Is GAA p.Val320Arg (c.958_959delinsAG) pathogenic?

GAA p.Val320Arg (c.958959delinsAG) is classified Uncertain significance in GAA (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-03). Absent from gnomAD; Associated with glycogen storage disease II.

What condition is associated with GAA p.Val320Arg (c.958_959delinsAG)?

GAA p.Val320Arg (c.958_959delinsAG) is associated with glycogen storage disease II (ClinVar).

How common is GAA p.Val320Arg (c.958_959delinsAG) in the general population?

GAA p.Val320Arg (c.958_959delinsAG) is absent from gnomAD (gnomAD).

GAA p.Val320Arg

Q: How is Glycogen storage disease due to acid maltase deficiency inherited?

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

c.958_959delinsAG · rs2510361849 · VCV1716223

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

glycogen storage disease II

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.7	GERP 1.9, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 15 kb · p 0.22 · regional, not allelic

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: GAA
Protein: p.Val320Arg
Coding: c.958_959delinsAG
MANE Select: NM_000152
dbSNP: rs2510361849
Type: Indel
Location: chr17:80108292 (GRCh38)
Gene constraint: LOEUF 1.008 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.32 · 19 PDB
Residue 320: a β-strand

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

Disease context

glycogen storage disease II — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Glycogen storage disease due to acid maltase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Antenatal, Childhood, Infancy, Neonatal
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

GAA p.Val320= Likely benign ★ same residue
GAA p.Ala761fs Pathogenic ★★★ same condition
GAA p.Asn535fs Likely pathogenic ★★★ same condition
GAA p.Ser529Val Likely pathogenic ★★★ same condition
GAA p.Trp376fs Pathogenic ★★★ same condition
GAA p.Tyr256fs Pathogenic ★★★ same condition
GAA p.Val723_Leu727delinsCysAspValVal Pathogenic ★★★ same condition
GAA p.Leu267fs Pathogenic/Likely pathogenic ★★ 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/gaa-p-val320arg (accessed [today's date]).

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