Is ALG1 p.Lys439= (c.1317G>A) pathogenic?

ALG1 p.Lys439= (c.1317G>A) is classified Likely benign in ALG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-29). Absent from gnomAD v4.1; Associated with ALG1-congenital disorder of glycosylation.

What condition is associated with ALG1 p.Lys439= (c.1317G>A)?

ALG1 p.Lys439= (c.1317G>A) is associated with ALG1-congenital disorder of glycosylation (ClinVar).

How common is ALG1 p.Lys439= (c.1317G>A) in the general population?

ALG1 p.Lys439= (c.1317G>A) is absent from gnomAD v4.1 (gnomAD).

How is ALG1-CDG inherited?

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

ALG1 p.Lys439=

c.1317G>A · rs2505880151 · VCV2817215

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

ALG1-congenital disorder of glycosylation

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

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 4.9	GERP 0.69, phastCons 1
Overall
CADD	7.789	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ALG1
Protein: p.Lys439=
Coding: c.1317G>A
MANE Select: NM_019109
dbSNP: rs2505880151
Type: single nucleotide variant
Location: chr16:5084803 (GRCh38)

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

Disease context

ALG1-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For ALG1-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/alg1-p-lys439 (accessed [today's date]).

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