POGLUT2

protein O-glucosyltransferase 2, the group of Glycosyltransferase family 90

Basic information

Region (hg38): 13:102784281-102799040

Previous symbols: [ "KDELC1" ]

Links

ENSG00000134901 ∙ NCBI:79070 ∙ OMIM:611613 ∙ HGNC:19350 ∙ Uniprot:Q6UW63 ∙ 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 POGLUT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POGLUT2 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			48	1		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	1	0

Variants in POGLUT2

This is a list of pathogenic ClinVar variants found in the POGLUT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-102786264-C-T		not specified	Uncertain significance (Jan 16, 2024)
13-102786287-C-A		not specified	Uncertain significance (Feb 27, 2024)
13-102786302-C-T		not specified	Uncertain significance (Jun 17, 2024)
13-102786329-T-C		not specified	Likely benign (Sep 16, 2021)
13-102786332-G-C		not specified	Uncertain significance (Apr 11, 2023)
13-102787862-A-G		not specified	Uncertain significance (Nov 11, 2024)
13-102789016-T-C		not specified	Uncertain significance (Feb 13, 2024)
13-102789016-T-G		not specified	Uncertain significance (Dec 18, 2023)
13-102789031-G-A		not specified	Uncertain significance (Apr 23, 2024)
13-102789037-T-G		not specified	Uncertain significance (Nov 07, 2022)
13-102789056-C-A		not specified	Uncertain significance (Aug 04, 2024)
13-102789082-T-C		not specified	Uncertain significance (Dec 13, 2023)
13-102789127-A-G		not specified	Uncertain significance (Aug 20, 2024)
13-102789160-A-G		not specified	Uncertain significance (Apr 28, 2022)
13-102789185-C-T		not specified	Uncertain significance (May 23, 2024)
13-102789217-T-G		not specified	Uncertain significance (Oct 07, 2024)
13-102789220-T-C		not specified	Uncertain significance (Aug 10, 2021)
13-102790912-C-A		not specified	Uncertain significance (Jan 23, 2024)
13-102790936-T-A		not specified	Uncertain significance (Feb 26, 2025)
13-102790936-T-C		not specified	Uncertain significance (Jan 01, 2025)
13-102790944-T-C		not specified	Uncertain significance (May 31, 2023)
13-102790959-T-C		not specified	Uncertain significance (Apr 07, 2023)
13-102791032-C-T		not specified	Uncertain significance (Dec 21, 2022)
13-102791068-C-T		not specified	Uncertain significance (Jun 11, 2021)
13-102791085-C-T		not specified	Uncertain significance (Sep 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POGLUT2	protein_coding	protein_coding	ENST00000376004	10	14727

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.91e-9	0.833	125657	0	91	125748	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0150	273	274	0.997	0.0000140	3334
Missense in Polyphen		112	120	0.93337		1435
Synonymous	0.297	101	105	0.963	0.00000612	913
Loss of Function	1.61	17	25.8	0.658	0.00000135	309

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000773	0.000772
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00157	0.00157
European (Non-Finnish)	0.000221	0.000220
Middle Eastern	0.000272	0.000272
South Asian	0.000134	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0976

Intolerance Scores

• loftool: 0.590
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.92

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.267
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.239

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kdelc1

Gene ontology

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