B3GALNT2

beta-1,3-N-acetylgalactosaminyltransferase 2, the group of Beta 3-glycosyltransferases

Basic information

Region (hg38): 1:235447189-235504452

Links

ENSG00000162885 ∙ NCBI:148789 ∙ OMIM:610194 ∙ HGNC:28596 ∙ Uniprot:Q8NCR0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 (Strong), mode of inheritance: AR
• muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 (Strong), mode of inheritance: AR
• muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 (Moderate), mode of inheritance: AR
• muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 (Strong), mode of inheritance: AR
• muscular dystrophy-dystroglycanopathy, type A (Supportive), mode of inheritance: AR
• muscle-eye-brain disease (Supportive), mode of inheritance: AR
• autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
• intellectual disability (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 11	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Cardiovascular; Musculoskeletal; Neurologic; Ophthalmologic	23453667

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the B3GALNT2 gene.

• Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 (371 variants)
• not provided (138 variants)
• Inborn genetic diseases (27 variants)
• not specified (22 variants)
• Hypoparathyroidism-retardation-dysmorphism syndrome (13 variants)
• Encephalopathy, progressive, with amyotrophy and optic atrophy (1 variants)
• Autosomal recessive Kenny-Caffey syndrome (1 variants)
• B3GALNT2-related condition (1 variants)
• - (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GALNT2 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	87		88
missense		1	176	2	2	181
nonsense	8	3	2	1		14
start loss			1			1
frameshift	12	1	3	1		17
inframe indel		1	7			8
splice donor/acceptor (+/-2bp)	2	9	1			12
splice region			15	15	1	31
non coding			19	71	36	126
Total	22	15	210	162	38

Highest pathogenic variant AF is 0.0000197

Variants in B3GALNT2

This is a list of pathogenic ClinVar variants found in the B3GALNT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-235448125-G-A			Likely benign (Jul 09, 2018)
1-235448206-A-C			Likely benign (Oct 06, 2019)
1-235448220-CA-C			Benign (Oct 06, 2019)
1-235448220-C-CA			Benign (Oct 05, 2019)
1-235448220-C-CAA			Benign (Oct 07, 2019)
1-235448220-C-CAAA			Benign (Oct 07, 2019)
1-235448329-C-A			Likely benign (Jul 07, 2023)
1-235448330-T-G			Likely benign (Jan 24, 2023)
1-235448331-T-G			Likely benign (Jul 29, 2023)
1-235448332-T-C			Likely benign (Aug 31, 2023)
1-235448335-T-C		Hypoparathyroidism-retardation-dysmorphism syndrome	Benign/Likely benign (Jan 31, 2024)
1-235448337-G-A			Likely benign (Dec 15, 2023)
1-235448341-T-TTTGA			Likely benign (Oct 05, 2023)
1-235448350-C-T			Likely benign (Oct 22, 2023)
1-235448358-C-CAATTCAAAAGGTGAAGGGATTGCTG		Encephalopathy, progressive, with amyotrophy and optic atrophy	Uncertain significance (May 26, 2020)
1-235448365-A-G			Likely benign (Dec 27, 2022)
1-235448368-G-A			Likely benign (Jun 14, 2022)
1-235448371-G-GAAGGGATTGCTGTCACGTCTTCTCAAAGTTCCT		Inborn genetic diseases	Uncertain significance (Sep 20, 2022)
1-235448374-G-A			Likely benign (Sep 27, 2023)
1-235448377-A-T			Likely benign (May 19, 2023)
1-235448378-T-C			Likely benign (Jan 21, 2024)
1-235448382-T-C			Uncertain significance (Jun 11, 2022)
1-235448387-C-T			Uncertain significance (Jun 04, 2022)
1-235448388-G-A		Inborn genetic diseases	Uncertain significance (Jul 12, 2022)
1-235448392-T-C			Likely benign (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B3GALNT2	protein_coding	protein_coding	ENST00000366600	12	54544

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.81e-7	0.982	125635	0	113	125748	0.000449

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.951	222	266	0.836	0.0000144	3252
Missense in Polyphen		53	62.714	0.84511		732
Synonymous	0.716	95	104	0.911	0.00000631	961
Loss of Function	2.20	15	27.4	0.547	0.00000147	309

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000477	0.000477
Ashkenazi Jewish	0.000993	0.000993
East Asian	0.000600	0.000598
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000660	0.000642
Middle Eastern	0.000600	0.000598
South Asian	0.0000654	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Beta-1,3-N-acetylgalactosaminyltransferase that synthesizes a unique carbohydrate structure, GalNAc-beta-1- 3GlcNAc, on N- and O-glycans. Has no galactose nor galactosaminyl transferase activity toward any acceptor substrate. Involved in alpha-dystroglycan (DAG1) glycosylation: acts coordinately with GTDC2/POMGnT2 to synthesize a GalNAc-beta3-GlcNAc-beta-terminus at the 4-position of protein O-mannose in the biosynthesis of the phosphorylated O-mannosyl trisaccharide (N-acetylgalactosamine- beta-3-N-acetylglucosamine-beta-4-(phosphate-6-)mannose), a carbohydrate structure present in alpha-dystroglycan, which is required for binding laminin G-like domain-containing extracellular proteins with high affinity. {ECO:0000269|PubMed:14724282, ECO:0000269|PubMed:23453667, ECO:0000269|PubMed:23929950}.
• Disease: DISEASE: Muscular dystrophy-dystroglycanopathy congenital with brain and eye anomalies A11 (MDDGA11) [MIM:615181]: An autosomal recessive disorder characterized by congenital muscular dystrophy associated with cobblestone lissencephaly and other brain anomalies, eye malformations, profound mental retardation, and death usually in the first years of life. Included diseases are the more severe Walker-Warburg syndrome and the slightly less severe muscle-eye-brain disease. {ECO:0000269|PubMed:23453667}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Mannose type O-glycan biosynthesis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;O-linked glycosylation (Consensus)

Intolerance Scores

• loftool: 0.850
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.5

Haploinsufficiency Scores

• pHI: 0.0926
• hipred: N
• hipred_score: 0.333
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.155

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B3galnt2

Zebrafish Information Network

• Gene name: b3galnt2
• Affected structure: skeletal muscle cell
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: protein glycosylation;protein O-linked glycosylation
• Cellular component: Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;Golgi apparatus;integral component of membrane
• Molecular function: acetylglucosaminyltransferase activity;acetylgalactosaminyltransferase activity;galactosyltransferase activity