Is FCGRT p.Pro6Arg (c.17C>G) pathogenic?

FCGRT p.Pro6Arg (c.17C>G) is classified Uncertain significance in FCGRT (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-05). AlphaMissense: likely benign (0.0702); Ultra-rare (popmax 0.0301%, mid).

How common is FCGRT p.Pro6Arg (c.17C>G) in the general population?

FCGRT p.Pro6Arg (c.17C>G) is ultra-rare (popmax 0.0301%, mid) (gnomAD).

What do computational predictors say about FCGRT p.Pro6Arg (c.17C>G)?

AlphaMissense predicts likely benign (score 0.0702) — an in-silico prediction, not a clinical call.

FCGRT p.Pro6Arg

c.17C>G · rs2079985451 · VCV3094082

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0702 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0301%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0702	likely benign
REVEL	0.052	moderately benign-leaning
SaProt	LLR -7.19	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.21	acceptor gain · deltas
Constraint at this position
Conservation	phyloP 1.9	GERP -0.014, phastCons 0.014
Regional constraint	o/e 0.86	unconstrained · MANE · 881 bp · p 0.069 · regional, not allelic
Overall
CADD	17.73	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 0.0301% Middle Eastern · 1/3,322 alleles

Filtering AF 0.008% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00522%

Overall 0.000482% 6/1,245,384 alleles · ultra-rare exomes 5/1,093,422 · genomes 1/151,962 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0301%	3,322
South Asian	0.0205%	4,889

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.Pro6Arg
Coding: c.17C>G
MANE Select: NM_001136019
dbSNP: rs2079985451
Type: single nucleotide variant
Location: chr19:49513417 (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-pro6arg (accessed [today's date]).

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