Is FLG p.Ala3288= (c.9864A>G) pathogenic?

FLG p.Ala3288= (c.9864A>G) is classified Likely benign in FLG (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-05). Ultra-rare (popmax 0.0848%, eas).

How common is FLG p.Ala3288= (c.9864A>G) in the general population?

FLG p.Ala3288= (c.9864A>G) is ultra-rare (popmax 0.0848%, eas) (gnomAD).

FLG p.Ala3288=

c.9864A>G · VCV4911411

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0848%, eas)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -8.6	GERP -2.9
Overall
CADD	0.87	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0848% East Asian · 38/44,814 alleles

Filtering AF 0.0635% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.056%

Overall 0.0052% 84/1,613,840 alleles · ultra-rare exomes 78/1,461,804 · genomes 6/152,036 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0848%	1,179
Remaining individualsnot grpmax-eligible	0.0048%	20,834
European (non-Finnish)	0.00339%	29,499
South Asian	0.0022%	45,490
African / African-American	0.00133%	74,964

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: FLG
Protein: p.Ala3288=
Coding: c.9864A>G
MANE Select: NM_002016
Type: single nucleotide variant
Location: chr1:152305022 (GRCh38)

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

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/flg-p-ala3288 (accessed [today's date]).

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