NM_000158.4:c.2053-3358_2053-3350delGTGTGGTGGinsTGTTTTTTACATTACAGGT

Variant names:

• chr3-81493813-CCACCACAC-ACCTGTAATGTAAAAAACA
• rs869320698
• NM_000158.4:c.2053-3358_2053-3350delGTGTGGTGGinsTGTTTTTTACATTACAGGT

Variant summary

Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PM2 PP5_Very_Strong

The NM_000158.4(GBE1):​c.2053-3358_2053-3350delGTGTGGTGGinsTGTTTTTTACATTACAGGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: GBE1 NM_000158.4 intron
• Clinical Significance: Likely pathogenic criteria provided, multiple submitters, no conflicts P:3
• Conservation: PhyloP100: 0.749
• Publications: 0 publications found

Genes affected

GBE1 (HGNC:4180): (1,4-alpha-glucan branching enzyme 1) The protein encoded by this gene is a glycogen branching enzyme that catalyzes the transfer of alpha-1,4-linked glucosyl units from the outer end of a glycogen chain to an alpha-1,6 position on the same or a neighboring glycogen chain. Branching of the chains is essential to increase the solubility of the glycogen molecule and, consequently, in reducing the osmotic pressure within cells. Highest level of this enzyme are found in liver and muscle. Mutations in this gene are associated with glycogen storage disease IV (also known as Andersen's disease). [provided by RefSeq, Jul 2008]

GBE1 Gene-Disease associations (from GenCC):

• glycogen storage disease due to glycogen branching enzyme deficiency

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Laboratory for Molecular Medicine, Ambry Genetics, G2P, ClinGen
• adult polyglucosan body disease

  Inheritance: AR Classification: MODERATE, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics

ACMG classification

Our verdict: Pathogenic. The variant received 10 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 3-81493813-CCACCACAC-ACCTGTAATGTAAAAAACA is Pathogenic according to our data. Variant chr3-81493813-CCACCACAC-ACCTGTAATGTAAAAAACA is described in ClinVar as Likely_pathogenic. ClinVar VariationId is 2635394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000158.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GBE1	NM_000158.4	MANE Select	c.2053-3358_2053-3350delGTGTGGTGGinsTGTTTTTTACATTACAGGT		intron	N/A	NP_000149.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GBE1	ENST00000429644.7	TSL:1 MANE Select	c.2053-3358_2053-3350delGTGTGGTGGinsTGTTTTTTACATTACAGGT		intron	N/A	ENSP00000410833.2
	GBE1	ENST00000895874.1		c.2047-3358_2047-3350delGTGTGGTGGinsTGTTTTTTACATTACAGGT		intron	N/A	ENSP00000565933.1
	GBE1	ENST00000942742.1		c.2047-3358_2047-3350delGTGTGGTGGinsTGTTTTTTACATTACAGGT		intron	N/A	ENSP00000612801.1

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

ClinVar submissions as Germline

Significance: Likely pathogenic

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
1	-	-	GBE1-related disorder (1)
1	-	-	Glycogen storage disease, type IV (1)
1	-	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs869320698; hg19: chr3-81542964;