UGGT1

UDP-glucose glycoprotein glucosyltransferase 1, the group of UDP-glucose glycoprotein glucosyltransferases

Basic information

Region (hg38): 2:128091200-128195677

Previous symbols: [ "UGCGL1" ]

Links

ENSG00000136731 ∙ NCBI:56886 ∙ OMIM:605897 ∙ HGNC:15663 ∙ Uniprot:Q9NYU2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• disorder of protein N-glycosylation (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UGGT1 gene.

• not_specified (167 variants)
• not_provided (21 variants)
• CONGENITAL_DISORDER_OF_GLYCOSYLATION,_TYPE_IIcc (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UGGT1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020120.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	7	8
missense	4		159	8	5	176
nonsense	1		1			2
start loss						0
frameshift	2					2
splice donor/acceptor (+/-2bp)			1			1
Total	7	0	161	9	12

Highest pathogenic variant AF is 0.0000065706477

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UGGT1	protein_coding	protein_coding	ENST00000259253	41	104478

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.19e-10	1.00	125675	0	72	125747	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	737	824	0.894	0.0000426	10273
Missense in Polyphen		181	264.38	0.68463		3211
Synonymous	1.27	274	302	0.907	0.0000167	2858
Loss of Function	5.56	33	89.9	0.367	0.00000444	1101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000568	0.000568
Ashkenazi Jewish	0.00	0.00
East Asian	0.000278	0.000272
Finnish	0.0000933	0.0000924
European (Non-Finnish)	0.000398	0.000396
Middle Eastern	0.000278	0.000272
South Asian	0.000167	0.000163
Other	0.00	0.00

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. {ECO:0000269|PubMed:10694380}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);er associated degradation (erad) pathway;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: 0.118

Intolerance Scores

• loftool: 0.814
• rvis_EVS: -1.16
• rvis_percentile_EVS: 6.08

Haploinsufficiency Scores

• pHI: 0.562
• hipred: N
• hipred_score: 0.492
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.990

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Uggt1
• Phenotype: cellular phenotype; immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: protein N-linked glycosylation via asparagine;'de novo' posttranslational protein folding;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;extracellular exosome
• Molecular function: UDP-glucose:glycoprotein glucosyltransferase activity;protein binding;unfolded protein binding