GBGT1

protein-coding

globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 (FORS blood group), the group of Blood group antigens|Glycosyltransferase family 6

Gene summary

This gene encodes a glycosyltransferase that plays a role in the synthesis of Forssman glycolipid (FG), a member of the globoseries glycolipid family. Glycolipids such as FG form attachment sites for the binding of pathogens to cells; expression of this protein may determine host tropism to microorganisms. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

MANE transcript

NM_021996.6

Inheritance

—

ClinVar variants

U:60B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.04

Max pathogenic AF

—

Genomic locus

chr9:133,152,948-133,163,933

External References & Databases

Ensembl (ENSG00000148288)

Transcript & Mutation Effects

hg38 • Region Span ~11.0 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 GBGT1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 64

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021996.6. 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					1 clinvar	1
missense			60 clinvar	7 clinvar		67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	60	7	1	68

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 72 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021996.6	RefSeq	NP_068836.2	6	MANE Select
ENST00000372040.9	Ensembl	ENSP00000361110.3	6	MANE Select
NM_001282629.2	RefSeq	NP_001269558.1	6	Standard
NM_001282632.2	RefSeq	NP_001269561.1	5	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)

Biological Process

carbohydrate metabolic process
protein glycosylation
glycolipid biosynthetic process
lipid glycosylation

Molecular Function

transferase activity, transferring glycosyl groups
metal ion binding
globoside alpha-N-acetylgalactosaminyltransferase activity

Cellular Component

Golgi membrane
Golgi apparatus
integral component of membrane
vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372040
Coding exons: 6
Length: 10993
Individuals with no LoFs: 125691
Homozygous LoFs: 0
Heterozygous LoFs: 51
Defined: 125742
p: 0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0443	215	217	0.992	0.0000134	2247
Missense (PolyPhen)		76	69.917	1.087		780
Synonymous	0.0236	87	87.3	0.997	0.00000522	699
Loss of Function	-0.140	15	14.4	1.04	6.13e-7	166

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00028	0.00027	rare
South Asian	0.00033	0.00033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalyzes the formation of some glycolipid via the addition of N-acetylgalactosamine (GalNAc) in alpha-1,3-linkage to some substrate. Glycolipids probably serve for adherence of some pathogens.;

Recessive Scores

pRec: 0.163

Intolerance Scores

LoFtool: 0.846
RVIS EVS: 1.67
RVIS percentile EVS: 96.3

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.144

Gene Damage Prediction

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