B3GNT3

UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3, the group of Beta 3-glycosyltransferases

Basic information

Region (hg38): 19:17794827-17813576

Previous symbols: [ "TMEM3" ]

Links

ENSG00000179913 ∙ NCBI:10331 ∙ OMIM:605863 ∙ HGNC:13528 ∙ Uniprot:Q9Y2A9 ∙ 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 B3GNT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GNT3 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				1	1	2
missense			18	3	1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	4	2

Variants in B3GNT3

This is a list of pathogenic ClinVar variants found in the B3GNT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-17807854-C-T		not specified	Uncertain significance (Jul 13, 2022)
19-17807928-C-T		not specified	Uncertain significance (Feb 01, 2023)
19-17807929-C-T		not specified	Uncertain significance (Nov 29, 2021)
19-17807939-C-T			Benign (Mar 29, 2018)
19-17807986-C-A		not specified	Uncertain significance (Nov 03, 2022)
19-17807994-G-A		not specified	Uncertain significance (Jan 16, 2024)
19-17808034-A-G		not specified	Uncertain significance (Aug 04, 2023)
19-17808049-A-G		not specified	Likely benign (Dec 17, 2023)
19-17808098-C-G		not specified	Uncertain significance (Jun 17, 2024)
19-17808102-C-T		not specified	Uncertain significance (Apr 15, 2024)
19-17808103-C-A		not specified	Uncertain significance (Aug 21, 2023)
19-17808106-C-G		not specified	Uncertain significance (Oct 26, 2022)
19-17808217-G-A		not specified	Likely benign (Mar 01, 2023)
19-17808220-G-T		not specified	Uncertain significance (Mar 12, 2024)
19-17808232-G-A		not specified	Uncertain significance (May 04, 2022)
19-17811619-G-A		not specified	Uncertain significance (Jun 11, 2021)
19-17811619-G-C		not specified	Likely benign (Nov 14, 2023)
19-17811651-C-G		not specified	Uncertain significance (Oct 06, 2022)
19-17811683-A-G		not specified	Uncertain significance (Jan 08, 2024)
19-17811791-G-A		not specified	Uncertain significance (Dec 18, 2023)
19-17811839-C-T		not specified	Uncertain significance (Oct 17, 2023)
19-17811844-G-A		not specified	Uncertain significance (Sep 17, 2021)
19-17811959-C-T			Benign (Mar 29, 2018)
19-17811970-C-T		not specified	Uncertain significance (Sep 25, 2023)
19-17812036-C-T		not specified	Uncertain significance (Sep 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B3GNT3	protein_coding	protein_coding	ENST00000318683	2	18255

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.739	0.259	125626	0	14	125640	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.52	187	255	0.733	0.0000179	2381
Missense in Polyphen		49	99.012	0.49489		997
Synonymous	1.10	99	114	0.869	0.00000782	807
Loss of Function	2.43	1	8.76	0.114	3.75e-7	88

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000117	0.000114
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Beta-1,3-N-acetylglucosaminyltransferase involved in the synthesis of poly-N-acetyllactosamine. Has activity for type 2 oligosaccharides (PubMed:11042166). Also acts as a core1-1,3-N- acetylglucosaminyltransferase (Core1-beta3GlcNAcT) to form the 6- sulfo sialyl Lewis x on extended core1 O-glycans (PubMed:11439191). {ECO:0000269|PubMed:11042166, ECO:0000269|PubMed:11439191}.
• Pathway: Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human);Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;Post-translational protein modification;Metabolism of proteins;Metabolism;mucin core 1 and core 2 <i>O</i>-glycosylation;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.435
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.82

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.284

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.334

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B3gnt3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: protein glycosylation;O-glycan processing;keratan sulfate biosynthetic process;poly-N-acetyllactosamine biosynthetic process
• Cellular component: Golgi membrane;endoplasmic reticulum;Golgi apparatus;integral component of plasma membrane
• Molecular function: acetylgalactosaminyltransferase activity;UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity;N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity;beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity