GBGT1

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

Basic information

Region (hg38): 9:133152947-133163933

Links

ENSG00000148288 ∙ NCBI:26301 ∙ OMIM:606074 ∙ HGNC:20460 ∙ Uniprot:Q8N5D6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GBGT1 gene.

• Inborn genetic diseases (20 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GBGT1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			17	3		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	3	1

Variants in GBGT1

This is a list of pathogenic ClinVar variants found in the GBGT1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-133153620-C-T		not specified	Uncertain significance (Feb 28, 2023)
9-133153621-G-A		not specified	Uncertain significance (Aug 11, 2022)
9-133153672-C-T		not specified	Uncertain significance (Apr 13, 2022)
9-133153708-A-C		not specified	Uncertain significance (Aug 15, 2023)
9-133153764-T-C		not specified	Uncertain significance (Oct 12, 2021)
9-133153767-G-A		not specified	Uncertain significance (Aug 01, 2022)
9-133153780-T-C		not specified	Uncertain significance (Jan 08, 2024)
9-133153870-C-A		not specified	Uncertain significance (May 25, 2022)
9-133153899-T-C		not specified	Uncertain significance (Mar 24, 2023)
9-133153915-G-A		not specified	Uncertain significance (Dec 20, 2021)
9-133153924-C-T		not specified	Likely benign (Nov 17, 2022)
9-133153925-G-A			Benign (Apr 09, 2018)
9-133153980-G-A		not specified	Uncertain significance (Dec 15, 2023)
9-133154031-C-T		not specified	Uncertain significance (Oct 18, 2021)
9-133154076-C-T		not specified	Uncertain significance (Oct 14, 2023)
9-133154077-G-A		not specified	Uncertain significance (Oct 26, 2021)
9-133154125-T-C		not specified	Uncertain significance (Nov 07, 2022)
9-133154155-C-T		not specified	Likely benign (Jul 29, 2022)
9-133154170-G-C		not specified	Uncertain significance (Jun 07, 2023)
9-133154199-C-T		not specified	Likely benign (Oct 12, 2022)
9-133154205-C-T		not specified	Uncertain significance (Mar 06, 2023)
9-133154257-T-C		not specified	Uncertain significance (May 03, 2023)
9-133155185-C-T		not specified	Uncertain significance (Sep 13, 2023)
9-133155205-A-G		not specified	Uncertain significance (Aug 06, 2021)
9-133156022-C-T		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GBGT1	protein_coding	protein_coding	ENST00000372040	6	10993

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.08e-10	0.0483	125691	0	51	125742	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0443	215	217	0.992	0.0000134	2247
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000460	0.000460
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000551	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000275	0.000273
Middle Eastern	0.0000551	0.0000544
South Asian	0.000327	0.000327
Other	0.000164	0.000163

dbNSFP

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.
• Pathway: Glycosphingolipid biosynthesis - globo and isoglobo series - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.163

Intolerance Scores

• loftool: 0.846
• rvis_EVS: 1.67
• rvis_percentile_EVS: 96.3

Haploinsufficiency Scores

• pHI: 0.0962
• hipred: N
• hipred_score: 0.219
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.144

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gbgt1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: carbohydrate metabolic process;protein glycosylation;glycolipid biosynthetic process;lipid glycosylation
• Cellular component: Golgi membrane;Golgi apparatus;integral component of membrane;vesicle
• Molecular function: transferase activity, transferring glycosyl groups;metal ion binding;globoside alpha-N-acetylgalactosaminyltransferase activity