Is FLNA p.Ser968fs (c.2904_2925del) pathogenic?

FLNA p.Ser968fs (c.29042925del) is classified Pathogenic in FLNA (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-29). Associated with heterotopia, periventricular, X-linked dominant.

What condition is associated with FLNA p.Ser968fs (c.2904_2925del)?

FLNA p.Ser968fs (c.2904_2925del) is associated with heterotopia, periventricular, X-linked dominant, otopalatodigital syndrome type 2, Melnick-Needles syndrome (ClinVar).

FLNA p.Ser968fs

c.2904_2925del · VCV4785432

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

heterotopia, periventricular, X-linked dominant

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 20 of 48
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6	GERP 0.75, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: FLNA
Protein: p.Ser968fs
Coding: c.2904_2925del
MANE Select: NM_001110556
Type: Deletion
Location: chrX:154361689 (GRCh38)
Structure: AlphaFold pLDDT 77.37 · 26 PDB
Residue 968: a modified residue (phosphoserine)

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

Disease context

heterotopia, periventricular, X-linked dominant — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: otopalatodigital syndrome type 2 Melnick-Needles syndrome frontometaphyseal dysplasia

Similar variants

FLNA p.Arg674fs Pathogenic ★★ same condition
FLNA p.Gln378fs Pathogenic/Likely pathogenic ★★ same condition
FLNA p.Ter2648SerextTer? Pathogenic/Likely pathogenic ★★ same condition
FLNA p.Val2212fs Pathogenic ★★ same condition
FLNA p.Lys531del Uncertain significance ★★ same condition
FLNA p.Ser1747_Pro1750del Uncertain significance ★★ same condition
FLNA c.1065+15del Likely benign ★★ same condition
FLNA c.1066-20del Likely benign ★★ 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-ser968fs (accessed [today's date]).

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