Is GBE1 p.Asp571= (c.1713C>T) pathogenic?

GBE1 p.Asp571= (c.1713C>T) is classified Likely benign in GBE1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-05). Rare (popmax 0.146%, afr); Associated with Glycogen storage disease IV, classic hepatic.

What condition is associated with GBE1 p.Asp571= (c.1713C>T)?

GBE1 p.Asp571= (c.1713C>T) is associated with Glycogen storage disease IV, classic hepatic, glycogen storage disease due to glycogen branching enzyme deficiency, adult polyglucosan body disease (ClinVar).

How common is GBE1 p.Asp571= (c.1713C>T) in the general population?

GBE1 p.Asp571= (c.1713C>T) is rare (popmax 0.146%, afr) (gnomAD).

GBE1 p.Asp571=

c.1713C>T · rs373148836 · VCV709076

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.146%, afr)

Conditions

Glycogen storage disease IV, classic hepatic

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 1.9	GERP -4.9, phastCons 1
Overall
CADD	7.634	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.146% African / African-American · 107/73,394 alleles

Filtering AF 0.123% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.115%

Overall 0.0141% 225/1,591,044 alleles · rare exomes 161/1,438,952 · genomes 64/152,092 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.146%	686
East Asian	0.0442%	2,261
Admixed American	0.0265%	3,771
Remaining individualsnot grpmax-eligible	0.0195%	5,135
South Asian	0.0115%	8,662
European (non-Finnish)	0.00521%	19,179
Finnishnot grpmax-eligible	0.00157%	63,788

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: GBE1
Protein: p.Asp571=
Coding: c.1713C>T
MANE Select: NM_000158
dbSNP: rs373148836
Type: single nucleotide variant
Location: chr3:81537001 (GRCh38)
Gene constraint: LOEUF 1.211 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.30 · 3 PDB

Full GBE1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Glycogen storage disease IV, classic hepatic — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: glycogen storage disease due to glycogen branching enzyme deficiency adult polyglucosan body disease

Similar variants

GBE1 p.Asp571Val Uncertain significance ★ ⚠ same residue
GBE1 c.1109-1G>T Likely pathogenic ★★ same condition
GBE1 c.1236+1G>A Likely pathogenic ★★ same condition
GBE1 c.1336-1G>A Pathogenic/Likely pathogenic ★★ same condition
GBE1 c.143+1G>A Pathogenic ★★ same condition
GBE1 c.143+2T>C Pathogenic/Likely pathogenic ★★ same condition
GBE1 c.144-1G>C Pathogenic/Likely pathogenic ★★ same condition
GBE1 c.1618+1G>A Pathogenic/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/gbe1-p-asp571 (accessed [today's date]).

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