B3GNT4

UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4, the group of Beta 3-glycosyltransferases

Basic information

Region (hg38): 12:122203680-122208952

Links

ENSG00000176383 ∙ NCBI:79369 ∙ OMIM:605864 ∙ HGNC:15683 ∙ Uniprot:Q9C0J1 ∙ 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 B3GNT4 gene.

• not provided (20 variants)
• Inborn genetic diseases (17 variants)
• not specified (5 variants)
• DIABLO-related condition (1 variants)
• Hearing impairment (1 variants)
• Autosomal dominant nonsyndromic hearing loss 64 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GNT4 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			14	3		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			7	10	5	22
Total	0	0	21	13	5

Variants in B3GNT4

This is a list of pathogenic ClinVar variants found in the B3GNT4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-122204670-G-A		not specified	Uncertain significance (Dec 03, 2021)
12-122206360-A-G		not specified	Uncertain significance (Apr 05, 2023)
12-122206454-C-T		not specified	Uncertain significance (Jan 31, 2024)
12-122206468-C-T		not specified	Uncertain significance (Jan 03, 2024)
12-122206519-C-T		not specified	Uncertain significance (Sep 06, 2022)
12-122206568-C-G		not specified	Uncertain significance (Nov 10, 2022)
12-122206597-A-G		not specified	Likely benign (Dec 28, 2022)
12-122206720-T-C		not specified	Uncertain significance (Oct 29, 2021)
12-122206824-C-A		not specified	Uncertain significance (Oct 30, 2023)
12-122206855-C-A		not specified	Uncertain significance (May 17, 2023)
12-122206883-C-T		not specified	Uncertain significance (Jun 06, 2023)
12-122206899-G-T		not specified	Uncertain significance (Jun 22, 2023)
12-122206924-G-A		not specified	Uncertain significance (Oct 05, 2023)
12-122206933-G-A		not specified	Uncertain significance (Nov 01, 2021)
12-122207020-A-G		not specified	Uncertain significance (Jan 09, 2024)
12-122207047-A-G		not specified	Uncertain significance (Aug 17, 2022)
12-122207053-A-G		not specified	Uncertain significance (Dec 15, 2022)
12-122207120-G-A		not specified	Likely benign (Jul 14, 2021)
12-122207161-G-A		not specified	Uncertain significance (Oct 05, 2022)
12-122207242-C-T		not specified	Uncertain significance (Sep 29, 2023)
12-122207246-G-A		not specified	Likely benign (Nov 30, 2022)
12-122207281-G-A		not specified	Uncertain significance (Sep 26, 2023)
12-122207284-C-G		not specified	Uncertain significance (Oct 14, 2023)
12-122207300-G-A		not specified	Uncertain significance (Nov 01, 2022)
12-122207320-T-G		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B3GNT4	protein_coding	protein_coding	ENST00000324189	2	5410

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.68e-7	0.299	125497	1	249	125747	0.000995

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.40	340	236	1.44	0.0000142	2419
Missense in Polyphen		135	85.364	1.5815		990
Synonymous	-3.50	141	97.2	1.45	0.00000545	826
Loss of Function	0.338	10	11.2	0.891	6.48e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00141	0.00141
Ashkenazi Jewish	0.00219	0.00218
East Asian	0.000435	0.000435
Finnish	0.0000473	0.0000462
European (Non-Finnish)	0.00118	0.00117
Middle Eastern	0.000435	0.000435
South Asian	0.00155	0.00147
Other	0.000825	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Beta-1,3-N-acetylglucosaminyltransferase involved in the synthesis of poly-N-acetyllactosamine. Has activity for type 2 oligosaccharides. {ECO:0000269|PubMed:11042166}.
• 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;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.153

Intolerance Scores

• loftool: 0.919
• rvis_EVS: 1.07
• rvis_percentile_EVS: 91.61

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.170
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.225

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B3gnt4

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 membrane
• Molecular function: acetylgalactosaminyltransferase activity;UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity;N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity