FLNA p.Phe2202=
c.6606T>C · rs781801702 · VCV2424075
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00887%, eas)
Conditions
4
Melnick-Needles syndrome
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 -2 | GERP -3.7 |
| Overall | ||
| CADD | 1.711 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00887%
East Asian · 3/33,835 alleles
Filtering AF
0.00235%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00125%
Overall
0.000273%
3/1,097,940 alleles · very rare
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
- FLNA
- Protein
- p.Phe2202=
- Coding
- c.6606T>C
- MANE Select
- NM_001110556
- dbSNP
- rs781801702
- Type
- single nucleotide variant
- Location
- chrX:154352344 (GRCh38)
- Structure
- AlphaFold pLDDT 77.37 · 26 PDB
Similar variants
- FLNA c.1066-1G>A Pathogenic/Likely pathogenic ★★ same condition
- FLNA c.2022+1G>A Pathogenic ★★ same condition
- FLNA c.4598+1G>A Pathogenic/Likely pathogenic ★★ same condition
- FLNA c.5417-2A>G Likely pathogenic ★★ same condition
- FLNA c.868+1G>A Likely pathogenic ★★ same condition
- FLNA c.987+1G>A Likely pathogenic ★★ same condition
- FLNA p.Ala1188Thr Pathogenic/Likely pathogenic ★★ same condition
- FLNA p.Arg1515Ter 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/flna-p-phe2202 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown