Is ALG1 p.Glu288fs (c.839_860dup) pathogenic?

ALG1 p.Glu288fs (c.839860dup) is classified Likely pathogenic in ALG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-01). Absent from gnomAD.

How common is ALG1 p.Glu288fs (c.839_860dup) in the general population?

ALG1 p.Glu288fs (c.839_860dup) is absent from gnomAD (gnomAD).

ALG1 p.Glu288fs

c.839_860dup · rs2142716129 · VCV1298653

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
NMD	predicted	premature termination codon in exon 7 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.5	GERP -2.1, phastCons 1
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

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: ALG1
Protein: p.Glu288fs
Coding: c.839_860dup
MANE Select: NM_019109
dbSNP: rs2142716129
Type: Duplication
Location: chr16:5078853 (GRCh38)
Gene constraint: LOEUF 1.419 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.24

Full ALG1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ALG1 p.Glu288Gly Uncertain significance ★★ ⚠ same residue
ALG1 p.Leu15_Pro16insAlaLeuCysLeuLeuLeu Uncertain significance ★★ same type
ALG1 p.Asn171fs Pathogenic ★ same type
ALG1 p.Gln102fs Pathogenic ★ same type
ALG1 p.Ile163fs Pathogenic ★ same type
ALG1 p.Leu56fs Pathogenic ★ same type
ALG1 p.Val107fs Pathogenic ★ same type
ALG1 p.Cys12_Leu17dup Conflicting classifications of pathogenicity ★ 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/alg1-p-glu288fs (accessed [today's date]).

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