Is ALG3 p.Ser202Gly (c.604A>G) pathogenic?

ALG3 p.Ser202Gly (c.604A>G) is classified Uncertain significance in ALG3 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-06-03). AlphaMissense: ambiguous (0.5272); No allele count reported in gnomAD v4.1 (AN 1,613,722); Associated with Inborn genetic diseases.

What condition is associated with ALG3 p.Ser202Gly (c.604A>G)?

ALG3 p.Ser202Gly (c.604A>G) is associated with Inborn genetic diseases (ClinVar).

How common is ALG3 p.Ser202Gly (c.604A>G) in the general population?

ALG3 p.Ser202Gly (c.604A>G) is no allele count reported in gnomAD v4.1 (AN 1,613,722) (gnomAD).

What do computational predictors say about ALG3 p.Ser202Gly (c.604A>G)?

AlphaMissense predicts ambiguous (score 0.5272) — an in-silico prediction, not a clinical call.

ALG3 p.Ser202Gly

c.604A>G · rs1553828635 · VCV2231151

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5272 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,722)

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.5272	ambiguous
REVEL	0.96	strongly pathogenic-leaning
SaProt	LLR -11.02	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense makes no call.
Splicing
SpliceAI	Δ0.59	donor loss, 1 bp away · masked 0 · deltas
Pangolin	Δ0.72	loss · gain 0.06 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 7.9	GERP 1.6, phastCons 1
Regional constraint	o/e 1.09	unconstrained · MANE · 3,742 bp · p 0.14 · regional, not allelic
Overall
CADD	33.0	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

No allele count reported in gnomAD v4.1 (AN 1,613,722). 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: ALG3
Protein: p.Ser202Gly
Coding: c.604A>G
MANE Select: NM_005787
dbSNP: rs1553828635
Type: single nucleotide variant
Location: chr3:184245199 (GRCh38)
Gene constraint: LOEUF 0.972 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.05

Full ALG3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ALG3 p.Ser202Arg Uncertain significance ★ ⚠ same residue
ALG3 p.Ala102Ser Uncertain significance ★★ ⚠ same condition
ALG3 p.Arg229Cys Uncertain significance ★★ ⚠ same condition
ALG3 p.Arg27Gly Uncertain significance ★★ ⚠ same condition
ALG3 p.Arg378Cys Uncertain significance ★★ ⚠ same condition
ALG3 p.Asn83Ser Uncertain significance ★★ ⚠ same condition
ALG3 p.Cys21Gly Uncertain significance ★★ ⚠ same condition
ALG3 p.Cys21Phe Uncertain significance ★★ ⚠ 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/alg3-p-ser202gly (accessed [today's date]).

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