Is AAGAB p.Ala2= (c.6T>C) pathogenic?

AAGAB p.Ala2= (c.6T>C) is classified Likely benign in AAGAB (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-09-17). Absent from gnomAD v4.1; Associated with AAGAB-related disorder.

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

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

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

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

AAGAB p.Ala2=

c.6T>C · VCV3355721

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

AAGAB-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 1.6	GERP -0.78, phastCons 1
Overall
CADD	10.7	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: AAGAB
Protein: p.Ala2=
Coding: c.6T>C
MANE Select: NM_024666
Type: single nucleotide variant
Location: chr15:67254626 (GRCh38)
Gene constraint: LOEUF 1.156 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 80.41 · 3 PDB

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

Disease context

AAGAB-related disorder

Similar variants

AAGAB p.Ala2Gly Uncertain significance ★ ⚠ same residue
AAGAB p.Ala2Thr Uncertain significance ★ ⚠ same residue
AAGAB p.Arg124Ter Pathogenic ★★ same condition
AAGAB c.451+1G>A Pathogenic ★ same condition
AAGAB c.619-2A>G Likely pathogenic ★ same condition
AAGAB c.74-1G>C Likely pathogenic ★ same condition
AAGAB c.821-1G>T Likely pathogenic ★ same condition
AAGAB p.Ser189Ter 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/aagab-p-ala2 (accessed [today's date]).

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