Is FLG p.Arg3879= (c.11637A>G) pathogenic?

FLG p.Arg3879= (c.11637A>G) is classified Likely benign in FLG (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-01). Ultra-rare (popmax 0.0164%, mid).

How common is FLG p.Arg3879= (c.11637A>G) in the general population?

FLG p.Arg3879= (c.11637A>G) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

FLG p.Arg3879=

c.11637A>G · VCV4083951

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

⚠ 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.
Splicing
SpliceAI	—	not looked up on this page · why
Overall
CADD	0.335	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0164% Middle Eastern · 1/6,084 alleles

Filtering AF 0.000183% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00012%

Overall 0.00062% 10/1,613,782 alleles · ultra-rare exomes 8/1,461,862 · genomes 2/151,920 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,084
Remaining individualsnot grpmax-eligible	0.0032%	31,243
South Asian	0.0011%	91,036
European (non-Finnish)	0.000508%	196,664

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.Arg3879=
Coding: c.11637A>G
MANE Select: NM_002016
Type: single nucleotide variant
Location: chr1:152303249 (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-arg3879 (accessed [today's date]).

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