Is ALG9 p.Gly37Asp (c.110G>A) pathogenic?

ALG9 p.Gly37Asp (c.110G>A) is classified Uncertain significance in ALG9 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-14). AlphaMissense: likely benign (0.1256); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with ALG9 p.Gly37Asp (c.110G>A)?

ALG9 p.Gly37Asp (c.110G>A) is associated with Inborn genetic diseases (ClinVar).

How common is ALG9 p.Gly37Asp (c.110G>A) in the general population?

ALG9 p.Gly37Asp (c.110G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ALG9 p.Gly37Asp (c.110G>A)?

AlphaMissense predicts likely benign (score 0.1256) — an in-silico prediction, not a clinical call.

ALG9 p.Gly37Asp

c.110G>A · VCV4038418

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1256 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1256	likely benign
REVEL	0.074	moderately benign-leaning
SaProt	LLR -7.13	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.9	GERP 0.41, phastCons 0.15
Regional constraint	o/e 0.88	unconstrained · MANE · 27 kb · p 0.019 · regional, not allelic
Overall
CADD	22.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

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: ALG9
Protein: p.Gly37Asp
Coding: c.110G>A
MANE Select: NM_024740
Type: single nucleotide variant
Location: chr11:111871373 (GRCh38)
Gene constraint: LOEUF 0.853 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.35 · 2 PDB

Full ALG9 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

ALG9 p.Arg607Gln Uncertain significance ★★ ⚠ same condition
ALG9 p.Gln526Glu Uncertain significance ★★ ⚠ same condition
ALG9 p.Ile130Val Uncertain significance ★★ ⚠ same condition
ALG9 p.Ser17Thr Uncertain significance ★★ ⚠ same condition
ALG9 p.Ala421Pro Uncertain significance ★ ⚠ same condition
ALG9 p.Arg42Trp Uncertain significance ★ ⚠ same condition
ALG9 p.Arg517Trp Uncertain significance ★ ⚠ same condition
ALG9 p.Arg584Trp Conflicting classifications of pathogenicity ★ ⚠ 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/alg9-p-gly37asp (accessed [today's date]).

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