Is FLNB p.Ser1821fs (c.5461del) pathogenic?

FLNB p.Ser1821fs (c.5461del) is classified Pathogenic in FLNB (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-29). Absent from gnomAD.

How common is FLNB p.Ser1821fs (c.5461del) in the general population?

FLNB p.Ser1821fs (c.5461del) is absent from gnomAD (gnomAD).

FLNB p.Ser1821fs

c.5461del · rs2471197087 · VCV2764430

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 33 of 46
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.8	GERP 2.7, 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: FLNB
Protein: p.Ser1821fs
Coding: c.5461del
MANE Select: NM_001457
dbSNP: rs2471197087
Type: Deletion
Location: chr3:58145956 (GRCh38)
Gene constraint: LOEUF 0.504 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 76.96 · 23 PDB

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

Similar variants

FLNB p.Ser1821Asn Uncertain significance ★ ⚠ same residue
FLNB p.Glu1000fs Likely pathogenic ★★ same type
FLNB p.Glu1792del Likely pathogenic ★★ same type
FLNB c.2056-15_2056-10del Uncertain significance ★★ same type
FLNB c.2055+274del Benign ★★ same type
FLNB c.3724+13_3724+15del Likely benign ★★ same type
FLNB c.3724+35_3724+36del Benign/Likely benign ★★ same type
FLNB c.3724+36del Benign/Likely benign ★★ 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/flnb-p-ser1821fs (accessed [today's date]).

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