GYG2

protein-coding

glycogenin 2, the group of Glycosyltransferase family 8

Gene summary

This gene encodes a member of the the glycogenin family. Glycogenin is a self-glucosylating protein involved in the initiation reactions of glycogen biosynthesis. A gene on chromosome 3 encodes the muscle glycogenin and this X-linked gene encodes the glycogenin mainly present in liver; both are involved in blood glucose homeostasis. This gene has a short version on chromosome Y, which is 3' truncated and can not make a functional protein. Multiple alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, May 2010]

MANE transcript

NM_001079855.2

Inheritance

—

ClinVar variants

U:120B:50

Top phenotype

GYG2-related disorder

gnomAD constraint

pLI —, LoF o/e 1.01

Max pathogenic AF

—

Genomic locus

chrX:2,828,822-2,882,818

External References & Databases

Ensembl (ENSG00000056998)

Transcript & Mutation Effects

hg38 • Region Span ~54.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GYG2 variants in ClinVar

5 Conditions Cataloged

not providedTotal: 140

not specifiedTotal: 78

GYG2-related disorderTotal: 11

Abnormality of neuronal migrationTotal: 1

Atypical Leigh syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001079855.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	25 clinvar	5 clinvar	35
missense			99 clinvar	15 clinvar	5 clinvar	119
nonsense			5 clinvar			5
start loss						0
frameshift			3 clinvar			3
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	120	40	10	170

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 120 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001079855.2	RefSeq	NP_001073324.1	10	MANE Select
ENST00000398806.8	Ensembl	ENSP00000381786.3	10	MANE Select
NM_001184702.2	RefSeq	NP_001171631.1	10	Standard
NM_001184703.2	RefSeq	NP_001171632.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Starch and sucrose metabolism - Homo sapiens (human)
Glycogen Metabolism
Metabolism of carbohydrates
Metabolism
glycogen biosynthesis

Biological Process

glycogen biosynthetic process

Molecular Function

glycogenin glucosyltransferase activity
UDP-alpha-D-glucose:glucosyl-glycogenin alpha-D-glucosyltransferase activity

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000381163
Coding exons: 11
Length: 54031
Individuals with no LoFs: 125679
Homozygous LoFs: 18
Heterozygous LoFs: 26
Defined: 125723
p: 0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0760	199	202	0.985	0.0000168	3271
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000076	0.000062	rare
Latino/Admixed American	0.00023	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000072	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00019	0.00013	rare
South Asian	0.0010	0.00062	notable
Other	0.00046	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Self-glucosylates, via an inter-subunit mechanism, to form an oligosaccharide primer that serves as substrate for glycogen synthase.;

Intolerance Scores

LoFtool: 0.966
RVIS EVS: 0.2
RVIS percentile EVS: 67.3

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.591

Gene Damage Prediction

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