Is ALG12 p.Arg311fs (c.930_931del) pathogenic?

ALG12 p.Arg311fs (c.930931del) is classified Pathogenic in ALG12 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-03-09). Absent from gnomAD; Associated with ALG12-congenital disorder of glycosylation.

What condition is associated with ALG12 p.Arg311fs (c.930_931del)?

ALG12 p.Arg311fs (c.930_931del) is associated with ALG12-congenital disorder of glycosylation (ClinVar).

How common is ALG12 p.Arg311fs (c.930_931del) in the general population?

ALG12 p.Arg311fs (c.930_931del) is absent from gnomAD (gnomAD).

How is ALG12-CDG inherited?

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

ALG12 p.Arg311fs

c.930_931del · rs1569174722 · VCV560937

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

ALG12-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	predicted	premature termination codon in exon 7 of 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.4	GERP 1.6, 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: ALG12
Protein: p.Arg311fs
Coding: c.930_931del
MANE Select: NM_024105
dbSNP: rs1569174722
Type: Deletion
Location: chr22:49907782 (GRCh38)
Gene constraint: LOEUF 0.965 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.26

Full ALG12 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ALG12-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For ALG12-CDG (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

ALG12 p.Arg311Cys Uncertain significance ★★ ⚠ same residue
ALG12 p.Arg311= Conflicting classifications of pathogenicity ★ same residue
ALG12 p.Asn334fs Pathogenic/Likely pathogenic ★★ same condition
ALG12 p.Gln40fs Pathogenic ★★ same condition
ALG12 p.Leu12fs Pathogenic/Likely pathogenic ★★ same condition
ALG12 p.Lys416fs Likely pathogenic ★★ same condition
ALG12 p.Arg486fs Uncertain significance ★★ same condition
ALG12 c.439_469+19del 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/alg12-p-arg311fs (accessed [today's date]).

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