B3GNT2

protein-coding

UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2, the group of Beta 3-glycosyltransferases|MicroRNA protein coding host genes

Gene summary

This gene encodes a member of the beta-1,3-N-acetylglucosaminyltransferase family. This enzyme is a type II transmembrane protein. It prefers the substrate of lacto-N-neotetraose, and is involved in the biosynthesis of poly-N-acetyllactosamine chains. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jan 2016]

Previous symbols:

B3GNT1

MANE transcript

NM_006577.6

Inheritance

ClinVar variants

U:32B:18

Top phenotype

B3GNT2-related disorder

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr2:62,196,115-62,224,731

External References & Databases

Ensembl (ENSG00000170340)

Transcript & Mutation Effects

hg38 • Region Span ~28.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

muscular dystrophy-dystroglycanopathyMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0018276

Submitter: PanelApp Australia

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0014120

Submitter: Genomics England PanelApp

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to B3GNT2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 31

not providedTotal: 16

B3GNT2-related disorderTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006577.6. 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				13 clinvar	2 clinvar	15
missense			32 clinvar	1 clinvar	2 clinvar	35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	32	14	4	50

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_006577.6	RefSeq	NP_006568.2	1	MANE Select
ENST00000301998.5	Ensembl	ENSP00000305595.4	1	MANE Select
NM_001319075.2	RefSeq	NP_001306004.1	1	Standard
ENST00000405767.1	Ensembl	ENSP00000384692.1	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)
Glycosaminoglycan biosynthesis - keratan sulfate - Homo sapiens (human)
Metabolism of carbohydrates
Keratan sulfate biosynthesis
Keratan sulfate/keratin metabolism

Biological Process

protein glycosylation
axon guidance
sensory perception of smell
O-glycan processing
keratan sulfate biosynthetic process

Molecular Function

protein binding
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: ENST00000301998
Coding exons: 1
Length: 28619
Individuals with no LoFs: 125687
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125689
p: 0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.28	168	221	0.759	0.0000121	2644
Missense (PolyPhen)		37	88.579	0.41771		1057
Synonymous	0.154	89	90.9	0.979	0.00000553	753
Loss of Function	2.87	1	11.5	0.0871	6.38e-7	145

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Beta-1,3-N-acetylglucosaminyltransferase involved in the synthesis of poly-N-acetyllactosamine. Catalyzes the initiation and elongation of poly-N-acetyllactosamine chains. Shows a marked preference for Gal(beta1-4)Glc(NAc)-based acceptors (PubMed:9892646). Probably constitutes the main polylactosamine synthase. {ECO:0000269|PubMed:11042166, ECO:0000269|PubMed:25279697, ECO:0000269|PubMed:9892646}.;

Recessive Scores

pRec: 0.123

Intolerance Scores

LoFtool: 0.207
RVIS EVS: -0.07
RVIS percentile EVS: 48.35

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): K
Indispensability pred.: N
Indispensability score: 0.231

Gene Damage Prediction

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