B4GALT5

protein-coding

beta-1,4-galactosyltransferase 5, 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 function of the enzyme encoded by this gene is not clear. This gene was previously designated as B4GALT4 but was renamed to B4GALT5. In the literature it is also referred to as beta4GalT2. [provided by RefSeq, Jul 2008]

MANE transcript

NM_004776.4

Inheritance

—

ClinVar variants

U:28B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr20:49,632,945-49,713,878

External References & Databases

Ensembl (ENSG00000158470)

Transcript & Mutation Effects

hg38 • Region Span ~80.9 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 B4GALT5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 27

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004776.4. 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					3 clinvar	3
missense			27 clinvar	2 clinvar		29
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	28	2	3	33

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004776.4	RefSeq	NP_004767.1	9	MANE Select
ENST00000371711.4	Ensembl	ENSP00000360776.4	9	MANE Select
ENST00000921904.1	Ensembl	ENSP00000591963.1	8	Standard
ENST00000921904.2	Ensembl	ENSP00000591963.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Mucin type O-glycan biosynthesis - Homo sapiens (human)
Metabolism of carbohydrates
Keratan sulfate biosynthesis
Keratan sulfate/keratin metabolism
Glycosaminoglycan metabolism

Biological Process

O-glycan processing
keratan sulfate biosynthetic process
poly-N-acetyllactosamine 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
integral component of membrane
Golgi cisterna membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371711
Coding exons: 9
Length: 80934
Individuals with no LoFs: 125742
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125746
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.37	126	226	0.557	0.0000126	2552
Missense (PolyPhen)		30	101.99	0.29413		1109
Synonymous	0.182	81	83.1	0.975	0.00000473	724
Loss of Function	4.12	0	19.7	0.00	9.62e-7	228

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	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. {ECO:0000269|PubMed:9435216}.;

Recessive Scores

pRec: 0.140

Intolerance Scores

LoFtool: 0.0764
RVIS EVS: 0.19
RVIS percentile EVS: 67.03

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.186

Gene Damage Prediction

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