B4GALT2

beta-1,4-galactosyltransferase 2, the group of Beta 4-glycosyltransferases

Basic information

Region (hg38): 1:43978943-43991170

Links

ENSG00000117411 ∙ NCBI:8704 ∙ OMIM:604013 ∙ HGNC:925 ∙ Uniprot:O60909 ∙ 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 B4GALT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B4GALT2 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						0
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			1			1
Total	0	0	27	0	0

Variants in B4GALT2

This is a list of pathogenic ClinVar variants found in the B4GALT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-43981111-C-G		not specified	Uncertain significance (Jan 09, 2024)
1-43981141-G-T		not specified	Uncertain significance (Apr 27, 2022)
1-43981204-C-T		not specified	Uncertain significance (May 14, 2024)
1-43981209-C-A		not specified	Uncertain significance (Sep 26, 2023)
1-43981242-G-A		not specified	Uncertain significance (May 03, 2023)
1-43981260-G-A		not specified	Uncertain significance (Jul 05, 2023)
1-43981290-C-T		not specified	Uncertain significance (Apr 13, 2023)
1-43981291-G-A		not specified	Uncertain significance (Jun 28, 2022)
1-43981303-G-A		not specified	Uncertain significance (Sep 21, 2023)
1-43981351-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-43981365-C-T		not specified	Uncertain significance (Mar 31, 2022)
1-43981366-G-A		not specified	Uncertain significance (Dec 20, 2023)
1-43981371-A-G		not specified	Uncertain significance (Aug 17, 2021)
1-43981384-C-T		not specified	Uncertain significance (Oct 13, 2021)
1-43981392-G-A		not specified	Uncertain significance (Oct 12, 2021)
1-43981422-G-T		not specified	Uncertain significance (Jun 24, 2022)
1-43981446-C-T		not specified	Uncertain significance (Mar 17, 2023)
1-43981689-T-C		not specified	Uncertain significance (Oct 02, 2023)
1-43981794-C-T		not specified	Uncertain significance (Jul 29, 2022)
1-43981877-A-G		not specified	Uncertain significance (Apr 07, 2022)
1-43981886-C-T		not specified	Uncertain significance (Jan 02, 2024)
1-43981898-C-T		not specified	Uncertain significance (Feb 22, 2024)
1-43985000-C-T		not specified	Uncertain significance (Aug 13, 2021)
1-43985001-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-43985351-C-T		not specified	Uncertain significance (Apr 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B4GALT2	protein_coding	protein_coding	ENST00000309519	7	12226

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.198	0.800	125739	0	5	125744	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.88	194	283	0.685	0.0000198	2583
Missense in Polyphen		69	119.58	0.57704		1045
Synonymous	-0.317	125	121	1.04	0.00000885	848
Loss of Function	2.70	4	15.5	0.259	8.28e-7	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Responsible for the synthesis of complex-type N-linked oligosaccharides in many glycoproteins as well as the carbohydrate moieties of glycolipids. Can produce lactose.
• Pathway: N-Glycan biosynthesis - Homo sapiens (human);Other types of O-glycan biosynthesis - Homo sapiens (human);Mannose type O-glycan biosynthesis - Homo sapiens (human);Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human);Galactose metabolism - Homo sapiens (human);Glycosaminoglycan biosynthesis - keratan sulfate - Homo sapiens (human);Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;Post-translational protein modification;N-Glycan antennae elongation;N-glycan antennae elongation in the medial/trans-Golgi;Metabolism of proteins;Metabolism;terminal <i>O</i>-glycans residues modification;Galactose metabolism;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;N-Glycan biosynthesis;Galactose metabolism (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.259
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.0636
• hipred: Y
• hipred_score: 0.728
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.941

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B4galt2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: carbohydrate metabolic process;protein glycosylation;memory;locomotory behavior;visual learning;keratan sulfate biosynthetic process;cerebellar Purkinje cell layer development
• Cellular component: Golgi membrane;nucleoplasm;Golgi apparatus;integral component of membrane;Golgi cisterna membrane;intracellular membrane-bounded organelle
• Molecular function: beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity;N-acetyllactosamine synthase activity;lactose synthase activity;galactosyltransferase activity;metal ion binding