POGLUT3

protein O-glucosyltransferase 3, the group of Glycosyltransferase family 90

Basic information

Region (hg38): 11:108472112-108498405

Previous symbols: [ "KDELC2" ]

Links

ENSG00000178202 ∙ NCBI:143888 ∙ OMIM:618503 ∙ HGNC:28496 ∙ Uniprot:Q7Z4H8 ∙ 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 POGLUT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POGLUT3 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						0
missense			50	2		52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	50	2	0

Variants in POGLUT3

This is a list of pathogenic ClinVar variants found in the POGLUT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-108474840-C-G		not specified	Uncertain significance (Apr 09, 2024)
11-108474858-T-A		not specified	Uncertain significance (Oct 24, 2023)
11-108474895-G-A		not specified	Uncertain significance (May 10, 2024)
11-108474916-G-A		not specified	Uncertain significance (Nov 15, 2021)
11-108474931-T-A		not specified	Uncertain significance (Feb 23, 2023)
11-108477626-T-C		not specified	Uncertain significance (Aug 21, 2024)
11-108479309-A-G		not specified	Uncertain significance (Mar 25, 2024)
11-108479329-T-C		not specified	Uncertain significance (Feb 12, 2025)
11-108479348-T-C		not specified	Uncertain significance (Jun 25, 2024)
11-108479410-T-G		not specified	Uncertain significance (Aug 14, 2023)
11-108479432-C-G		not specified	Uncertain significance (May 24, 2023)
11-108479444-A-G		not specified	Uncertain significance (Mar 29, 2024)
11-108479465-C-A		not specified	Uncertain significance (Jan 30, 2024)
11-108481227-T-C		not specified	Uncertain significance (Jan 17, 2024)
11-108481256-G-A		not specified	Uncertain significance (Jan 17, 2025)
11-108481289-T-G		not specified	Uncertain significance (Aug 16, 2022)
11-108481302-C-A		not specified	Uncertain significance (Oct 24, 2024)
11-108481302-C-T		not specified	Uncertain significance (May 24, 2023)
11-108481313-C-T		not specified	Uncertain significance (Sep 10, 2024)
11-108481322-C-T		not specified	Uncertain significance (Sep 11, 2024)
11-108482014-C-T		not specified	Uncertain significance (Jan 23, 2025)
11-108482021-T-G		not specified	Uncertain significance (Jan 31, 2024)
11-108482045-C-A		not specified	Uncertain significance (Jul 12, 2023)
11-108482047-C-T		not specified	Uncertain significance (Feb 08, 2025)
11-108482048-G-A		not specified	Uncertain significance (Nov 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POGLUT3	protein_coding	protein_coding	ENST00000323468	8	26328

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.14e-10	0.313	124431	2	362	124795	0.00146

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.490	230	252	0.913	0.0000124	3273
Missense in Polyphen		111	120.19	0.92352		1510
Synonymous	0.248	93	96.1	0.968	0.00000500	978
Loss of Function	0.934	18	22.8	0.789	0.00000111	298

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0135	0.0128
Ashkenazi Jewish	0.00	0.00
East Asian	0.000292	0.000278
Finnish	0.000511	0.000510
European (Non-Finnish)	0.000908	0.000892
Middle Eastern	0.000292	0.000278
South Asian	0.000138	0.000131
Other	0.00187	0.00182

dbNSFP

Source: dbNSFP

• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase (Consensus)

Intolerance Scores

• loftool: 0.668
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.9

Haploinsufficiency Scores

• pHI: 0.158
• hipred: N
• hipred_score: 0.282
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.469

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kdelc2

Gene ontology

• Biological process: biological_process;protein O-linked glycosylation via serine
• Cellular component: cellular_component;endoplasmic reticulum lumen
• Molecular function: molecular_function;UDP-glucosyltransferase activity;UDP-xylosyltransferase activity;glucosyltransferase activity