Is FLNB p.Ser2403= (c.7209G>A) pathogenic?

FLNB p.Ser2403= (c.7209G>A) is classified Benign in FLNB (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-02-04). Common (popmax 11.2%, nfe) — too common for a highly-penetrant pathogenic allele; Associated with FLNB-Related Spectrum Disorders.

What condition is associated with FLNB p.Ser2403= (c.7209G>A)?

FLNB p.Ser2403= (c.7209G>A) is associated with FLNB-Related Spectrum Disorders (ClinVar).

FLNB p.Ser2403=

Q: How common is FLNB p.Ser2403= (c.7209G>A) in the general population?

FLNB p.Ser2403= (c.7209G>A) is common (popmax 11.2%, nfe) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.7209G>A · rs13079906 · VCV258121

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Common

common (popmax 11.2%, nfe) — too common for a highly-penetrant pathogenic allele

Conditions

FLNB-Related Spectrum Disorders

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.20 · evaluated, not missing
Constraint at this position
Conservation	phyloP -3.5	GERP -5.7
Overall
CADD	10.12	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 11.2% European (non-Finnish) · 132,238/1,178,064 alleles

Filtering AF 11.2% ClinGen BA1/BS1 input FAF95, joint · FAF99 11.2%

Overall 10.2% 165,037/1,612,022 alleles · common

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	16.2%	6
Finnishnot grpmax-eligible	14.5%	7
European (non-Finnish)grpmax	11.2%	9
Remaining individualsnot grpmax-eligible	9.01%	11
Admixed American	8.52%	12
South Asian	6.64%	15
Ashkenazi Jewishnot grpmax-eligible	6.44%	16
African / African-American	5.9%	17
Middle Eastern	3.6%	28
East Asian	0.0535%	1,870

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: FLNB
Protein: p.Ser2403=
Coding: c.7209G>A
MANE Select: NM_001457
dbSNP: rs13079906
Type: single nucleotide variant
Location: chr3:58168450 (GRCh38)
Gene constraint: LOEUF 0.504 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 76.96 · 23 PDB
Residue 2403: a β-strand; the 'interaction with inppl1' region

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

Disease context

FLNB-Related Spectrum Disorders

Similar variants

FLNB p.Ser2403Leu Likely benign ★ ⚠ same residue
FLNB p.Glu1661Lys Uncertain significance ★★ ⚠ same condition
FLNB p.Glu78Gly Uncertain significance ★★ ⚠ same condition
FLNB p.His1117Arg Uncertain significance ★★ ⚠ same condition
FLNB p.Leu1440Pro Uncertain significance ★★ ⚠ same condition
FLNB p.Pro396Ser Uncertain significance ★★ ⚠ same condition
FLNB p.Ser1096Phe Uncertain significance ★★ ⚠ same condition
FLNB p.Ser188Cys 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/flnb-p-ser2403 (accessed [today's date]).

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