B3GNT5

UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5, the group of Beta 3-glycosyltransferases

Basic information

Region (hg38): 3:183253253-183298504

Links

ENSG00000176597 ∙ NCBI:84002 ∙ OMIM:615333 ∙ HGNC:15684 ∙ Uniprot:Q9BYG0 ∙ 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 B3GNT5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GNT5 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			23	2		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			15	1		16
Total	0	0	38	3	0

Variants in B3GNT5

This is a list of pathogenic ClinVar variants found in the B3GNT5 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-183269811-G-C		not specified	Uncertain significance (Sep 29, 2023)
3-183269821-G-C		not specified	Uncertain significance (Jun 22, 2021)
3-183269835-T-C		not specified	Uncertain significance (Sep 07, 2022)
3-183269901-A-C		not specified	Uncertain significance (Dec 03, 2024)
3-183269904-G-A		not specified	Uncertain significance (Mar 04, 2024)
3-183270060-G-A		not specified	Uncertain significance (Jul 02, 2024)
3-183270091-C-T		not specified	Uncertain significance (Sep 14, 2023)
3-183270114-G-A		not specified	Uncertain significance (May 25, 2022)
3-183270183-T-A		not specified	Uncertain significance (Aug 11, 2022)
3-183270205-C-T		not specified	Uncertain significance (Jun 16, 2023)
3-183270226-A-G		not specified	Uncertain significance (Jan 24, 2023)
3-183270264-A-G		not specified	Likely benign (Oct 27, 2023)
3-183270298-A-G		not specified	Uncertain significance (Dec 11, 2024)
3-183270352-A-G		not specified	Uncertain significance (Mar 01, 2023)
3-183270448-A-C		not specified	Uncertain significance (Oct 28, 2024)
3-183270463-G-A		not specified	Uncertain significance (Feb 28, 2024)
3-183270520-A-G		not specified	Uncertain significance (Sep 14, 2023)
3-183270582-G-A		not specified	Likely benign (Feb 03, 2022)
3-183270603-T-G		not specified	Uncertain significance (Aug 22, 2023)
3-183270606-G-A		not specified	Uncertain significance (Dec 01, 2022)
3-183270618-A-G		not specified	Uncertain significance (Feb 02, 2024)
3-183270651-T-C		not specified	Uncertain significance (Mar 16, 2022)
3-183270681-A-G		not specified	Uncertain significance (Jul 19, 2023)
3-183270688-C-T		not specified	Uncertain significance (Aug 25, 2021)
3-183270745-A-G		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B3GNT5	protein_coding	protein_coding	ENST00000326505	1	45261

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.726	0.274	125727	0	17	125744	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	167	210	0.796	0.0000109	2521
Missense in Polyphen		60	81.195	0.73896		974
Synonymous	0.744	68	76.3	0.892	0.00000435	694
Loss of Function	2.82	2	13.0	0.154	6.14e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000333	0.000333
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.000272	0.000272
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Beta-1,3-N-acetylglucosaminyltransferase that plays a key role in the synthesis of lacto- or neolacto-series carbohydrate chains on glycolipids, notably by participating in biosynthesis of HNK-1 and Lewis X carbohydrate structures. Has strong activity toward lactosylceramide (LacCer) and neolactotetraosylceramide (nLc(4)Cer; paragloboside), resulting in the synthesis of Lc(3)Cer and neolactopentaosylceramide (nLc(5)Cer), respectively. Probably plays a central role in regulating neolacto-series glycolipid synthesis during embryonic development.
• Pathway: Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human);Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Post-translational protein modification;Metabolism of proteins;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.530
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.103
• hipred: Y
• hipred_score: 0.504
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B3gnt5
• Phenotype: hematopoietic system phenotype; growth/size/body region phenotype; reproductive system 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); immune system phenotype

Gene ontology

• Biological process: protein glycosylation;central nervous system development;brain development;glycolipid biosynthetic process;O-glycan processing;poly-N-acetyllactosamine biosynthetic process
• Cellular component: Golgi membrane;endoplasmic reticulum;Golgi apparatus;integral component of membrane
• Molecular function: acetylgalactosaminyltransferase activity;beta-galactosyl-N-acetylglucosaminylgalactosylglucosyl-ceramide beta-1,3-acetylglucosaminyltransferase activity;UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity;N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity;lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase activity