B4GALT3

protein-coding

beta-1,4-galactosyltransferase 3, the group of Beta 4-glycosyltransferases

Gene summary

This gene is one of seven beta-1,4-galactosyltransferase (beta4GalT) genes. They encode type II membrane-bound glycoproteins that appear to have exclusive specificity for the donor substrate UDP-galactose; all transfer galactose in a beta1,4 linkage to similar acceptor sugars: GlcNAc, Glc, and Xyl. Each beta4GalT has a distinct function in the biosynthesis of different glycoconjugates and saccharide structures. As type II membrane proteins, they have an N-terminal hydrophobic signal sequence that directs the protein to the Golgi apparatus and which then remains uncleaved to function as a transmembrane anchor. By sequence similarity, the beta4GalTs form four groups: beta4GalT1 and beta4GalT2, beta4GalT3 and beta4GalT4, beta4GalT5 and beta4GalT6, and beta4GalT7. This gene encodes an enzyme that may be mainly involved in the synthesis of the first N-acetyllactosamine unit of poly-N-acetyllactosamine chains. Multiple alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Dec 2010]

MANE transcript

NM_003779.4

Inheritance

—

ClinVar variants

U:45B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr1:161,171,310-161,177,968

External References & Databases

Ensembl (ENSG00000158850)

Transcript & Mutation Effects

hg38 • Region Span ~6.7 kb

Loading mutation effect viewer...

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 B4GALT3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 37

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003779.4. 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			2
missense			41 clinvar	1 clinvar		42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	45	1	0	46

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 112 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003779.4	RefSeq	NP_003770.1	6	MANE Select
ENST00000319769.10	Ensembl	ENSP00000320965.5	6	MANE Select
NM_001199873.1	RefSeq	NP_001186802.1	6	Standard
NM_001199874.1	RefSeq	NP_001186803.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

N-Glycan biosynthesis - Homo sapiens (human)
Other types of O-glycan biosynthesis - Homo sapiens (human)
Mannose type O-glycan biosynthesis - Homo sapiens (human)
Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human)
Glycosaminoglycan biosynthesis - keratan sulfate - Homo sapiens (human)

Biological Process

carbohydrate metabolic process
protein glycosylation
galactosylceramide biosynthetic process
keratan sulfate biosynthetic process

Molecular Function

beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity
N-acetyllactosamine synthase activity
galactosyltransferase activity
metal ion binding

Cellular Component

Golgi membrane
Golgi apparatus
cytosol
integral component of membrane
Golgi cisterna membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000319769
Coding exons: 6
Length: 6188
Individuals with no LoFs: 125728
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125747
p: 0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.46	188	253	0.742	0.0000165	2494
Missense (PolyPhen)		48	88.254	0.54389		949
Synonymous	0.486	88	94.0	0.936	0.00000480	883
Loss of Function	2.76	7	20.5	0.342	0.00000148	182

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00032	0.00032	rare
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Responsible for the synthesis of complex-type N-linked oligosaccharides in many glycoproteins as well as the carbohydrate moieties of glycolipids.;

Recessive Scores

pRec: 0.120

Intolerance Scores

LoFtool: 0.626
RVIS EVS: -0.16
RVIS percentile EVS: 41.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.895

Gene Damage Prediction

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