B3GALNT1

protein-coding

beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group), the group of Beta 3-glycosyltransferases|Blood group antigens

Gene summary

This gene is a member of the beta-1,3-galactosyltransferase (beta3GalT) gene family. This family encodes type II membrane-bound glycoproteins with diverse enzymatic functions using different donor substrates (UDP-galactose and UDP-N-acetylglucosamine) and different acceptor sugars (N-acetylglucosamine, galactose, N-acetylgalactosamine). The beta3GalT genes are distantly related to the Drosophila Brainiac gene and have the protein coding sequence contained in a single exon. The beta3GalT proteins also contain conserved sequences not found in the beta4GalT or alpha3GalT proteins. The carbohydrate chains synthesized by these enzymes are designated as type 1, whereas beta4GalT enzymes synthesize type 2 carbohydrate chains. The ratio of type 1:type 2 chains changes during embryogenesis. By sequence similarity, the beta3GalT genes fall into at least two groups: beta3GalT4 and 4 other beta3GalT genes (beta3GalT1-3, beta3GalT5). The encoded protein of this gene does not use N-acetylglucosamine as an acceptor sugar at all. [provided by RefSeq, Mar 2017]

Previous symbols:

B3GALT3

MANE transcript

NM_003781.4

Inheritance

ClinVar variants

U:35B:1

Top phenotype

Blood group, globoside system; Blood group, P1PK system

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr3:161,083,883-161,105,411

External References & Databases

Ensembl (ENSG00000169255)

Transcript & Mutation Effects

hg38 • Region Span ~21.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

Clinical Genomic Database (CGD)

Blood group, globoside system; Blood group, P1PK systemBG

Manifestation: Hematologic; Neurologic

Intervention: Hematologic

Rationale: Variants associated with a blood group may be important in specific situations (eg, related to transfusion)

Refs: 12023287

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to B3GALNT1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 32

p phenotypeTotal: 4

B3GALNT1-related disorderTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003781.4. 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			33 clinvar			33
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	35	1	0	36

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 312 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003781.4	RefSeq	NP_003772.1	1	MANE Select
ENST00000320474.10	Ensembl	ENSP00000323479.4	1	MANE Select
NM_001038628.2	RefSeq	NP_001033717.1	1	Standard
NM_001349130.2	RefSeq	NP_001336059.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glycosphingolipid biosynthesis - globo and isoglobo series - Homo sapiens (human)
Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human)
Metabolism of Spingolipids in ER and Golgi apparatus
Metabolism of lipids
Metabolism

Biological Process

protein glycosylation
protein N-linked glycosylation
glycosphingolipid metabolic process
oligosaccharide biosynthetic process

Molecular Function

acetylgalactosaminyltransferase activity
UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity
galactosylgalactosylglucosylceramide beta-D-acetylgalactosaminyltransferase 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: ENST00000392781
Coding exons: 1
Length: 21502
Individuals with no LoFs: 125693
Homozygous LoFs: 0
Heterozygous LoFs: 54
Defined: 125747
p: 0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.749	145	173	0.840	0.00000859	2190
Missense (PolyPhen)		25	49.6	0.50403		650
Synonymous	-0.250	70	67.4	1.04	0.00000351	614
Loss of Function	1.58	6	11.9	0.506	6.57e-7	152

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	0.00011	0.00011	rare
Finnish	0.0011	0.0011	notable
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00020	0.00020	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transfers N-acetylgalactosamine onto globotriaosylceramide (PubMed:10993897). Plays a critical role in preimplantation stage embryonic development (By similarity). {ECO:0000250|UniProtKB:Q920V1, ECO:0000269|PubMed:10993897}.;

Recessive Scores

pRec: 0.180

Intolerance Scores

LoFtool: 0.278
RVIS EVS: -0.25
RVIS percentile EVS: 35.75

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0707

Gene Damage Prediction

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