Is MOGS p.Ile402fs (c.1204del) pathogenic?

MOGS p.Ile402fs (c.1204del) is classified Pathogenic in MOGS (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-24). No gnomAD frequency available for this variant; Associated with MOGS-congenital disorder of glycosylation.

What condition is associated with MOGS p.Ile402fs (c.1204del)?

MOGS p.Ile402fs (c.1204del) is associated with MOGS-congenital disorder of glycosylation (ClinVar).

How common is MOGS p.Ile402fs (c.1204del) in the general population?

MOGS p.Ile402fs (c.1204del) is no gnomAD frequency available for this variant (gnomAD).

How is MOGS-CDG inherited?

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

MOGS p.Ile402fs

c.1204del · rs2529496158 · VCV2022184

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

MOGS-congenital disorder of glycosylation

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (4 of 4) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.4, 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: MOGS
Protein: p.Ile402fs
Coding: c.1204del
MANE Select: NM_006302
dbSNP: rs2529496158
Type: Deletion
Location: chr2:74462585 (GRCh38)
Gene constraint: LOEUF 0.85 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.42

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

Disease context

MOGS-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For MOGS-CDG (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

MOGS p.Ile402Thr Uncertain significance ★★ ⚠ same residue
MOGS p.Ile402= Likely benign ★ same residue
MOGS p.Glu295fs Pathogenic/Likely pathogenic ★★ same condition
MOGS p.Val216fs Pathogenic/Likely pathogenic ★★ same condition
MOGS p.Asp141fs Pathogenic ★ same condition
MOGS p.Asp212fs Pathogenic ★ same condition
MOGS p.Gln408fs Pathogenic ★ same condition
MOGS p.His151fs 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/mogs-p-ile402fs (accessed [today's date]).

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