UGGT2

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

Basic information

Region (hg38): 13:95801579-96053482

Previous symbols: [ "UGCGL2" ]

Links

ENSG00000102595 ∙ NCBI:55757 ∙ OMIM:605898 ∙ HGNC:15664 ∙ Uniprot:Q9NYU1 ∙ 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 UGGT2 gene.

• Inborn genetic diseases (64 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UGGT2 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				3		3
missense			61	6	2	69
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	61	9	3

Variants in UGGT2

This is a list of pathogenic ClinVar variants found in the UGGT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-95832929-G-T		not specified	Uncertain significance (Feb 28, 2023)
13-95832950-A-G		not specified	Uncertain significance (Mar 17, 2023)
13-95837096-G-A		not specified	Uncertain significance (Mar 27, 2023)
13-95837173-G-A			Likely benign (Mar 01, 2023)
13-95853550-A-T		not specified	Uncertain significance (Jul 28, 2021)
13-95853587-G-C		not specified	Uncertain significance (Jul 06, 2022)
13-95853655-G-A		not specified	Uncertain significance (Dec 27, 2023)
13-95854321-T-C		not specified	Uncertain significance (Dec 19, 2022)
13-95854331-G-A		not specified	Uncertain significance (Jan 17, 2024)
13-95854379-C-T			Likely benign (Mar 29, 2018)
13-95854453-T-A		not specified	Uncertain significance (Feb 28, 2023)
13-95856193-C-G		not specified	Uncertain significance (Mar 04, 2024)
13-95856220-G-T		not specified	Uncertain significance (Nov 21, 2022)
13-95856268-G-A		not specified	Uncertain significance (Jul 05, 2023)
13-95856312-T-A			Benign (Aug 08, 2017)
13-95859624-C-G		not specified	Uncertain significance (Feb 16, 2023)
13-95859652-C-T		not specified	Uncertain significance (Aug 23, 2021)
13-95860803-T-C		not specified	Uncertain significance (Oct 06, 2021)
13-95860813-C-T		not specified	Uncertain significance (Feb 05, 2024)
13-95860828-A-C		not specified	Uncertain significance (Sep 20, 2023)
13-95863637-G-A			Likely benign (Mar 29, 2018)
13-95877294-A-G		not specified	Uncertain significance (Jun 06, 2023)
13-95877312-T-C		not specified	Uncertain significance (Nov 09, 2022)
13-95877706-C-T		not specified	Uncertain significance (Nov 02, 2023)
13-95877768-C-T		not specified	Likely benign (Apr 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UGGT2	protein_coding	protein_coding	ENST00000376747	39	251903

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.32e-41	0.0000716	125132	0	613	125745	0.00244

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0203	761	759	1.00	0.0000378	10040
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00249	0.00248
Ashkenazi Jewish	0.00368	0.00368
East Asian	0.000670	0.000653
Finnish	0.00135	0.00134
European (Non-Finnish)	0.00335	0.00333
Middle Eastern	0.000670	0.000653
South Asian	0.00257	0.00249
Other	0.00332	0.00326

dbNSFP

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}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);ER Quality Control Compartment (ERQC);Calnexin/calreticulin cycle;Post-translational protein modification;Metabolism of proteins;Asparagine N-linked glycosylation;N-glycan trimming in the ER and Calnexin/Calreticulin cycle (Consensus)

Recessive Scores

• pRec: 0.0970

Intolerance Scores

• loftool: 0.997
• rvis_EVS: 1.28
• rvis_percentile_EVS: 93.68

Haploinsufficiency Scores

• pHI: 0.0645
• hipred: N
• hipred_score: 0.484
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.977

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Uggt2

Gene ontology

• Biological process: protein N-linked glycosylation via asparagine;ER-associated misfolded protein catabolic process;UDP-glucosylation;endoplasmic reticulum mannose trimming
• Cellular component: endoplasmic reticulum;endoplasmic reticulum lumen;endoplasmic reticulum-Golgi intermediate compartment;protein-containing complex;endoplasmic reticulum quality control compartment
• Molecular function: UDP-glucose:glycoprotein glucosyltransferase activity;protein binding;unfolded protein binding