Is ALG11 p.Asn397= (c.1191C>T) pathogenic?

ALG11 p.Asn397= (c.1191C>T) is classified Likely benign in ALG11 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-11-30). Very rare (popmax 0.00988%, sas); Associated with ALG11-congenital disorder of glycosylation.

What condition is associated with ALG11 p.Asn397= (c.1191C>T)?

ALG11 p.Asn397= (c.1191C>T) is associated with ALG11-congenital disorder of glycosylation (ClinVar).

How common is ALG11 p.Asn397= (c.1191C>T) in the general population?

ALG11 p.Asn397= (c.1191C>T) is very rare (popmax 0.00988%, sas) (gnomAD).

How is ALG11-CDG inherited?

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

ALG11 p.Asn397=

c.1191C>T · rs141089354 · VCV1135135

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00988%, sas)

Conditions

ALG11-congenital disorder of glycosylation

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -7.5	GERP -3.4
Overall
CADD	3.959	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00988% South Asian · 9/91,078 alleles

Filtering AF 0.00514% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00375%

Overall 0.00248% 40/1,610,152 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00988%	10,120
Admixed American	0.005%	20,010
East Asian	0.00446%	22,437
European (non-Finnish)	0.00212%	47,200
Remaining individualsnot grpmax-eligible	0.0016%	62,484

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ALG11
Protein: p.Asn397=
Coding: c.1191C>T
MANE Select: NM_021645 · reported on NM_001004127
dbSNP: rs141089354
Type: single nucleotide variant
Location: chr13:52024921 (GRCh38)

Full ALG11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ALG11-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For ALG11-CDG (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

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/alg11-p-asn397 (accessed [today's date]).

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