UGGT2

protein-coding

UDP-glucose glycoprotein glucosyltransferase 2, the group of UDP-glucose glycoprotein glucosyltransferases

Gene summary

UDP-glucose:glycoprotein glucosyltransferase (UGT) is a soluble protein of the endoplasmic reticulum (ER) that selectively reglucosylates unfolded glycoproteins, thus providing quality control for protein transport out of the ER.[supplied by OMIM, Oct 2009]

Previous symbols:

UGCGL2

MANE transcript

NM_020121.4

Inheritance

—

ClinVar variants

U:210B:21

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr13:95,801,580-96,053,482

External References & Databases

Ensembl (ENSG00000102595)

Transcript & Mutation Effects

hg38 • Region Span ~251.9 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 UGGT2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 207

not providedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020121.4. 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			2 clinvar	3 clinvar		5
missense			198 clinvar	16 clinvar	2 clinvar	216
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	210	19	2	231

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 62 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020121.4	RefSeq	NP_064506.3	39	MANE Select
ENST00000376747.8	Ensembl	ENSP00000365938.3	39	MANE Select
ENST00000376712.4	Ensembl	ENSP00000365902.4	8	Standard
ENST00000376712.5	Ensembl	ENSP00000365902.4	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Protein processing in endoplasmic reticulum - Homo sapiens (human)
ER Quality Control Compartment (ERQC)
Calnexin/calreticulin cycle
Post-translational protein modification
Metabolism of proteins

Biological Process

protein N-linked glycosylation via asparagine
ER-associated misfolded protein catabolic process
UDP-glucosylation
endoplasmic reticulum mannose trimming

Molecular Function

UDP-glucose:glycoprotein glucosyltransferase activity
protein binding
unfolded protein binding

Cellular Component

endoplasmic reticulum
endoplasmic reticulum lumen
endoplasmic reticulum-Golgi intermediate compartment
protein-containing complex
endoplasmic reticulum quality control compartment

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000376747
Coding exons: 39
Length: 251903
Individuals with no LoFs: 125132
Homozygous LoFs: 0
Heterozygous LoFs: 613
Defined: 125745
p: 0.00244

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0203	761	759	1.00	0.0000378	10040
Missense (PolyPhen)		263	273.66	0.96106		3672
Synonymous	1.90	214	252	0.848	0.0000120	2688
Loss of Function	1.10	69	79.6	0.866	0.00000376	1072

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0013	0.0013	notable
Latino/Admixed American	0.0012	0.0012	notable
Ashkenazi Jewish	0.0037	0.0037	notable
East Asian	0.00067	0.00065	rare
Finnish	0.0013	0.0013	notable
European (Non-Finnish)	0.0034	0.0033	notable
South Asian	0.0026	0.0025	notable
Other	0.0033	0.0033	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Recognizes glycoproteins with minor folding defects. Reglucosylates single N-glycans near the misfolded part of the protein, thus providing quality control for protein folding in the endoplasmic reticulum. Reglucosylated proteins are recognized by calreticulin for recycling to the endoplasmic reticulum and refolding or degradation (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.0970

Intolerance Scores

LoFtool: 0.997
RVIS EVS: 1.28
RVIS percentile EVS: 93.68

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.977

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High