B3GALT4

beta-1,3-galactosyltransferase 4, the group of Beta 3-glycosyltransferases

Basic information

Region (hg38): 6:33277123-33284832

Links

ENSG00000235863 ∙ NCBI:8705 ∙ OMIM:603095 ∙ HGNC:919 ∙ Uniprot:O96024 ∙ 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 B3GALT4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GALT4 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			11	5		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	5	0

Variants in B3GALT4

This is a list of pathogenic ClinVar variants found in the B3GALT4 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-33277503-G-C		not specified	Likely benign (May 05, 2023)
6-33277546-G-A		not specified	Uncertain significance (Oct 06, 2022)
6-33277547-C-T		not specified	Uncertain significance (Feb 27, 2023)
6-33277612-A-G		not specified	Likely benign (Feb 05, 2024)
6-33277705-G-A		not specified	Likely benign (Oct 25, 2022)
6-33277850-A-G		not specified	Likely benign (Jul 31, 2023)
6-33277900-G-T		not specified	Uncertain significance (Mar 06, 2023)
6-33278015-G-C		not specified	Uncertain significance (Mar 06, 2023)
6-33278033-C-T		not specified	Uncertain significance (Sep 14, 2022)
6-33278035-C-A		not specified	Uncertain significance (Jan 10, 2023)
6-33278041-G-A		not specified	Likely benign (Dec 21, 2022)
6-33278080-G-A		not specified	Uncertain significance (Jun 07, 2024)
6-33278138-C-T		not specified	Uncertain significance (Nov 17, 2022)
6-33278266-C-T		not specified	Uncertain significance (Dec 14, 2023)
6-33278326-C-T		not specified	Uncertain significance (Nov 21, 2023)
6-33278462-G-C		not specified	Uncertain significance (Aug 16, 2021)
6-33278525-G-T		not specified	Uncertain significance (Oct 12, 2022)
6-33279308-G-A		not specified	Uncertain significance (Feb 16, 2023)
6-33279308-G-C		not specified	Uncertain significance (Nov 08, 2021)
6-33279328-T-C		not specified	Uncertain significance (Oct 29, 2021)
6-33279331-G-A		not specified	Uncertain significance (Jun 07, 2023)
6-33279334-T-G		not specified	Uncertain significance (Mar 06, 2023)
6-33279338-T-C		not specified	Uncertain significance (Mar 06, 2023)
6-33279357-G-C		not specified	Uncertain significance (Dec 18, 2023)
6-33279508-C-T		not specified	Uncertain significance (Nov 24, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B3GALT4	protein_coding	protein_coding	ENST00000451237	1	7693

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0298	0.961	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.45	166	227	0.730	0.0000130	2360
Missense in Polyphen		33	83.859	0.39352		839
Synonymous	-0.883	116	105	1.11	0.00000603	869
Loss of Function	2.28	5	14.3	0.350	9.12e-7	126

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in GM1/GD1B/GA1 ganglioside biosynthesis. {ECO:0000269|PubMed:9582303}.
• Pathway: Glycosphingolipid biosynthesis - ganglio series - Homo sapiens (human);Ganglio Sphingolipid Metabolism;Glycosphingolipid biosynthesis - ganglioseries (Consensus)

Intolerance Scores

• loftool: 0.549
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.150
• hipred: Y
• hipred_score: 0.572
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.758

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B3galt4

Gene ontology

• Biological process: ganglioside biosynthetic process;protein glycosylation
• Cellular component: Golgi membrane;endoplasmic reticulum;Golgi apparatus;integral component of membrane
• Molecular function: acetylgalactosaminyltransferase activity;UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity;ganglioside galactosyltransferase activity