B4GALNT3

protein-coding

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

Gene summary

B4GALNT3 transfers N-acetylgalactosamine (GalNAc) onto glucosyl residues to form N,N-prime-diacetyllactosediamine (LacdiNAc, or LDN), a unique terminal structure of cell surface N-glycans (Ikehara et al., 2006 [PubMed 16728562]).[supplied by OMIM, Aug 2008]

MANE transcript

NM_173593.4

Inheritance

—

ClinVar variants

P:1U:162B:23

Top phenotype

Susceptibility to severe COVID-19

gnomAD constraint

pLI —, LoF o/e 0.58

Max pathogenic AF

—

Genomic locus

chr12:459,939-563,509

External References & Databases

Ensembl (ENSG00000139044)

Transcript & Mutation Effects

hg38 • Region Span ~103.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to B4GALNT3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 160

not providedTotal: 9

Susceptibility to severe COVID-19Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173593.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar	2 clinvar	5
missense			151 clinvar	17 clinvar	3 clinvar	171
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)		1 clinvar	6 clinvar			7
Total	0	1	162	18	5	186

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173593.4	RefSeq	NP_775864.3	20	MANE Select
ENST00000266383.10	Ensembl	ENSP00000266383.5	20	MANE Select
ENST00000322843.3	Ensembl	ENSP00000322953.3	13	Standard
ENST00000933169.1	Ensembl	ENSP00000603228.1	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

acetylgalactosaminyltransferase activity
N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity

Cellular Component

integral component of membrane
Golgi cisterna membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000266383
Coding exons: 20
Length: 103146
Individuals with no LoFs: 125613
Homozygous LoFs: 0
Heterozygous LoFs: 135
Defined: 125748
p: 0.000537

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.710	544	593	0.918	0.0000365	6499
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00052	0.00049	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0014	0.0014	notable
Finnish	0.00037	0.00037	rare
European (Non-Finnish)	0.00058	0.00054	rare
South Asian	0.00065	0.00065	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.319

Gene Damage Prediction

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