Is FLNA p.Ala15fs (c.42del) pathogenic?

FLNA p.Ala15fs (c.42del) is classified Pathogenic in FLNA (ClinVar, Single submitter, 1 submitter; last evaluated 2013-01-30). No gnomAD frequency available for this variant.

How common is FLNA p.Ala15fs (c.42del) in the general population?

FLNA p.Ala15fs (c.42del) is no gnomAD frequency available for this variant (gnomAD).

FLNA p.Ala15fs

c.42del · rs398123619 · VCV93760

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 in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 2 of 48
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.4	GERP 1.3, phastCons 0.02

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: FLNA
Protein: p.Ala15fs
Coding: c.42del
MANE Select: NM_001110556
dbSNP: rs398123619
Type: Deletion
Location: chrX:154371204 (GRCh38)
Structure: AlphaFold pLDDT 77.37 · 26 PDB
Residue 15: the 'disordered' region; the 'actin-binding' region

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

Similar variants

FLNA p.Ala15Glu Uncertain significance ★★ ⚠ same residue
FLNA p.Ala15= Likely benign ★★ same residue
FLNA p.Ala15Ser Uncertain significance ★ ⚠ same residue
FLNA p.Ala15Thr Likely benign ★ same residue
FLNA c.4750_4755+18del Pathogenic/Likely pathogenic ★★ same type
FLNA p.Arg674fs Pathogenic ★★ same type
FLNA p.Gln378fs Pathogenic/Likely pathogenic ★★ same type
FLNA p.Glu1977fs Pathogenic ★★ 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/flna-p-ala15fs (accessed [today's date]).

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