B3GLCT

beta 3-glucosyltransferase, the group of Beta 3-glycosyltransferases

Basic information

Region (hg38): 13:31199974-31332276

Previous symbols: [ "B3GALTL" ]

Links

ENSG00000187676 ∙ NCBI:145173 ∙ OMIM:610308 ∙ HGNC:20207 ∙ Uniprot:Q6Y288 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Peters plus syndrome (Strong), mode of inheritance: AR
• Peters plus syndrome (Strong), mode of inheritance: AR
• Peters plus syndrome (Strong), mode of inheritance: AR
• Peters plus syndrome (Supportive), mode of inheritance: AR
• Peters plus syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Peters-plus syndrome	AR	Ophthalmologic	Individuals may be at high risk for ophthalmologic complications, including glaucoma, and surveillance may allow early interventions and management	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	16909395; 18199743; 18798333; 19796186; 20301637; 21067481; 21671750; 22759511

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the B3GLCT gene.

• Peters plus syndrome (195 variants)
• not provided (84 variants)
• Inborn genetic diseases (27 variants)
• not specified (17 variants)
• B3GLCT-related condition (3 variants)
• Marfanoid habitus and intellectual disability (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GLCT 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			7	29	2	38
missense		2	63	5	2	72
nonsense	2	1	2			5
start loss						0
frameshift	3	1	1			5
inframe indel			2			2
splice donor/acceptor (+/-2bp)	2	5				7
splice region			5	9	4	18
non coding			37	22	46	105
Total	7	9	112	56	50

Highest pathogenic variant AF is 0.000802

Variants in B3GLCT

This is a list of pathogenic ClinVar variants found in the B3GLCT region.

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

Position	Type	Phenotype	Significance	ClinVar
13-31200049-C-G		Peters plus syndrome	Uncertain significance (Jan 12, 2018)
13-31200101-G-A		Peters plus syndrome	Uncertain significance (Jun 19, 2023)
13-31200107-GGCTGCTCGCGCCGCCGGC-G		Peters plus syndrome	Uncertain significance (Aug 14, 2022)
13-31200112-C-T		Peters plus syndrome	Uncertain significance (Sep 07, 2022)
13-31200114-C-T		Peters plus syndrome	Uncertain significance (Jan 13, 2018)
13-31200116-C-A		Inborn genetic diseases	Uncertain significance (Dec 20, 2023)
13-31200123-G-C		Peters plus syndrome	Conflicting classifications of pathogenicity (Nov 28, 2023)
13-31200126-G-A			Likely benign (May 01, 2022)
13-31200140-T-C		Peters plus syndrome • Inborn genetic diseases	Uncertain significance (Jan 24, 2023)
13-31200145-T-G		Inborn genetic diseases	Uncertain significance (Dec 02, 2022)
13-31200159-G-A			Uncertain significance (Jan 24, 2017)
13-31200168-G-A		Peters plus syndrome	Likely benign (Oct 24, 2022)
13-31200283-C-G			Likely benign (Jul 10, 2018)
13-31215032-CT-C		not specified • Peters plus syndrome	Benign/Likely benign (Jul 14, 2021)
13-31215032-CTT-C			Benign (Dec 04, 2020)
13-31215042-T-C		not specified • Peters plus syndrome • B3GLCT-related disorder	Conflicting classifications of pathogenicity (Aug 30, 2023)
13-31215045-TTC-T		Peters plus syndrome	Likely benign (Dec 11, 2023)
13-31215050-G-T		Peters plus syndrome	Likely pathogenic (Nov 02, 2022)
13-31215067-T-A		Peters plus syndrome	Uncertain significance (Jan 12, 2018)
13-31215075-C-A		Inborn genetic diseases	Uncertain significance (Jun 29, 2022)
13-31215075-CAAAG-C		Peters plus syndrome	Pathogenic (Apr 03, 2020)
13-31215085-G-A		Peters plus syndrome	Uncertain significance (Jan 13, 2018)
13-31215093-A-G		Inborn genetic diseases	Uncertain significance (Dec 02, 2022)
13-31215094-G-C		Inborn genetic diseases	Uncertain significance (May 11, 2022)
13-31215110-C-A		Peters plus syndrome	Likely benign (Jun 23, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B3GLCT	protein_coding	protein_coding	ENST00000343307	15	132341

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.14e-17	0.0152	125450	1	297	125748	0.00119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.392	237	255	0.931	0.0000129	3264
Missense in Polyphen		83	94.793	0.87559		1187
Synonymous	-1.55	116	96.6	1.20	0.00000591	908
Loss of Function	0.347	26	28.0	0.929	0.00000125	359

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00152	0.00152
Ashkenazi Jewish	0.000699	0.000695
East Asian	0.000272	0.000272
Finnish	0.00413	0.00370
European (Non-Finnish)	0.00131	0.00129
Middle Eastern	0.000272	0.000272
South Asian	0.000426	0.000425
Other	0.000995	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: O-glucosyltransferase that transfers glucose toward fucose with a beta-1,3 linkage. Specifically glucosylates O-linked fucosylglycan on TSP type-1 domains of proteins, thereby contributing to elongation of O-fucosylglycan. {ECO:0000269|PubMed:16899492}.
• Pathway: Other types of O-glycan biosynthesis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;O-glycosylation of TSR domain-containing proteins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.138

Intolerance Scores

• rvis_EVS: 0.07
• rvis_percentile_EVS: 58.96

Haploinsufficiency Scores

• pHI: 0.222
• hipred: N
• hipred_score: 0.247
• ghis: 0.473

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: B3glct

Gene ontology

• Biological process: fucose metabolic process;protein O-linked fucosylation
• Cellular component: endoplasmic reticulum membrane;integral component of membrane
• Molecular function: acetylglucosaminyltransferase activity;transferase activity, transferring glycosyl groups