertain significance ★ ⚠ same type
FCER2 p.Ala33Thr Uncertain significance ★ ⚠ same type
FCER2 p.Ala36Val Uncertain significance ★ ⚠ same type
FCER2 p.Arg142Trp Uncertain significance ★ ⚠ same type
FCER2 p.Arg14Ser Uncertain significance ★ ⚠ same type
FCER2 p.Arg16Gln 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/fcer2-p-arg267pro (accessed [today's date]).

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