GYG2

glycogenin 2, the group of Glycosyltransferase family 8

Basic information

Region (hg38): X:2828822-2882818

Links

ENSG00000056998 ∙ NCBI:8908 ∙ OMIM:300198 ∙ HGNC:4700 ∙ Uniprot:O15488 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GYG2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GYG2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				20	5	25
missense			49	7	8	64
nonsense			1			1
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			3	3		6
non coding				40	41	81
Total	0	0	52	67	54

Variants in GYG2

This is a list of pathogenic ClinVar variants found in the GYG2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-2828979-CG-C			Likely benign (May 25, 2018)
X-2828984-G-C		not specified	Likely benign (Aug 09, 2016)
X-2828985-G-C		not specified	Likely benign (Apr 27, 2017)
X-2828989-T-C			Likely benign (May 25, 2018)
X-2828991-G-GC			Likely benign (May 25, 2018)
X-2830010-T-C			Benign (Jun 23, 2018)
X-2830027-G-A			Likely benign (Aug 03, 2018)
X-2830043-C-G			Likely benign (May 21, 2018)
X-2830052-C-A			Likely benign (Sep 24, 2018)
X-2830140-C-T		not specified	Likely benign (Feb 12, 2018)
X-2830166-C-G		not specified	Likely benign (Mar 22, 2016)
X-2830212-G-C		not specified	Benign (Feb 03, 2025)
X-2830251-C-G			Benign (Jun 23, 2018)
X-2830380-G-A			Benign (Jun 14, 2018)
X-2842935-T-G			Benign (Jun 23, 2018)
X-2842979-A-AT			Benign (Aug 30, 2022)
X-2843009-C-T		not specified	Benign (Feb 03, 2025)
X-2843024-G-T			Uncertain significance (Nov 28, 2024)
X-2843032-C-G		GYG2-related disorder	Likely benign (Sep 16, 2020)
X-2843052-A-G		not specified	Uncertain significance (Oct 26, 2021)
X-2843067-C-A			Conflicting classifications of pathogenicity (Oct 14, 2024)
X-2843104-C-T		not specified	Likely benign (May 22, 2017)
X-2843218-G-T			Uncertain significance (Dec 02, 2021)
X-2843236-C-T		not specified	Likely benign (Dec 27, 2016)
X-2843245-A-C		GYG2-related disorder	Benign/Likely benign (Sep 17, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GYG2	protein_coding	protein_coding	ENST00000381163	11	54031

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.06e-10	0.0750	125679	18	26	125723	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0760	199	202	0.985	0.0000168	3271
Missense in Polyphen		56	62.169	0.90077		1033
Synonymous	-0.0238	96	95.7	1.00	0.00000918	985
Loss of Function	-0.0337	14	13.9	1.01	8.78e-7	259

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000306	0.000292
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000722	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000191	0.000132
Middle Eastern	0.0000722	0.0000544
South Asian	0.00102	0.000621
Other	0.000459	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Self-glucosylates, via an inter-subunit mechanism, to form an oligosaccharide primer that serves as substrate for glycogen synthase.
• Pathway: Starch and sucrose metabolism - Homo sapiens (human);Glycogen Metabolism;Metabolism of carbohydrates;Metabolism;glycogen biosynthesis;Glycogen breakdown (glycogenolysis);Glycogen synthesis;Glycogen metabolism (Consensus)

Intolerance Scores

• loftool: 0.966
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.3

Haploinsufficiency Scores

• pHI: 0.502
• hipred: N
• hipred_score: 0.182
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.591

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: glycogen biosynthetic process
• Cellular component: cytosol
• Molecular function: glycogenin glucosyltransferase activity;UDP-alpha-D-glucose:glucosyl-glycogenin alpha-D-glucosyltransferase activity