Is FCGRT p.Pro202Ala (c.604C>G) pathogenic?

FCGRT p.Pro202Ala (c.604C>G) is classified Uncertain significance in FCGRT (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-19). AlphaMissense: likely benign (0.1164); Ultra-rare (popmax 0.0166%, mid).

How common is FCGRT p.Pro202Ala (c.604C>G) in the general population?

FCGRT p.Pro202Ala (c.604C>G) is ultra-rare (popmax 0.0166%, mid) (gnomAD).

What do computational predictors say about FCGRT p.Pro202Ala (c.604C>G)?

AlphaMissense predicts likely benign (score 0.1164) — an in-silico prediction, not a clinical call.

FCGRT p.Pro202Ala

c.604C>G · VCV3849751

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1164 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0166%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1164	likely benign
REVEL	0.128	moderately benign-leaning
SaProt	LLR -7.88	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 4.7	GERP 1.3, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 12 kb · p 0.36 · regional, not allelic
Overall
CADD	21.6	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 0.0166% Middle Eastern · 1/6,020 alleles

Overall 0.000125% 2/1,605,102 alleles · ultra-rare exomes 2/1,452,838 · genomes 0/152,264 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0166%	6,020
Admixed American	0.00167%	59,836

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: FCGRT
Protein: p.Pro202Ala
Coding: c.604C>G
MANE Select: NM_001136019
Type: single nucleotide variant
Location: chr19:49524509 (GRCh38)
Gene constraint: LOEUF 0.706 · pLI 0.12 (gnomAD)
Structure: AlphaFold pLDDT 85.73 · 31 PDB
Residue 202: the ig-like c1-type domain; the 'alpha-3' region

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

Similar variants

FCGRT p.Lys132Asn Benign ★★ same type
FCGRT p.Pro42= Benign ★★ same type
FCGRT p.Thr340= Benign ★★ same type
FCGRT p.Ala280Thr Uncertain significance ★ ⚠ same type
FCGRT p.Ala280Val Uncertain significance ★ ⚠ same type
FCGRT p.Ala283Thr Uncertain significance ★ ⚠ same type
FCGRT p.Ala283Val Uncertain significance ★ ⚠ same type
FCGRT p.Ala294Gly 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/fcgrt-p-pro202ala (accessed [today's date]).

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