B4GALNT2

beta-1,4-N-acetyl-galactosaminyltransferase 2, the group of Beta 4-glycosyltransferases

Basic information

Region (hg38): 17:49132459-49176840

Previous symbols: [ "GALGT2" ]

Links

ENSG00000167080 ∙ NCBI:124872 ∙ OMIM:111730 ∙ HGNC:24136 ∙ Uniprot:Q8NHY0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Sid blood group antigen	BG	Hematologic	Variants associated with a blood group may be important in specific situations (eg, related to transfusion)	Hematologic	N/A

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the B4GALNT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B4GALNT2 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			28	4	2	34
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	28	4	3

Variants in B4GALNT2

This is a list of pathogenic ClinVar variants found in the B4GALNT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-49132804-C-A			Likely benign (May 01, 2022)
17-49133051-G-A		not specified	Uncertain significance (Nov 14, 2023)
17-49133084-G-A		not specified	Uncertain significance (Aug 01, 2022)
17-49133102-C-T		not specified	Uncertain significance (Jan 29, 2024)
17-49133126-G-C		not specified	Uncertain significance (Apr 25, 2022)
17-49133177-C-T		not specified	Uncertain significance (Apr 09, 2024)
17-49133190-T-G		not specified	Uncertain significance (Jun 07, 2024)
17-49141281-A-C		not specified	Likely benign (Apr 07, 2023)
17-49141303-T-C		not specified	Likely benign (Feb 14, 2023)
17-49141359-G-C		not specified	Uncertain significance (Dec 14, 2023)
17-49141366-C-G		not specified	Uncertain significance (Jan 23, 2024)
17-49141384-T-C		not specified	Likely benign (Nov 29, 2023)
17-49141414-G-A		not specified	Likely benign (Jul 26, 2022)
17-49142071-C-A		not specified	Uncertain significance (Dec 01, 2022)
17-49142142-G-T		not specified	Uncertain significance (Nov 21, 2022)
17-49142144-C-G		not specified	Uncertain significance (May 11, 2022)
17-49142166-A-G		not specified	Uncertain significance (Jun 22, 2023)
17-49152892-C-T		not specified	Uncertain significance (Dec 13, 2023)
17-49156590-C-T		not specified	Uncertain significance (Dec 15, 2023)
17-49159121-C-G		not specified	Uncertain significance (Feb 22, 2023)
17-49159170-A-G		not specified	Uncertain significance (Aug 16, 2022)
17-49159215-T-C		not specified	Uncertain significance (Jun 01, 2023)
17-49160611-G-C		not specified	Uncertain significance (Dec 03, 2021)
17-49160618-C-G		not specified	Uncertain significance (May 30, 2023)
17-49164212-C-G		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B4GALNT2	protein_coding	protein_coding	ENST00000300404	11	37530

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.74e-17	0.00345	125249	2	497	125748	0.00199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.389	297	316	0.938	0.0000176	3655
Missense in Polyphen		110	103.16	1.0663		1210
Synonymous	0.152	131	133	0.983	0.00000803	1149
Loss of Function	-0.235	25	23.8	1.05	0.00000116	269

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0166	0.0165
Ashkenazi Jewish	0.00359	0.00358
East Asian	0.000660	0.000653
Finnish	0.0000935	0.0000924
European (Non-Finnish)	0.00132	0.00130
Middle Eastern	0.000660	0.000653
South Asian	0.000360	0.000359
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the synthesis of the Sd(a) antigen (Sia- alpha2,3-[GalNAc-beta1,4]Gal-beta1,4-GlcNAc), a carbohydrate determinant expressed on erythrocytes, the colonic mucosa and other tissues. Transfers a beta-1,4-linked GalNAc to the galactose residue of an alpha-2,3-sialylated chain. {ECO:0000269|PubMed:12678917, ECO:0000269|PubMed:14688233}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Asparagine N-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.284

Intolerance Scores

• loftool: 0.975
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.69

Haploinsufficiency Scores

• pHI: 0.0578
• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.226

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B4galnt2
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; digestive/alimentary phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: UDP-N-acetylglucosamine metabolic process;protein N-linked glycosylation via asparagine;UDP-N-acetylgalactosamine metabolic process;negative regulation of cell-cell adhesion;lipid glycosylation
• Cellular component: Golgi membrane;integral component of membrane;integral component of Golgi membrane
• Molecular function: acetylgalactosaminyltransferase activity