Is FLNA p.Arg2001fs (c.6001del) pathogenic?

FLNA p.Arg2001fs (c.6001del) is classified Likely pathogenic in FLNA (ClinVar, Single submitter, 1 submitter; last evaluated 2020-08-28). Absent from gnomAD.

How common is FLNA p.Arg2001fs (c.6001del) in the general population?

FLNA p.Arg2001fs (c.6001del) is absent from gnomAD (gnomAD).

FLNA p.Arg2001fs

c.6001del · rs1603359417 · VCV818013

Likely pathogenic Single submitter

Classification

Likely 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 37 of 48
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 1.7, phastCons 1

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.Arg2001fs
Coding: c.6001del
MANE Select: NM_001110556
dbSNP: rs1603359417
Type: Deletion
Location: chrX:154353317 (GRCh38)
Structure: AlphaFold pLDDT 77.37 · 26 PDB
Residue 2001: a β-strand

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

Similar variants

FLNA p.Arg2001Trp Benign/Likely benign ★★ ⚠ same residue
FLNA p.Arg2001Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
FLNA p.Arg2001Leu Uncertain significance ★ ⚠ 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
FLNA p.Leu2082fs 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-arg2001fs (accessed [today's date]).

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