Is FLAD1 p.Phe134fs (c.401_404del) pathogenic?

FLAD1 p.Phe134fs (c.401404del) is classified Pathogenic in FLAD1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2016-03-14). No gnomAD frequency available for this variant; Associated with myopathy with abnormal lipid metabolism.

What condition is associated with FLAD1 p.Phe134fs (c.401_404del)?

FLAD1 p.Phe134fs (c.401_404del) is associated with myopathy with abnormal lipid metabolism, multiple acyl-CoA dehydrogenase deficiency (ClinVar).

How common is FLAD1 p.Phe134fs (c.401_404del) in the general population?

FLAD1 p.Phe134fs (c.401_404del) is no gnomAD frequency available for this variant (gnomAD).

FLAD1 p.Phe134fs

c.401_404del · rs876661313 · VCV224732

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

myopathy with abnormal lipid metabolism

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 7
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.32	GERP -0.79, phastCons 0.99

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: FLAD1
Protein: p.Phe134fs
Coding: c.401_404del
MANE Select: NM_025207
dbSNP: rs876661313
Type: Microsatellite
Location: chr1:154988129 (GRCh38)
Gene constraint: LOEUF 0.809 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.34 · 2 PDB
Residue 134: the 'fad diphosphatase' region; an α-helix

Full FLAD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

myopathy with abnormal lipid metabolism — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: multiple acyl-CoA dehydrogenase deficiency

Similar variants

FLAD1 p.Arg148Ter Pathogenic ★★ same condition
FLAD1 p.Arg249Ter Pathogenic ★★ same condition
FLAD1 p.Arg530Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
FLAD1 p.Cys136Ter Pathogenic/Likely pathogenic ★★ same condition
FLAD1 p.Cys537Ser Uncertain significance ★★ ⚠ same condition
FLAD1 p.Met268Arg Uncertain significance ★★ same condition
FLAD1 c.372+24_372+25del Likely benign ★★ same condition
FLAD1 p.Phe243= Benign/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/flad1-p-phe134fs (accessed [today's date]).

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