Is FMO3 p.Ala6fs (c.16del) pathogenic?

FMO3 p.Ala6fs (c.16del) is classified Pathogenic in FMO3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-17). No gnomAD frequency available for this variant.

How common is FMO3 p.Ala6fs (c.16del) in the general population?

FMO3 p.Ala6fs (c.16del) is no gnomAD frequency available for this variant (gnomAD).

FMO3 p.Ala6fs

c.16del · rs2526256749 · VCV2696531

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 9
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.3	GERP 0.8, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: FMO3
Protein: p.Ala6fs
Coding: c.16del
MANE Select: NM_001002294
dbSNP: rs2526256749
Type: Deletion
Location: chr1:171092673 (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

Similar variants

FMO3 c.1183+1del Pathogenic/Likely pathogenic ★★ same type
FMO3 p.Arg131fs Pathogenic/Likely pathogenic ★★ same type
FMO3 p.Asn80fs Pathogenic/Likely pathogenic ★★ same type
FMO3 p.Phe242fs Pathogenic/Likely pathogenic ★★ same type
FMO3 p.Pro380fs Pathogenic/Likely pathogenic ★★ same type
FMO3 p.Val187fs Pathogenic/Likely pathogenic ★★ same type
FMO3 c.825_827+16del Likely pathogenic ★ same type
FMO3 p.Ala120fs Pathogenic ★ 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/fmo3-p-ala6fs (accessed [today's date]).

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