Is FCGRT p.Pro329Arg (c.986C>G) pathogenic?

FCGRT p.Pro329Arg (c.986C>G) is classified Uncertain significance in FCGRT (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-30). AlphaMissense: likely benign (0.1604); Ultra-rare (popmax 0.0434%, amr).

How common is FCGRT p.Pro329Arg (c.986C>G) in the general population?

FCGRT p.Pro329Arg (c.986C>G) is ultra-rare (popmax 0.0434%, amr) (gnomAD).

What do computational predictors say about FCGRT p.Pro329Arg (c.986C>G)?

AlphaMissense predicts likely benign (score 0.1604) — an in-silico prediction, not a clinical call.

FCGRT p.Pro329Arg

c.986C>G · rs142797093 · VCV2365488

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1604 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0434%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1604	likely benign
REVEL	0.124	moderately benign-leaning
SaProt	LLR -7.61	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Pangolin	Δ0.25	loss · gain 0.02 · SpliceAI below 0.2 · independent
Constraint at this position
Conservation	phyloP 2.4	GERP 1.5, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 12 kb · p 0.36 · regional, not allelic
Overall
CADD	25.0	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 0.0434% Admixed American · 26/59,920 alleles

Filtering AF 0.0304% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.026%

Overall 0.0028% 45/1,606,114 alleles · ultra-rare exomes 35/1,454,100 · genomes 10/152,014 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0434%	2,305
Remaining individualsnot grpmax-eligible	0.00965%	10,361
Ashkenazi Jewishnot grpmax-eligible	0.00677%	14,781
African / African-American	0.00134%	74,712
European (non-Finnish)	0.000852%	117,426

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.Pro329Arg
Coding: c.986C>G
MANE Select: NM_001136019
dbSNP: rs142797093
Type: single nucleotide variant
Location: chr19:49525571 (GRCh38)
Gene constraint: LOEUF 0.706 · pLI 0.12 (gnomAD)
Structure: AlphaFold pLDDT 85.73 · 31 PDB

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-pro329arg (accessed [today's date]).

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