B3GALNT1

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

Basic information

Region (hg38): 3:161083883-161105411

Previous symbols: [ "B3GALT3" ]

Links

ENSG00000169255 ∙ NCBI:8706 ∙ OMIM:603094 ∙ HGNC:918 ∙ Uniprot:O75752 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Blood group, globoside system; Blood group, P1PK system	BG	Hematologic	Variants associated with a blood group may be important in specific situations (eg, related to transfusion)	Hematologic; Neurologic	12023287

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the B3GALNT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GALNT1 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						0
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				4	2	6
Total	0	0	10	4	2

Variants in B3GALNT1

This is a list of pathogenic ClinVar variants found in the B3GALNT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-161085766-T-C		not specified	Uncertain significance (Oct 01, 2024)
3-161085944-C-T		p phenotype	Affects (Aug 16, 2002)
3-161085958-T-G		p phenotype	Affects (Aug 16, 2002)
3-161085983-C-G		not specified	Uncertain significance (Jun 24, 2022)
3-161085989-T-C		not specified	Uncertain significance (Dec 12, 2023)
3-161085994-T-C		not specified	Uncertain significance (Jun 28, 2024)
3-161086053-G-C		not specified	Uncertain significance (Oct 26, 2022)
3-161086090-G-T		not specified	Uncertain significance (Nov 23, 2021)
3-161086184-C-T		not specified	Uncertain significance (Nov 22, 2021)
3-161086217-C-CT		p phenotype	Affects (Aug 16, 2002)
3-161086241-T-C		not specified	Uncertain significance (Nov 13, 2024)
3-161086256-T-C		not specified	Uncertain significance (Dec 26, 2023)
3-161086339-A-C		not specified	Uncertain significance (Jun 22, 2023)
3-161086421-C-A		not specified	Uncertain significance (Nov 21, 2024)
3-161086501-G-A		not specified	Uncertain significance (Dec 04, 2024)
3-161086524-A-T		not specified	Uncertain significance (Jun 02, 2024)
3-161086532-G-A		not specified	Uncertain significance (Nov 08, 2022)
3-161086553-G-A		p phenotype	Affects (Aug 16, 2002)
3-161086558-G-A		not specified	Uncertain significance (Mar 20, 2023)
3-161086630-T-C		not specified	Uncertain significance (Nov 21, 2024)
3-161086693-C-A		not specified	Uncertain significance (Oct 04, 2022)
3-161086781-C-T		B3GALNT1-related disorder	Benign (Oct 15, 2019)
3-161090047-C-A		B3GALNT1-related disorder	Likely benign (Mar 22, 2019)
3-161090059-A-T		B3GALNT1-related disorder	Benign (Oct 15, 2019)
3-161101213-G-A		B3GALNT1-related disorder	Likely benign (Mar 22, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B3GALNT1	protein_coding	protein_coding	ENST00000392781	1	21502

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00221	0.927	125693	0	54	125747	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.749	145	173	0.840	0.00000859	2190
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00106	0.00106
European (Non-Finnish)	0.000169	0.000167
Middle Eastern	0.000109	0.000109
South Asian	0.000204	0.000196
Other	0.000326	0.000326

dbNSFP

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}.
• Pathway: 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;Glycosphingolipid metabolism;Sphingolipid metabolism (Consensus)

Recessive Scores

• pRec: 0.180

Intolerance Scores

• loftool: 0.278
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.763
• hipred: N
• hipred_score: 0.418
• ghis: 0.589

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0707

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B3galnt1
• Phenotype: normal 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); reproductive system phenotype

Gene ontology

• Biological process: protein glycosylation;protein N-linked glycosylation;glycosphingolipid metabolic process;oligosaccharide biosynthetic process
• Cellular component: Golgi membrane;endoplasmic reticulum;Golgi apparatus;integral component of membrane
• Molecular function: acetylgalactosaminyltransferase activity;UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity;galactosylgalactosylglucosylceramide beta-D-acetylgalactosaminyltransferase activity