Is GBE1 p.Pro405= (c.1215C>T) pathogenic?

GBE1 p.Pro405= (c.1215C>T) is classified Likely benign in GBE1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-27). Very rare (popmax 0.00672%, amr); Associated with Glycogen storage disease IV, classic hepatic.

What condition is associated with GBE1 p.Pro405= (c.1215C>T)?

GBE1 p.Pro405= (c.1215C>T) is associated with Glycogen storage disease IV, classic hepatic, glycogen storage disease due to glycogen branching enzyme deficiency (ClinVar).

How common is GBE1 p.Pro405= (c.1215C>T) in the general population?

GBE1 p.Pro405= (c.1215C>T) is very rare (popmax 0.00672%, amr) (gnomAD).

GBE1 p.Pro405=

c.1215C>T · rs373029683 · VCV1140742

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00672%, amr)

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 -0.13	GERP -2.2, phastCons 0.78
Overall
CADD	6.324	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00672% Admixed American · 4/59,528 alleles

Filtering AF 0.00227% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00136%

Overall 0.000995% 16/1,608,730 alleles · very rare exomes 13/1,456,676 · genomes 3/152,054 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00672%	14,882
Ashkenazi Jewishnot grpmax-eligible	0.00339%	29,460
South Asian	0.00333%	30,025
East Asian	0.00224%	44,670
Remaining individualsnot grpmax-eligible	0.00161%	62,244
European (non-Finnish)	0.00051%	196,191

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.Pro405=
Coding: c.1215C>T
MANE Select: NM_000158
dbSNP: rs373029683
Type: single nucleotide variant
Location: chr3:81591058 (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

Similar variants

GBE1 p.Pro405Ser 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-pro405 (accessed [today's date]).

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