Is ALG5 p.Ala2= (c.6T>A) pathogenic?

ALG5 p.Ala2= (c.6T>A) is classified Likely benign in ALG5 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-05-02). Absent from gnomAD v4.1; Associated with ALG5-related disorder.

What condition is associated with ALG5 p.Ala2= (c.6T>A)?

ALG5 p.Ala2= (c.6T>A) is associated with ALG5-related disorder (ClinVar).

How common is ALG5 p.Ala2= (c.6T>A) in the general population?

ALG5 p.Ala2= (c.6T>A) is absent from gnomAD v4.1 (gnomAD).

ALG5 p.Ala2=

c.6T>A · VCV3346692

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

ALG5-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.1	GERP -4
Overall
CADD	3.897	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: ALG5
Protein: p.Ala2=
Coding: c.6T>A
MANE Select: NM_013338
Type: single nucleotide variant
Location: chr13:36999295 (GRCh38)
Gene constraint: LOEUF 0.823 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 92.29

Full ALG5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ALG5-related disorder

Similar variants

ALG5 p.Arg212Cys Uncertain significance ★ ⚠ same condition
ALG5 p.Ala19Ser Uncertain significance ⚠ same condition
ALG5 p.Arg79Gln Uncertain significance ⚠ same condition
ALG5 p.Ala18= Benign same condition
ALG5 p.Gly12= Benign same condition
ALG5 p.Leu11Val Likely benign same condition
ALG5 p.Thr249= Likely benign same condition
ALG5 p.Trp60Arg Likely benign 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/alg5-p-ala2 (accessed [today's date]).

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