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.

not_specified (47 variants)
not_provided (2 variants)

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. These statistics are base on transcript: NM_000145236.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			45 clinvar	3 clinvar		48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	45	4	0

Loading clinvar variants...

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