B4GALT5

beta-1,4-galactosyltransferase 5, the group of Beta 4-glycosyltransferases

Basic information

Region (hg38): 20:49632945-49713878

Links

ENSG00000158470 ∙ NCBI:9334 ∙ OMIM:604016 ∙ HGNC:928 ∙ Uniprot:O43286 ∙ 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 B4GALT5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B4GALT5 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	3
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	10	0	4

Variants in B4GALT5

This is a list of pathogenic ClinVar variants found in the B4GALT5 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-49636332-C-G		not specified	Uncertain significance (Jan 05, 2022)
20-49636457-T-C		not specified	Uncertain significance (Apr 22, 2022)
20-49637431-G-A		not specified	Uncertain significance (Dec 20, 2021)
20-49639744-C-T		not specified	Uncertain significance (Sep 16, 2021)
20-49639776-G-A			Benign (Apr 04, 2018)
20-49639787-C-T		not specified	Uncertain significance (Nov 10, 2024)
20-49640538-T-A		not specified	Uncertain significance (Jun 12, 2023)
20-49642499-C-T		not specified	Uncertain significance (Nov 10, 2022)
20-49642593-G-A			Benign (Apr 10, 2018)
20-49643588-T-C		not specified	Uncertain significance (Feb 08, 2023)
20-49643628-C-T		not specified	Uncertain significance (May 13, 2024)
20-49643642-T-C		not specified	Uncertain significance (Sep 17, 2021)
20-49656596-G-A			Benign (Jun 19, 2018)
20-49656622-C-T		not specified	Uncertain significance (Nov 14, 2023)
20-49656683-C-G		not specified	Uncertain significance (May 15, 2024)
20-49713631-G-A			Benign (Apr 10, 2018)
20-49713638-G-A		not specified	Uncertain significance (Nov 07, 2022)
20-49713656-C-T		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B4GALT5	protein_coding	protein_coding	ENST00000371711	9	80934

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00111	125742	0	4	125746	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.37	126	226	0.557	0.0000126	2552
Missense in Polyphen		30	101.99	0.29413		1109
Synonymous	0.182	81	83.1	0.975	0.00000473	724
Loss of Function	4.12	0	19.7	0.00	9.62e-7	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

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. {ECO:0000269|PubMed:9435216}.
• Pathway: Mucin type O-glycan biosynthesis - 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;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;N-Glycan biosynthesis;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.0764
• rvis_EVS: 0.19
• rvis_percentile_EVS: 67.03

Haploinsufficiency Scores

• pHI: 0.284
• hipred: Y
• hipred_score: 0.646
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.186

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B4galt5
• Phenotype: 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: O-glycan processing;keratan sulfate biosynthetic process;poly-N-acetyllactosamine biosynthetic process
• Cellular component: Golgi membrane;integral component of membrane;Golgi cisterna membrane
• Molecular function: beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity;N-acetyllactosamine synthase activity;galactosyltransferase activity;metal ion binding