B3GNT6

UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6, the group of Beta 3-glycosyltransferases

Basic information

Region (hg38): 11:77034398-77041973

Links

ENSG00000198488 ∙ NCBI:192134 ∙ OMIM:615315 ∙ HGNC:24141 ∙ Uniprot:Q6ZMB0 ∙ 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 B3GNT6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GNT6 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		1	28			29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	28	0	0

Variants in B3GNT6

This is a list of pathogenic ClinVar variants found in the B3GNT6 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-77039567-C-T		not specified	Uncertain significance (Oct 02, 2023)
11-77039684-G-A		not specified	Uncertain significance (Jul 09, 2021)
11-77039686-G-T		not specified	Uncertain significance (Jun 02, 2023)
11-77039726-G-A		not specified	Uncertain significance (Oct 21, 2021)
11-77039756-C-T		not specified	Uncertain significance (Mar 15, 2024)
11-77039814-G-T		not specified	Uncertain significance (Feb 05, 2024)
11-77039819-C-A		not specified	Uncertain significance (Dec 14, 2023)
11-77039886-C-T		not specified	Uncertain significance (Feb 23, 2023)
11-77039891-G-A		not specified	Uncertain significance (Dec 13, 2023)
11-77039963-C-T		not specified	Uncertain significance (Dec 09, 2023)
11-77039985-G-C		not specified	Uncertain significance (Sep 06, 2022)
11-77040002-G-A		not specified	Uncertain significance (Jan 22, 2024)
11-77040005-C-T		not specified	Uncertain significance (Dec 20, 2023)
11-77040006-G-A		not specified	Uncertain significance (Nov 09, 2021)
11-77040008-C-T		not specified	Uncertain significance (Oct 18, 2021)
11-77040012-T-C		not specified	Uncertain significance (May 31, 2023)
11-77040023-G-T		not specified	Uncertain significance (Jun 06, 2023)
11-77040024-G-A		not specified	Uncertain significance (Dec 18, 2023)
11-77040036-C-T		not specified	Uncertain significance (Dec 20, 2021)
11-77040039-A-T		not specified	Uncertain significance (Jun 10, 2024)
11-77040041-G-A		not specified	Uncertain significance (Oct 13, 2023)
11-77040103-C-G		Childhood-onset schizophrenia	Likely pathogenic (Jan 01, 2014)
11-77040104-G-A		not specified	Uncertain significance (May 01, 2024)
11-77040194-G-C		not specified	Uncertain significance (Nov 22, 2021)
11-77040221-G-A		not specified	Uncertain significance (Nov 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B3GNT6	protein_coding	protein_coding	ENST00000533140	1	7712

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.09e-9	0.0267	124594	0	48	124642	0.000193

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.216	247	238	1.04	0.0000152	2359
Missense in Polyphen		96	85.173	1.1271		918
Synonymous	0.400	108	113	0.952	0.00000782	826
Loss of Function	-0.935	12	8.98	1.34	4.47e-7	82

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000766	0.000684
Ashkenazi Jewish	0.00	0.00
East Asian	0.000229	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.000207	0.000186
Middle Eastern	0.000229	0.000223
South Asian	0.000211	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Beta-1,3-N-acetylglucosaminyltransferase that synthesizes the core 3 structure of the O-glycan, an important precursor in the biosynthesis of mucin-type glycoproteins. Plays an important role in the synthesis of mucin-type O-glycans in digestive organs.
• Pathway: Mucin type O-glycan biosynthesis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;O-Glycan biosynthesis;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.285

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B3gnt6
• Phenotype: digestive/alimentary phenotype; immune system phenotype; neoplasm; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region 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); homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: protein glycosylation;glycoprotein biosynthetic process;O-glycan processing;O-glycan processing, core 3;poly-N-acetyllactosamine biosynthetic process
• Cellular component: Golgi membrane;endoplasmic reticulum;Golgi apparatus;membrane;integral component of membrane
• Molecular function: acetylgalactosaminyltransferase activity;galactosyltransferase 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;acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity