B3GNT9

protein-coding

UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9, the group of Beta 3-glycosyltransferases

Gene summary

Predicted to enable UDP-glycosyltransferase activity. Predicted to be involved in poly-N-acetyllactosamine biosynthetic process. Predicted to be located in membrane. Predicted to be active in Golgi membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_033309.3

Inheritance

—

ClinVar variants

U:66B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.06

Max pathogenic AF

—

Genomic locus

chr16:67,148,104-67,150,998

External References & Databases

Ensembl (ENSG00000237172)

Transcript & Mutation Effects

hg38 • Region Span ~2.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to B3GNT9 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 66

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033309.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			66 clinvar	1 clinvar		67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	66	1	0	67

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033309.3	RefSeq	NP_171608.2	1	MANE Select
ENST00000449549.4	Ensembl	ENSP00000400157.3	1	MANE Select
ENST00000885217.1	Ensembl	ENSP00000555276.1	1	Standard
ENST00001112417.1	Ensembl	ENSP00000782222.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational protein modification
Metabolism of proteins
O-linked glycosylation of mucins
O-linked glycosylation

Biological Process

protein glycosylation
poly-N-acetyllactosamine biosynthetic process

Molecular Function

acetylgalactosaminyltransferase activity
galactosyltransferase activity
N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity

Cellular Component

Golgi membrane
fibrillar center
endoplasmic reticulum
Golgi apparatus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000449549
Coding exons: 1
Length: 3110
Individuals with no LoFs: 124543
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 124560
p: 0.0000682

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.09	176	222	0.794	0.0000148	2443
Missense (PolyPhen)		80	99.916	0.80067		1141
Synonymous	-0.572	122	114	1.07	0.00000880	907
Loss of Function	-0.133	7	6.63	1.06	3.18e-7	82

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00013	0.00013	rare
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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