B4GALNT3

beta-1,4-N-acetyl-galactosaminyltransferase 3, the group of Beta 4-glycosyltransferases

Basic information

Region (hg38): 12:459939-563509

Links

ENSG00000139044 ∙ NCBI:283358 ∙ OMIM:612220 ∙ HGNC:24137 ∙ Uniprot:Q6L9W6 ∙ 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 B4GALNT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B4GALNT3 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			84	13	3	100
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region					1	1
non coding						0
Total	0	1	85	14	4

Variants in B4GALNT3

This is a list of pathogenic ClinVar variants found in the B4GALNT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-460420-C-G		not specified	Uncertain significance (Jan 23, 2025)
12-460440-C-A		not specified	Uncertain significance (Aug 02, 2021)
12-460460-G-A			Benign (Apr 20, 2018)
12-460479-G-A		not specified	Uncertain significance (Jul 14, 2021)
12-460524-G-A		not specified	Uncertain significance (Mar 11, 2022)
12-460534-C-T		not specified	Uncertain significance (Sep 14, 2022)
12-535179-G-C		not specified	Uncertain significance (Nov 15, 2021)
12-535196-C-T		not specified	Uncertain significance (Oct 08, 2024)
12-535198-C-G		not specified	Uncertain significance (Feb 27, 2024)
12-535267-G-A		not specified	Likely benign (Sep 30, 2021)
12-536248-AACAG-A			Uncertain significance (Jan 01, 2019)
12-544349-G-A		not specified	Likely benign (Jan 18, 2025)
12-544349-G-C		not specified	Uncertain significance (Nov 08, 2024)
12-544357-C-G		not specified	Uncertain significance (Aug 12, 2021)
12-544363-G-A		not specified	Uncertain significance (Dec 01, 2024)
12-544386-C-G		not specified	Uncertain significance (Jan 17, 2025)
12-544390-A-C		not specified	Uncertain significance (Mar 12, 2024)
12-544433-A-G		not specified	Uncertain significance (Jun 18, 2021)
12-544910-T-C		not specified	Uncertain significance (Dec 28, 2023)
12-544939-C-T		not specified	Uncertain significance (Feb 01, 2025)
12-544945-T-C		not specified	Uncertain significance (Feb 05, 2024)
12-545459-G-T		not specified	Uncertain significance (Dec 02, 2024)
12-546650-G-T		not specified	Uncertain significance (Jan 30, 2024)
12-546661-A-G		not specified	Uncertain significance (Mar 25, 2024)
12-546678-T-G		not specified	Uncertain significance (Nov 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B4GALNT3	protein_coding	protein_coding	ENST00000266383	20	103146

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.79e-15	0.997	125613	0	135	125748	0.000537

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.710	544	593	0.918	0.0000365	6499
Missense in Polyphen		171	237.95	0.71865		2566
Synonymous	0.255	233	238	0.979	0.0000144	1955
Loss of Function	2.92	32	55.4	0.577	0.00000298	554

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000751	0.000724
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00141	0.00141
Finnish	0.000372	0.000370
European (Non-Finnish)	0.000576	0.000536
Middle Eastern	0.00141	0.00141
South Asian	0.000654	0.000653
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transfers N-acetylgalactosamine (GalNAc) from UDP-GalNAc to N-acetylglucosamine-beta-benzyl with a beta-1,4-linkage to form N,N'-diacetyllactosediamine, GalNAc-beta-1,4-GlcNAc structures in N-linked glycans and probably O-linked glycans. Mediates the N,N'- diacetyllactosediamine formation on gastric mucosa. {ECO:0000269|PubMed:16728562}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.908
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.05

Haploinsufficiency Scores

• pHI: 0.192
• hipred: N
• hipred_score: 0.492
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.319

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B4galnt3
• Phenotype: hematopoietic system phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Cellular component: integral component of membrane;Golgi cisterna membrane
• Molecular function: acetylgalactosaminyltransferase activity;N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity