B4GALNT4

beta-1,4-N-acetyl-galactosaminyltransferase 4, the group of Beta 4-glycosyltransferases

Basic information

Region (hg38): 11:369499-382117

Links

ENSG00000182272 ∙ NCBI:338707 ∙ OMIM:618560 ∙ HGNC:26315 ∙ Uniprot:Q76KP1 ∙ 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 B4GALNT4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B4GALNT4 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				4	1	5
missense			100	7	1	108
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	101	11	2

Variants in B4GALNT4

This is a list of pathogenic ClinVar variants found in the B4GALNT4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-369916-A-G		not specified	Uncertain significance (Jul 09, 2024)
11-369948-G-C		not specified	Uncertain significance (Jan 19, 2024)
11-369949-G-A		not specified	Uncertain significance (Aug 21, 2024)
11-372126-A-G		not specified	Likely benign (Nov 15, 2021)
11-372145-G-C		not specified	Uncertain significance (Jan 20, 2025)
11-372147-G-A		not specified	Uncertain significance (Sep 03, 2024)
11-372148-T-C		not specified	Uncertain significance (Jul 27, 2021)
11-372153-G-A		not specified	Uncertain significance (Mar 14, 2023)
11-372196-G-T		not specified	Uncertain significance (Dec 03, 2024)
11-372207-C-A		not specified	Uncertain significance (Mar 06, 2023)
11-372211-C-A		not specified	Uncertain significance (Dec 25, 2024)
11-372211-C-T		not specified	Likely benign (Aug 31, 2022)
11-372683-A-G		not specified	Uncertain significance (Jun 25, 2024)
11-372696-G-C		not specified	Likely benign (Mar 17, 2023)
11-372696-G-T		not specified	Uncertain significance (Nov 14, 2024)
11-373027-C-T		not specified	Uncertain significance (Mar 20, 2023)
11-373053-G-A		not specified	Uncertain significance (Jul 26, 2024)
11-373061-C-T			Benign (Dec 31, 2019)
11-373220-G-C		not specified	Uncertain significance (Nov 24, 2024)
11-373252-G-C		not specified	Uncertain significance (Feb 08, 2025)
11-373265-G-T		not specified	Uncertain significance (May 17, 2023)
11-373286-G-A			not provided (-)
11-373468-C-T		not specified	Uncertain significance (Jul 30, 2024)
11-373763-C-T		not specified	Uncertain significance (Jan 24, 2023)
11-373799-G-A		not specified	Uncertain significance (Aug 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B4GALNT4	protein_coding	protein_coding	ENST00000329962	20	12321

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000225	1.00	125429	0	134	125563	0.000534

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.36	433	595	0.728	0.0000452	6539
Missense in Polyphen		91	146.58	0.6208		1627
Synonymous	-0.587	284	272	1.05	0.0000226	2176
Loss of Function	3.84	18	46.1	0.390	0.00000268	492

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00136	0.00136
Ashkenazi Jewish	0.00122	0.000895
East Asian	0.000405	0.000381
Finnish	0.00180	0.00166
European (Non-Finnish)	0.000404	0.000361
Middle Eastern	0.000405	0.000381
South Asian	0.000134	0.000131
Other	0.000407	0.000327

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transfers N-acetylgalactosamine (GalNAc) from UDP-GalNAc to N-acetylglucosamine-beta-benzyl with a beta-1,4-linkage to form N,N'-diacetyllactosediamine, GalNAc-beta-1,4-GlcNAc structures in N-linked glycans and probably O-linked glycans.

Recessive Scores

• pRec: 0.0924

Haploinsufficiency Scores

• pHI: 0.135
• hipred: Y
• hipred_score: 0.725
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.103

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B4galnt4

Gene ontology

• Cellular component: integral component of membrane;Golgi cisterna membrane
• Molecular function: acetylgalactosaminyltransferase activity;N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity