B4GALT4

protein-coding

beta-1,4-galactosyltransferase 4, 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. The enzyme encoded by this gene appears to mainly play a role in glycolipid biosynthesis. Two alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_003778.4

Inheritance

—

ClinVar variants

U:41B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.7

Max pathogenic AF

—

Genomic locus

chr3:119,211,732-119,240,946

External References & Databases

Ensembl (ENSG00000121578)

Transcript & Mutation Effects

hg38 • Region Span ~29.2 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 B4GALT4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 40

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003778.4. 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			37 clinvar	3 clinvar		40
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	41	3	0	44

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 120 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003778.4	RefSeq	NP_003769.1	6	MANE Select
ENST00000393765.7	Ensembl	ENSP00000377360.2	6	MANE Select
NM_212543.2	RefSeq	NP_997708.1	6	Standard
ENST00000359213.7	Ensembl	ENSP00000352144.3	6	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

carbohydrate metabolic process
protein glycosylation
membrane lipid metabolic 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
integral component of membrane
Golgi cisterna membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000483209
Coding exons: 6
Length: 29372
Individuals with no LoFs: 125723
Homozygous LoFs: 0
Heterozygous LoFs: 25
Defined: 125748
p: 0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.19	143	189	0.757	0.00000995	2258
Missense (PolyPhen)		56	80.052	0.69955		944
Synonymous	0.334	69	72.6	0.950	0.00000390	643
Loss of Function	1.14	12	17.1	0.702	9.60e-7	201

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00013	0.00013	rare
South Asian	0.000099	0.000098	rare
Other	0.00017	0.00016	rare

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. {ECO:0000269|PubMed:9792633}.;

Recessive Scores

pRec: 0.125

Intolerance Scores

LoFtool: 0.659
RVIS EVS: 0.26
RVIS percentile EVS: 70.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.118

Gene Damage Prediction

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