B3GNT7

UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7, the group of Beta 3-glycosyltransferases

Basic information

Region (hg38): 2:231395671-231408799

Links

ENSG00000156966 ∙ NCBI:93010 ∙ OMIM:615313 ∙ HGNC:18811 ∙ Uniprot:Q8NFL0 ∙ 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 B3GNT7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GNT7 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			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	3	0

Variants in B3GNT7

This is a list of pathogenic ClinVar variants found in the B3GNT7 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-231397741-G-A		not specified	Likely benign (Aug 29, 2024)
2-231397748-G-A		not specified	Uncertain significance (Jul 06, 2021)
2-231397777-G-A			Uncertain significance (Oct 01, 2022)
2-231397816-C-G		not specified	Uncertain significance (Mar 08, 2024)
2-231397883-T-C		not specified	Uncertain significance (Mar 29, 2022)
2-231397892-C-G		not specified	Uncertain significance (Feb 19, 2025)
2-231397930-C-T		not specified	Uncertain significance (Aug 10, 2024)
2-231398033-A-T		not specified	Uncertain significance (Jul 27, 2024)
2-231398039-A-C		not specified	Uncertain significance (Aug 28, 2024)
2-231398044-C-T		not specified	Uncertain significance (Dec 28, 2022)
2-231398071-C-T		not specified	Uncertain significance (Oct 26, 2022)
2-231398098-C-G		not specified	Uncertain significance (Jul 05, 2023)
2-231398170-G-A		not specified	Uncertain significance (Sep 27, 2022)
2-231398180-G-A		not specified	Uncertain significance (Aug 14, 2024)
2-231398213-G-A		not specified	Uncertain significance (Apr 18, 2023)
2-231398275-C-T		not specified	Uncertain significance (Jul 05, 2022)
2-231398323-G-A		not specified	Uncertain significance (Jul 19, 2023)
2-231398347-G-A		not specified	Uncertain significance (Oct 26, 2024)
2-231398351-C-A		not specified	Uncertain significance (Aug 20, 2023)
2-231398366-C-G		not specified	Uncertain significance (Jun 16, 2023)
2-231398379-C-G		not specified	Uncertain significance (Jun 13, 2023)
2-231398389-A-G		not specified	Uncertain significance (May 23, 2023)
2-231398567-A-T		not specified	Uncertain significance (Jan 15, 2025)
2-231398587-G-A		not specified	Likely benign (Jun 07, 2023)
2-231398620-G-A		not specified	Uncertain significance (Sep 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B3GNT7	protein_coding	protein_coding	ENST00000287590	2	5622

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.706	0.293	124620	0	15	124635	0.0000602

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.19	221	277	0.799	0.0000195	2587
Missense in Polyphen		65	111.86	0.58108		1074
Synonymous	-0.401	141	135	1.04	0.0000104	850
Loss of Function	2.79	2	12.7	0.157	6.24e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000249	0.000247
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.0000357	0.0000354
Middle Eastern	0.00	0.00
South Asian	0.0000331	0.0000327
Other	0.000520	0.000495

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in keratane sulfate biosynthesis. Transfers N-acetylgalactosamine on to keratan sulfate-related glycans. May play a role in preventing cells from migrating out of the original tissues and invading surrounding tissues. {ECO:0000269|PubMed:12061784}.
• Pathway: Glycosaminoglycan biosynthesis - keratan sulfate - Homo sapiens (human);Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;Post-translational protein modification;Metabolism of proteins;Metabolism;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.354
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.34

Haploinsufficiency Scores

• pHI: 0.432
• hipred: Y
• hipred_score: 0.684
• ghis: 0.393

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.220

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B3gnt7
• Phenotype: vision/eye phenotype; immune system phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: protein glycosylation;O-glycan processing;keratan sulfate biosynthetic process;poly-N-acetyllactosamine 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;N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity