B3GNT4

protein-coding

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

Gene summary

This gene encodes a member of the beta-1,3-N-acetylglucosaminyltransferase protein family. The encoded enzyme is involved in the biosynthesis of poly-N-acetyllactosamine chains and prefers lacto-N-neotetraose as a substrate. It is a type II transmembrane protein. [provided by RefSeq, Jul 2008]

MANE transcript

NM_030765.4

Inheritance

—

ClinVar variants

U:86B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.89

Max pathogenic AF

—

Genomic locus

chr12:122,203,681-122,208,952

External References & Databases

Ensembl (ENSG00000176383)

Transcript & Mutation Effects

hg38 • Region Span ~5.3 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 B3GNT4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 92

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030765.4. 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			1 clinvar			1
missense			84 clinvar	9 clinvar		93
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	86	9	0	95

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030765.4	RefSeq	NP_110392.1	2	MANE Select
ENST00000324189.5	Ensembl	ENSP00000319636.4	2	MANE Select
NM_001330492.2	RefSeq	NP_001317421.1	1	Standard
ENST00000535274.1	Ensembl	ENSP00000444534.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human)
Metabolism of carbohydrates
Keratan sulfate biosynthesis
Keratan sulfate/keratin metabolism
Glycosaminoglycan metabolism

Biological Process

protein glycosylation
O-glycan processing
keratan sulfate biosynthetic process
poly-N-acetyllactosamine biosynthetic process

Molecular Function

acetylgalactosaminyltransferase activity
UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity
N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity

Cellular Component

Golgi membrane
endoplasmic reticulum
Golgi apparatus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000324189
Coding exons: 2
Length: 5410
Individuals with no LoFs: 125497
Homozygous LoFs: 1
Heterozygous LoFs: 249
Defined: 125747
p: 0.000995

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-2.40	340	236	1.44	0.0000142	2419
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00068	0.00068	rare
Latino/Admixed American	0.00073	0.00072	rare
Ashkenazi Jewish	0.0022	0.0022	notable
East Asian	0.00044	0.00044	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.0012	0.0012	notable
South Asian	0.0016	0.0015	notable
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.153

Intolerance Scores

LoFtool: 0.919
RVIS EVS: 1.07
RVIS percentile EVS: 91.61

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.225

Gene Damage Prediction

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