Is ALG1 p.Pro346Thr (c.1036C>A) pathogenic?

ALG1 p.Pro346Thr (c.1036C>A) is classified Conflicting classifications of pathogenicity in ALG1 (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2025-01-26). AlphaMissense: likely benign (0.3247); Ultra-rare (popmax 0.0802%, afr); Associated with ALG1-congenital disorder of glycosylation.

What condition is associated with ALG1 p.Pro346Thr (c.1036C>A)?

ALG1 p.Pro346Thr (c.1036C>A) is associated with ALG1-congenital disorder of glycosylation (ClinVar).

How common is ALG1 p.Pro346Thr (c.1036C>A) in the general population?

ALG1 p.Pro346Thr (c.1036C>A) is ultra-rare (popmax 0.0802%, afr) (gnomAD).

How is ALG1-CDG inherited?

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

What do computational predictors say about ALG1 p.Pro346Thr (c.1036C>A)?

AlphaMissense predicts likely benign (score 0.3247) — an in-silico prediction, not a clinical call.

ALG1 p.Pro346Thr

c.1036C>A · rs143676440 · VCV803209

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.3247 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0802%, afr)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

ALG1-congenital disorder of glycosylation

Computational evidence

Protein change
AlphaMissense	0.3247	likely benign
REVEL	0.662	pathogenic-leaning
SaProt	LLR -12.08	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP 1.8, phastCons 1
Regional constraint	o/e 1.27	unconstrained · MANE · 13 kb · p 3.2e-11 · regional, not allelic
Overall
CADD	25.3	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0802% African / African-American · 60/74,848 alleles

Filtering AF 0.0639% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.058%

Overall 0.00376% 60/1,596,272 alleles · ultra-rare

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: ALG1
Protein: p.Pro346Thr
Coding: c.1036C>A
MANE Select: NM_019109
dbSNP: rs143676440
Type: single nucleotide variant
Location: chr16:5081020 (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

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

Similar variants

ALG1 p.Pro346Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
ALG1 p.Pro346= Likely benign ★ same residue
ALG1 c.1187+1G>A Pathogenic/Likely pathogenic ★★ same condition
ALG1 c.1187+2T>C Pathogenic ★★ same condition
ALG1 c.1188-2A>G Pathogenic/Likely pathogenic ★★ same condition
ALG1 c.209-2A>G Likely pathogenic ★★ same condition
ALG1 c.539+1G>A Pathogenic/Likely pathogenic ★★ same condition
ALG1 c.630-2A>G 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/alg1-p-pro346thr (accessed [today's date]).

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