B4GALT1

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

Basic information

Region (hg38): 9:33104081-33167356

Previous symbols: [ "GGTB2" ]

Links

ENSG00000086062 ∙ NCBI:2683 ∙ OMIM:137060 ∙ HGNC:924 ∙ Uniprot:P15291 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• B4GALT1-congenital disorder of glycosylation (Strong), mode of inheritance: AR
• B4GALT1-congenital disorder of glycosylation (Moderate), mode of inheritance: AR
• B4GALT1-congenital disorder of glycosylation (Supportive), mode of inheritance: AR
• B4GALT1-congenital disorder of glycosylation (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital disorder of glycosylation, type IId	AR	Hematologic; Gastrointestinal	Awareness of coagulopathies may be beneficial in terms of medical management, especially in situations such as surgery; Individuals have been described with hepatosplenomegaly and transient cholestatic jaundice, which was treated with ursodeoxycholic acid	Biochemical; Cardiovascular; Hematologic; Gastrointestinal; Musculoskeletal; Neurologic; Renal	11901181; 11930273; 21920538; 32157688; 34855475
Hepatic-metabolized agents should be avoided

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the B4GALT1 gene.

• not provided (70 variants)
• Inborn genetic diseases (17 variants)
• Congenital disorder of glycosylation (13 variants)
• not specified (9 variants)
• B4GALT1-congenital disorder of glycosylation (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B4GALT1 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			3	13	1	17
missense			36	3		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			10	15	15	40
Total	0	0	49	31	16

Variants in B4GALT1

This is a list of pathogenic ClinVar variants found in the B4GALT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-33110736-C-G		Congenital disorder of glycosylation	Uncertain significance (Jun 14, 2016)
9-33111055-AG-A		Congenital disorder of glycosylation	Uncertain significance (Jun 14, 2016)
9-33111250-CAAAA-C		Congenital disorder of glycosylation	Uncertain significance (Jun 14, 2016)
9-33111276-AAAC-A		Congenital disorder of glycosylation	Uncertain significance (Jun 14, 2016)
9-33111277-AACAAC-A		Congenital disorder of glycosylation	Uncertain significance (Jun 14, 2016)
9-33111563-GA-G		Congenital disorder of glycosylation	Likely benign (Jun 14, 2016)
9-33111580-G-A		Congenital disorder of glycosylation	Uncertain significance (Jun 14, 2016)
9-33111778-G-GA		Congenital disorder of glycosylation	Likely benign (Jun 14, 2016)
9-33112366-A-AG		Congenital disorder of glycosylation	Uncertain significance (Jun 14, 2016)
9-33112716-GTTCT-G		Congenital disorder of glycosylation	Uncertain significance (Jun 14, 2016)
9-33112740-C-G		Congenital disorder of glycosylation	Uncertain significance (Jun 14, 2016)
9-33112748-T-TA		Congenital disorder of glycosylation	Uncertain significance (Jun 14, 2016)
9-33113198-G-T			Benign (Jul 27, 2018)
9-33113300-C-T			Likely benign (Oct 29, 2019)
9-33113301-G-A			Likely benign (May 14, 2021)
9-33113324-C-T			Benign (Jun 29, 2018)
9-33113457-G-C		Inborn genetic diseases	Uncertain significance (Dec 02, 2021)
9-33113502-T-A			Uncertain significance (Apr 22, 2022)
9-33113521-T-C			Uncertain significance (Aug 26, 2021)
9-33113539-A-C		Inborn genetic diseases	Uncertain significance (Sep 01, 2021)
9-33113555-T-A			Uncertain significance (Nov 21, 2023)
9-33113555-T-C		Inborn genetic diseases	Uncertain significance (Jan 17, 2023)
9-33113591-A-G			Likely benign (Dec 15, 2023)
9-33113598-A-T		not specified	Likely benign (Dec 08, 2016)
9-33113742-G-C			Likely benign (May 24, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B4GALT1	protein_coding	protein_coding	ENST00000379731	6	63275

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0374	0.956	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.976	184	225	0.817	0.0000128	2549
Missense in Polyphen		69	98.431	0.701		1137
Synonymous	-0.472	100	94.2	1.06	0.00000499	833
Loss of Function	2.38	5	14.9	0.335	7.31e-7	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000706	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The Golgi complex form catalyzes the production of lactose in the lactating mammary gland and could also be responsible for the synthesis of complex-type N-linked oligosaccharides in many glycoproteins as well as the carbohydrate moieties of glycolipids.
• Disease: DISEASE: Congenital disorder of glycosylation 2D (CDG2D) [MIM:607091]: A multisystem disorder caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N- glycoproteins during embryonic development, differentiation, and maintenance of cell functions. {ECO:0000269|PubMed:11901181}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• 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);Galactose Metabolism;GLUT-1 deficiency syndrome;Congenital disorder of glycosylation CDG-IId;Lactose Synthesis;Galactosemia;Metabolism of Spingolipids in ER and Golgi apparatus;Neutrophil degranulation;Interaction With The Zona Pellucida;Signal Transduction;Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;Fertilization;Post-translational protein modification;N-Glycan antennae elongation;N-glycan antennae elongation in the medial/trans-Golgi;Metabolism of proteins;Reproduction;Innate Immune System;Immune System;Metabolism;Lactose synthesis;Pre-NOTCH Processing in Golgi;Pre-NOTCH Expression and Processing;Signaling by NOTCH;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: 0.210

Intolerance Scores

• loftool: 0.203
• rvis_EVS: -0.52
• rvis_percentile_EVS: 21.2

Haploinsufficiency Scores

• pHI: 0.609
• hipred: Y
• hipred_score: 0.572
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B4galt1
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); immune system phenotype; homeostasis/metabolism phenotype; cellular phenotype; respiratory 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); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; digestive/alimentary phenotype; 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: epithelial cell development;acute inflammatory response;lactose biosynthetic process;galactose metabolic process;protein N-linked glycosylation;cell adhesion;binding of sperm to zona pellucida;penetration of zona pellucida;negative regulation of cell population proliferation;oligosaccharide biosynthetic process;keratan sulfate biosynthetic process;extracellular matrix organization;positive regulation of apoptotic process;neutrophil degranulation;development of secondary sexual characteristics;leukocyte migration;protein homooligomerization;regulation of acrosome reaction;positive regulation of epithelial cell proliferation involved in wound healing;angiogenesis involved in wound healing
• Cellular component: Golgi trans cisterna;Golgi membrane;extracellular space;Golgi apparatus;plasma membrane;external side of plasma membrane;membrane;integral component of membrane;basolateral plasma membrane;desmosome;filopodium;secretory granule membrane;brush border membrane;Golgi cisterna membrane;azurophil granule membrane;extracellular exosome
• Molecular function: beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity;N-acetyllactosamine synthase activity;lactose synthase activity;galactosyltransferase activity;manganese ion binding;UDP-galactosyltransferase activity