B4GALNT4

protein-coding

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

Gene summary

Enables acetylgalactosaminyltransferase activity. Predicted to be located in Golgi cisterna membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_178537.5

Inheritance

—

ClinVar variants

U:203B:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr11:369,499-382,117

External References & Databases

Ensembl (ENSG00000182272)

Transcript & Mutation Effects

hg38 • Region Span ~12.6 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 B4GALNT4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 200

not providedTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178537.5. 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			1 clinvar	4 clinvar	1 clinvar	6
missense			196 clinvar	9 clinvar	1 clinvar	206
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	203	13	2	218

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178537.5	RefSeq	NP_848632.2	20	MANE Select
ENST00000329962.11	Ensembl	ENSP00000328277.6	20	MANE Select
ENST00000526584.2	Ensembl	ENSP00000434463.1	2	Standard
ENST00000534778.1	Ensembl	ENSP00000432372.1	2	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: ENST00000329962
Coding exons: 20
Length: 12321
Individuals with no LoFs: 125429
Homozygous LoFs: 0
Heterozygous LoFs: 134
Defined: 125563
p: 0.000534

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.36	433	595	0.728	0.0000452	6539
Missense (PolyPhen)		91	146.58	0.6208		1627
Synonymous	-0.587	284	272	1.05	0.0000226	2176
Loss of Function	3.84	18	46.1	0.390	0.00000268	492

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.0012	0.00095	notable
Ashkenazi Jewish	0.0012	0.00090	notable
East Asian	0.00040	0.00038	rare
Finnish	0.0018	0.0017	notable
European (Non-Finnish)	0.00040	0.00036	rare
South Asian	0.00013	0.00013	rare
Other	0.00041	0.00033	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.;

Recessive Scores

pRec: 0.0924

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.103

Gene Damage Prediction

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