B3GNTL1

UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase like 1, the group of Glycosyltransferase family 2

Basic information

Region (hg38): 17:82942148-83051809

Links

ENSG00000175711 ∙ NCBI:146712 ∙ OMIM:615337 ∙ HGNC:21727 ∙ Uniprot:Q67FW5 ∙ 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 B3GNTL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GNTL1 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			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	13		14
Total	0	0	29	14	1

Variants in B3GNTL1

This is a list of pathogenic ClinVar variants found in the B3GNTL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-82942429-T-C			Likely benign (Sep 23, 2023)
17-82942431-G-C			Likely benign (Feb 13, 2023)
17-82942433-C-T			Likely benign (Oct 13, 2023)
17-82942435-TGTCTC-T			Likely benign (Jan 31, 2024)
17-82942438-C-T			Likely benign (Apr 22, 2023)
17-82942440-C-A			Likely benign (Feb 14, 2023)
17-82942440-C-G			Likely benign (Apr 28, 2023)
17-82942440-CTT-C			Likely benign (Jun 29, 2023)
17-82942441-T-C			Likely benign (Aug 16, 2023)
17-82942442-T-C			Likely benign (Dec 02, 2021)
17-82942443-C-T			Likely benign (Sep 22, 2023)
17-82942444-T-C			Likely benign (Sep 03, 2023)
17-82942460-C-T			Likely benign (Jan 04, 2024)
17-82946930-C-G		not specified	Uncertain significance (Jun 23, 2023)
17-82946964-A-G		not specified	Uncertain significance (Jul 19, 2023)
17-82956723-C-T		not specified	Uncertain significance (Sep 26, 2022)
17-82956724-G-C		not specified	Uncertain significance (Nov 21, 2022)
17-82956753-C-T		not specified	Uncertain significance (Jul 11, 2023)
17-82956765-C-G		not specified	Uncertain significance (Jun 11, 2021)
17-82957192-C-T		not specified	Uncertain significance (Apr 07, 2022)
17-82957206-C-A		not specified	Uncertain significance (Jan 05, 2022)
17-82957231-C-T		not specified	Uncertain significance (Oct 05, 2021)
17-82957364-G-T		not specified	Uncertain significance (Jun 09, 2022)
17-82957382-A-G			Benign (Dec 26, 2018)
17-82957397-G-A		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B3GNTL1	protein_coding	protein_coding	ENST00000320865	12	109656

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.07e-28	0.00000254	125559	0	189	125748	0.000752

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0166	230	229	1.00	0.0000155	2331
Missense in Polyphen		68	66.304	1.0256		678
Synonymous	-1.50	110	91.7	1.20	0.00000686	679
Loss of Function	-1.80	36	26.1	1.38	0.00000156	246

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00407	0.00407
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.00310	0.00310
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000354	0.000343
Middle Eastern	0.00310	0.00310
South Asian	0.000531	0.000523
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative glycosyltransferase. {ECO:0000305}.
• Pathway: Post-translational protein modification;Metabolism of proteins;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.851
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62.14

Haploinsufficiency Scores

• pHI: 0.158
• hipred: N
• hipred_score: 0.251
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.485

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B3gntl1

Gene ontology

• Molecular function: transferase activity, transferring glycosyl groups