B3GNT9

UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9, the group of Beta 3-glycosyltransferases

Basic information

Region (hg38): 16:67148104-67150998

Links

ENSG00000237172 ∙ NCBI:84752 ∙ ∙ HGNC:28714 ∙ Uniprot:Q6UX72 ∙ 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 B3GNT9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GNT9 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in B3GNT9

This is a list of pathogenic ClinVar variants found in the B3GNT9 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-67149390-C-G		not specified	Uncertain significance (May 18, 2022)
16-67149444-G-A		not specified	Uncertain significance (Mar 18, 2024)
16-67149449-G-A		not specified	Uncertain significance (Feb 17, 2022)
16-67149483-C-A		not specified	Uncertain significance (Nov 01, 2022)
16-67149486-G-T		not specified	Uncertain significance (Nov 11, 2024)
16-67149509-A-C		not specified	Uncertain significance (Apr 05, 2023)
16-67149514-C-G		not specified	Uncertain significance (Nov 19, 2024)
16-67149566-G-A		not specified	Uncertain significance (May 20, 2024)
16-67149593-G-A		not specified	Uncertain significance (Oct 01, 2024)
16-67149621-C-T		not specified	Uncertain significance (Sep 27, 2024)
16-67149630-A-G		not specified	Uncertain significance (Mar 25, 2022)
16-67149692-C-T		not specified	Uncertain significance (Nov 28, 2024)
16-67149702-G-A		not specified	Uncertain significance (Mar 30, 2024)
16-67149729-G-T		not specified	Uncertain significance (Jul 26, 2022)
16-67149738-G-C		not specified	Uncertain significance (Jul 30, 2024)
16-67149776-C-T		not specified	Uncertain significance (Nov 15, 2024)
16-67149837-C-G		not specified	Uncertain significance (Jun 29, 2023)
16-67149848-G-C		not specified	Uncertain significance (Oct 05, 2023)
16-67149899-G-T		not specified	Uncertain significance (Sep 01, 2021)
16-67149947-G-A		not specified	Uncertain significance (Dec 09, 2024)
16-67150006-C-G		not specified	Uncertain significance (Dec 03, 2024)
16-67150031-C-G		not specified	Uncertain significance (Oct 09, 2024)
16-67150047-C-G		not specified	Uncertain significance (Dec 05, 2024)
16-67150059-C-T		not specified	Uncertain significance (Apr 12, 2024)
16-67150085-G-A		not specified	Uncertain significance (Mar 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B3GNT9	protein_coding	protein_coding	ENST00000449549	1	3110

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000174	0.268	124543	0	17	124560	0.0000682

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	176	222	0.794	0.0000148	2443
Missense in Polyphen		80	99.916	0.80067		1141
Synonymous	-0.572	122	114	1.07	0.00000880	907
Loss of Function	-0.133	7	6.63	1.06	3.18e-7	82

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)	0.000111	0.000106
Middle Eastern	0.00	0.00
South Asian	0.000134	0.000131
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Pathway: Post-translational protein modification;Metabolism of proteins;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.354
• ghis: 0.463

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B3gnt9

Gene ontology

• Biological process: protein glycosylation;poly-N-acetyllactosamine biosynthetic process
• Cellular component: Golgi membrane;fibrillar center;endoplasmic reticulum;Golgi apparatus;integral component of membrane
• Molecular function: acetylgalactosaminyltransferase activity;galactosyltransferase activity;N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity