Is ACADVL p.Phe259fs (c.776_777insA) pathogenic?

ACADVL p.Phe259fs (c.776777insA) is classified Pathogenic in ACADVL (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-24). Absent from gnomAD; Associated with very long chain acyl-CoA dehydrogenase deficiency.

What condition is associated with ACADVL p.Phe259fs (c.776_777insA)?

ACADVL p.Phe259fs (c.776_777insA) is associated with very long chain acyl-CoA dehydrogenase deficiency (ClinVar).

How common is ACADVL p.Phe259fs (c.776_777insA) in the general population?

ACADVL p.Phe259fs (c.776_777insA) is absent from gnomAD (gnomAD).

ACADVL p.Phe259fs

Q: How is Very long chain acyl-CoA dehydrogenase deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.776_777insA · rs2508303394 · VCV2711063

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

Conditions

very long chain acyl-CoA dehydrogenase deficiency

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 9 of 20
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.9	GERP 1.9, 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: ACADVL
Protein: p.Phe259fs
Coding: c.776_777insA
MANE Select: NM_000018
dbSNP: rs2508303394
Type: Insertion
Location: chr17:7222200 (GRCh38)
Gene constraint: LOEUF 1.077 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 90.65 · 3 PDB
Residue 259: a β-strand; the 'catalytic' region

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

Disease context

very long chain acyl-CoA dehydrogenase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Very long chain acyl-CoA dehydrogenase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

ACADVL p.Phe259= Likely benign ★ same residue
ACADVL p.Ala333fs Pathogenic ★★★ same condition
ACADVL p.Asn365fs Pathogenic ★ same condition
ACADVL p.Leu102fs Pathogenic ★ same condition
ACADVL p.Leu515fs Likely pathogenic ★ same condition
ACADVL p.Val284fs Likely pathogenic ★ same condition
ACADVL c.-72_-71insGAGGACGTGGGCGTG Uncertain significance ★ same condition
ACADVL c.132-186_132-185insGGGCGTGCAGGACGT 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/acadvl-p-phe259fs (accessed [today's date]).

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