Is AGL p.Arg342fs (c.1025_1026del) pathogenic?

AGL p.Arg342fs (c.10251026del) is classified Pathogenic in AGL (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-01). Absent from gnomAD.

How common is AGL p.Arg342fs (c.1025_1026del) in the general population?

AGL p.Arg342fs (c.1025_1026del) is absent from gnomAD (gnomAD).

AGL p.Arg342fs

c.1025_1026del · rs2524594680 · VCV2672341

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

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 8 of 34
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.12	GERP -0.41, phastCons 0.91

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: AGL
Protein: p.Arg342fs
Coding: c.1025_1026del
MANE Select: NM_000642
dbSNP: rs2524594680
Type: Deletion
Location: chr1:99874752 (GRCh38)
Gene constraint: LOEUF 0.72 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.88 · 1 PDB
Residue 342: the 'amylo-1,6-glucosidase' region

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

Similar variants

AGL p.Arg342Gly Uncertain significance ★★ ⚠ same residue
AGL c.293+1del Pathogenic/Likely pathogenic ★★ same type
AGL c.3481_3589-407del Pathogenic ★★ same type
AGL c.3588_3588+14del Pathogenic/Likely pathogenic ★★ same type
AGL p.Ala117fs Pathogenic ★★ same type
AGL p.Ala1222fs Pathogenic ★★ same type
AGL p.Ala1388_Pro1389insTer Pathogenic/Likely pathogenic ★★ same type
AGL p.Ala1400fs 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/agl-p-arg342fs (accessed [today's date]).

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