Is FLNB p.Ser2107= (c.6321C>T) pathogenic?

FLNB p.Ser2107= (c.6321C>T) is classified Likely benign in FLNB (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-03-01). Very rare (popmax 0.00833%, amr); Associated with Inborn genetic diseases.

What condition is associated with FLNB p.Ser2107= (c.6321C>T)?

FLNB p.Ser2107= (c.6321C>T) is associated with Inborn genetic diseases (ClinVar).

How common is FLNB p.Ser2107= (c.6321C>T) in the general population?

FLNB p.Ser2107= (c.6321C>T) is very rare (popmax 0.00833%, amr) (gnomAD).

FLNB p.Ser2107=

c.6321C>T · rs749772889 · VCV1569635

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00833%, amr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -8.6	GERP -5.4
Overall
CADD	0.079	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00833% Admixed American · 5/60,008 alleles

Filtering AF 0.00323% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00207%

Overall 0.00248% 40/1,614,072 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00833%	12,002
South Asian	0.00659%	15,181
Remaining individualsnot grpmax-eligible	0.0032%	31,243
East Asian	0.00223%	44,894
European (non-Finnish)	0.00212%	47,201
African / African-American	0.00133%	74,934

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.Ser2107=
Coding: c.6321C>T
MANE Select: NM_001457
dbSNP: rs749772889
Type: single nucleotide variant
Location: chr3:58150181 (GRCh38)
Gene constraint: LOEUF 0.504 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 76.96 · 23 PDB
Residue 2107: the 'interaction with the cytoplasmic tail of gp1ba' region; the 'interaction with flna 1' region; a modified residue (phosphoserine)

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

FLNB c.4862-3C>T Uncertain significance ★★ same condition
FLNB p.Ala1191Thr Uncertain significance ★★ ⚠ same condition
FLNB p.Ala1191Val Uncertain significance ★★ ⚠ same condition
FLNB p.Ala1391Thr Uncertain significance ★★ ⚠ same condition
FLNB p.Ala1427Val Uncertain significance ★★ ⚠ same condition
FLNB p.Ala1608Val Uncertain significance ★★ ⚠ same condition
FLNB p.Ala1704Ser Uncertain significance ★★ same condition
FLNB p.Ala2193Thr 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-ser2107 (accessed [today's date]).

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