FLNC p.Glu2009=
c.6027G>A · VCV4614183
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
Conditions
1
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.21 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.8 | phastCons 1 |
| Overall | ||
| CADD | 12.11 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,088 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000136%
Overall
0.000124%
2/1,613,908 alleles · very rare
exomes 2/1,461,550 · genomes 0/152,358 · joint denominator
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
- FLNC
- Protein
- p.Glu2009=
- Coding
- c.6027G>A
- MANE Select
- NM_001458
- Type
- single nucleotide variant
- Location
- chr7:128852850 (GRCh38)
- Gene constraint
- LOEUF 0.424 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 2009
- the 'required for interaction with pgm5' region
Similar variants
- FLNC c.1210+1G>A Likely pathogenic ★★ same condition
- FLNC c.2550+2T>C Pathogenic/Likely pathogenic ★★ same condition
- FLNC c.2930-1G>A Pathogenic/Likely pathogenic ★★ same condition
- FLNC c.5199+1G>T Pathogenic/Likely pathogenic ★★ same condition
- FLNC c.5398+1G>C Likely pathogenic ★★ same condition
- FLNC p.Arg1313Ter Pathogenic/Likely pathogenic ★★ same condition
- FLNC p.Arg1341Ter Pathogenic/Likely pathogenic ★★ same condition
- FLNC p.Arg1657Ter Pathogenic/Likely pathogenic ★★ 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/flnc-p-glu2009 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown