Is FLG p.Arg3907= (c.11721C>T) pathogenic?

FLG p.Arg3907= (c.11721C>T) is classified Likely benign in FLG (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-01). Ultra-rare (popmax 0.0318%, sas).

How common is FLG p.Arg3907= (c.11721C>T) in the general population?

FLG p.Arg3907= (c.11721C>T) is ultra-rare (popmax 0.0318%, sas) (gnomAD).

FLG p.Arg3907=

c.11721C>T · VCV4911226

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0318%, sas)

⚠ 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 -0.064	GERP -3.1, phastCons 0.004
Overall
CADD	0.199	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0318% South Asian · 29/91,082 alleles

Filtering AF 0.0228% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0196%

Overall 0.00434% 70/1,614,008 alleles · ultra-rare exomes 69/1,461,894 · genomes 1/152,114 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0318%	3,141
Middle Eastern	0.0164%	6,084
African / African-American	0.00534%	18,722
Remaining individualsnot grpmax-eligible	0.0048%	20,830
East Asian	0.00445%	22,447
European (non-Finnish)	0.00263%	38,066

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.Arg3907=
Coding: c.11721C>T
MANE Select: NM_002016
Type: single nucleotide variant
Location: chr1:152303165 (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-arg3907 (accessed [today's date]).

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