Is FMO3 p.Ala367Val (c.1100C>T) pathogenic?

FMO3 p.Ala367Val (c.1100C>T) is classified Uncertain significance in FMO3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-14). AlphaMissense: likely benign (0.2548); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with FMO3 p.Ala367Val (c.1100C>T)?

FMO3 p.Ala367Val (c.1100C>T) is associated with Inborn genetic diseases (ClinVar).

How common is FMO3 p.Ala367Val (c.1100C>T) in the general population?

FMO3 p.Ala367Val (c.1100C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about FMO3 p.Ala367Val (c.1100C>T)?

AlphaMissense predicts likely benign (score 0.2548) — an in-silico prediction, not a clinical call.

FMO3 p.Ala367Val

c.1100C>T · VCV4025895

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2548 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2548	likely benign
REVEL	0.288	benign-leaning
SaProt	LLR -10.97	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 3.9	GERP 1.9, phastCons 1
Regional constraint	o/e 1.04	unconstrained · MANE · 25 kb · p 0.27 · regional, not allelic
Overall
CADD	23.1	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: FMO3
Protein: p.Ala367Val
Coding: c.1100C>T
MANE Select: NM_001002294
Type: single nucleotide variant
Location: chr1:171114279 (GRCh38)
Gene constraint: LOEUF 1.314 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.50

Full FMO3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

FMO3 p.Tyr430His Uncertain significance ★★ same condition
FMO3 p.Thr532Ile Likely benign ★★ same condition
FMO3 p.Ala10Val Uncertain significance ★ ⚠ same condition
FMO3 p.Ala138Thr Uncertain significance ★ ⚠ same condition
FMO3 p.Ala378Val Uncertain significance ★ ⚠ same condition
FMO3 p.Ala458Val Uncertain significance ★ ⚠ same condition
FMO3 p.Arg500Gln Conflicting classifications of pathogenicity ★ ⚠ same condition
FMO3 p.Asn268Ser Uncertain significance ★ ⚠ same condition

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/fmo3-p-ala367val (accessed [today's date]).

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