Is FCGRT p.Val307Ala (c.920T>C) pathogenic?

FCGRT p.Val307Ala (c.920T>C) is classified Uncertain significance in FCGRT (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-19). AlphaMissense: likely benign (0.1798); Very rare (popmax 0.00636%, nfe).

How common is FCGRT p.Val307Ala (c.920T>C) in the general population?

FCGRT p.Val307Ala (c.920T>C) is very rare (popmax 0.00636%, nfe) (gnomAD).

What do computational predictors say about FCGRT p.Val307Ala (c.920T>C)?

AlphaMissense predicts likely benign (score 0.1798) — an in-silico prediction, not a clinical call.

FCGRT p.Val307Ala

c.920T>C · rs199588435 · VCV3094088

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1798 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00636%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1798	likely benign
REVEL	0.108	moderately benign-leaning
SaProt	LLR -8.06	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 5.7	GERP 1.3, phastCons 0.95
Regional constraint	o/e 1.05	unconstrained · MANE · 12 kb · p 0.36 · regional, not allelic
Overall
CADD	16.59	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 0.00636% European (non-Finnish) · 75/1,180,002 alleles

Filtering AF 0.00519% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00474%

Overall 0.00483% 78/1,613,864 alleles · very rare exomes 74/1,461,702 · genomes 4/152,162 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00636%	15,733
Remaining individualsnot grpmax-eligible	0.0032%	31,239
African / African-American	0.00133%	74,918

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.Val307Ala
Coding: c.920T>C
MANE Select: NM_001136019
dbSNP: rs199588435
Type: single nucleotide variant
Location: chr19:49525505 (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-val307ala (accessed [today's date]).

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