B3GNT9

Summary

B3GNT9 (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9, HGNC:28714) is a protein-coding gene on chromosome 16q22.1, encoding UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9 (Q6UX72).

Predicted to enable UDP-glycosyltransferase activity. Predicted to be involved in poly-N-acetyllactosamine biosynthetic process and protein O-linked glycosylation. Predicted to be located in Golgi apparatus and membrane. Predicted to be active in Golgi membrane.

Source: NCBI Gene 84752 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 72 total — 1 pathogenic
• MANE Select transcript: NM_033309

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28714
Approved symbol	B3GNT9
Name	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9
Location	16q22.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC4655
Ensembl gene	ENSG00000237172
Ensembl biotype	protein_coding
Entrez	84752

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000449549, ENST00000885217

RefSeq mRNA: 1 — MANE Select: NM_033309 NM_033309

CCDS: CCDS45509

Canonical transcript exons

ENST00000449549 — 2 exons

Exon	Start	End
ENSE00001593945	67148104	67150671
ENSE00002615638	67150865	67150998

Expression profiles

Bgee: expression breadth ubiquitous, 233 present calls, max score 89.95.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.3557 / max 55.0613, expressed in 1387 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
157740	8.3557	1387

Top tissues by expression

245 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
stromal cell of endometrium	CL:0002255	89.95	gold quality
cardiac muscle of right atrium	UBERON:0003379	89.59	silver quality
left ventricle myocardium	UBERON:0006566	87.39	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.32	gold quality
tendon of biceps brachii	UBERON:0008188	86.75	gold quality
parotid gland	UBERON:0001831	86.72	gold quality
buccal mucosa cell	CL:0002336	86.70	gold quality
adenohypophysis	UBERON:0002196	86.37	gold quality
myocardium	UBERON:0002349	85.80	silver quality
ascending aorta	UBERON:0001496	85.56	gold quality
pituitary gland	UBERON:0000007	85.52	gold quality
thoracic aorta	UBERON:0001515	85.47	gold quality
right coronary artery	UBERON:0001625	85.17	gold quality
left lobe of thyroid gland	UBERON:0001120	85.13	gold quality
right lobe of thyroid gland	UBERON:0001119	84.71	gold quality
thyroid gland	UBERON:0002046	84.57	gold quality
descending thoracic aorta	UBERON:0002345	84.13	gold quality
right ovary	UBERON:0002118	84.11	gold quality
left uterine tube	UBERON:0001303	83.94	gold quality
kidney epithelium	UBERON:0004819	83.53	gold quality
endocervix	UBERON:0000458	83.48	gold quality
cardiac atrium	UBERON:0002081	83.18	gold quality
right atrium auricular region	UBERON:0006631	83.07	gold quality
left coronary artery	UBERON:0001626	82.87	gold quality
aorta	UBERON:0000947	82.74	gold quality
coronary artery	UBERON:0001621	82.45	gold quality
mucosa of stomach	UBERON:0001199	82.43	gold quality
decidua	UBERON:0002450	82.41	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	82.41	gold quality
upper arm skin	UBERON:0004263	82.09	silver quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.05
E-MTAB-6058	no	3.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AP1, FOXN1, GLI2, KLF5, NKX3-1, PARP1, SP1, SP3, TBXT, THRA, TP53, USF1

miRNA regulators (miRDB)

82 targeting B3GNT9, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4713-3P	100.00	65.92	505
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-10401-5P	99.99	65.79	948
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-153-5P	99.89	73.86	6317
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-3177-5P	99.65	70.38	1174
HSA-MIR-891B	99.59	69.81	1083
HSA-MIR-2113	99.58	71.22	1521
HSA-MIR-105-5P	99.54	69.24	2060
HSA-MIR-7853-5P	99.54	69.30	2055
HSA-MIR-6727-3P	99.49	65.92	1333
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-889-3P	99.40	69.76	2103
HSA-MIR-3911	99.38	66.95	1087
HSA-MIR-5683	99.36	68.59	2083
HSA-MIR-4722-3P	99.35	65.22	1099

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	b3gnt9	ENSDARG00000041616
mus_musculus	B3gnt9	ENSMUSG00000069920
rattus_norvegicus	B3gnt9	ENSRNOG00000053895
drosophila_melanogaster	brn	FBGN0000221
caenorhabditis_elegans		WBGENE00000270
caenorhabditis_elegans		WBGENE00007096
caenorhabditis_elegans		WBGENE00017653

Paralogs (15): B3GNT7 (ENSG00000156966), B3GALT2 (ENSG00000162630), B3GALNT2 (ENSG00000162885), B3GALNT1 (ENSG00000169255), B3GNT2 (ENSG00000170340), B3GALT1 (ENSG00000172318), B3GALT6 (ENSG00000176022), B3GNT4 (ENSG00000176383), B3GNT5 (ENSG00000176597), B3GNT8 (ENSG00000177191), B3GNT3 (ENSG00000179913), B3GALT5 (ENSG00000183778), B3GNT6 (ENSG00000198488), B3GALT9 (ENSG00000214654), B3GALT4 (ENSG00000235863)

Protein

Protein identifiers

UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9 — Q6UX72 (reviewed: Q6UX72)

All UniProt accessions (1): Q6UX72

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Golgi apparatus membrane.

Similarity. Belongs to the glycosyltransferase 31 family.

RefSeq proteins (1): NP_171608* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002659	Glyco_trans_31	Family

Pfam: PF01762

UniProt features (6 total): topological domain 2, chain 1, transmembrane region 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UX72-F1	83.11	0.65

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-913709	O-linked glycosylation of mucins
R-HSA-392499	Metabolism of proteins
R-HSA-5173105	O-linked glycosylation
R-HSA-597592	Post-translational protein modification

MSigDB gene sets: 70 (showing top): chr16q22, WHITEHURST_PACLITAXEL_SENSITIVITY, CAGGTCC_MIR492, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_AMINOGLYCAN_BIOSYNTHETIC_PROCESS, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, USF_01, GOBP_AMINOGLYCAN_METABOLIC_PROCESS, RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_UP, MYCMAX_03, GOMF_HEXOSYLTRANSFERASE_ACTIVITY, MAX_01, ARNT_01, GOMF_GLYCOSYLTRANSFERASE_ACTIVITY

GO Biological Process (4): protein O-linked glycosylation (GO:0006493), poly-N-acetyllactosamine biosynthetic process (GO:0030311), obsolete protein glycosylation (GO:0006486), carbohydrate derivative biosynthetic process (GO:1901137)

GO Molecular Function (4): UDP-glycosyltransferase activity (GO:0008194), hexosyltransferase activity (GO:0016758), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757)

GO Cellular Component (3): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
O-linked glycosylation	1
Post-translational protein modification	1
Metabolism of proteins	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
glycosyltransferase activity	2
glycoprotein biosynthetic process	1
aminoglycan biosynthetic process	1
poly-N-acetyllactosamine metabolic process	1
biosynthetic process	1
carbohydrate derivative metabolic process	1
catalytic activity	1
transferase activity	1
Golgi apparatus	1
bounding membrane of organelle	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

448 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
B3GNT9	Q8WV35	Q8WV35	506
B3GNT9	QRICH1	Q2TAL8	506
B3GNT9	HHATL	Q9HCP6	491
B3GNT9	NUTM2D	Q5VT03	479
B3GNT9	MATCAP1	Q68EN5	473
B3GNT9	CHPF	Q8IZ52	462
B3GNT9	LFNG	Q8NES3	433
B3GNT9	RGS22	Q8NE09	426
B3GNT9	EXOSC1	Q9Y3B2	419
B3GNT9	MCMDC2	Q4G0Z9	411
B3GNT9	SDR42E2	A6NKP2	407
B3GNT9	ARFGAP3	Q9NP61	393
B3GNT9	EXOC3L1	Q86VI1	392
B3GNT9	FAM25A	B3EWG3	392
B3GNT9	A4GALT	Q9NPC4	392

IntAct

4 interactions, top by confidence:

A	B	Type	Score
B3GNT9	MDFI	psi-mi:“MI:0915”(physical association)	0.490
CFTR	SNHG32	psi-mi:“MI:0914”(association)	0.350

BioGRID (4): B3GNT9 (Proximity Label-MS), B3GNT9 (Negative Genetic), MDFI (Two-hybrid), B3GNT9 (Affinity Capture-MS)

ESM2 similar proteins: A0A8I5KY20, A2A9Q0, A9JSM3, C9JI98, D4A2Q0, D4ABX8, E7ERA6, F1SAM7, F2Z333, O94819, P0C7J6, P0CG25, P13224, P56400, Q04785, Q0GA42, Q17QZ8, Q1RMK9, Q2MJR0, Q2WF71, Q504Y2, Q50LG9, Q5RJI4, Q6IEE6, Q6IEE7, Q6IQX7, Q6P6N5, Q6PJG9, Q6UKI2, Q6UX72, Q6ZMC9, Q6ZT52, Q6ZVX7, Q7Z6J2, Q80XU8, Q86UD0, Q86VR8, Q8BQB4, Q8IZ52, Q8QZV0

Diamond homologs: A8MXE2, O43825, O54904, O54905, O75752, O88178, O96024, Q17QZ8, Q1RLK6, Q3USF0, Q5HZL5, Q5R5Y3, Q5RAL7, Q5TJE8, Q5XJP0, Q66H69, Q6AY39, Q6DE15, Q6P3P5, Q6UX72, Q793U7, Q7JK24, Q7JK25, Q7JK26, Q7T3S5, Q864U6, Q864U8, Q8BGY6, Q8K0J2, Q8L7F9, Q8NFL0, Q8VI16, Q920V1, Q99NB2, Q9BYG0, Q9C0J1, Q9JI67, Q9MYM7, Q9N293, Q9N294

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

72 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	68
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2424194	NC_000016.9:g.(?65821800)(67208957_?)del	Pathogenic

SpliceAI

150 predictions. Top by Δscore:

Variant	Effect	Δscore
16:67150863:A:AC	donor_gain	0.9900
16:67150864:C:CC	donor_gain	0.9900
16:67150864:CG:C	donor_gain	0.9900
16:67150864:CGCT:C	donor_gain	0.9800
16:67150856:GACAC:G	donor_loss	0.9200
16:67150857:ACACT:A	donor_loss	0.9200
16:67150858:CACTC:C	donor_loss	0.9200
16:67150859:AC:A	donor_loss	0.9200
16:67150860:C:CG	donor_loss	0.9200
16:67150861:T:TT	donor_loss	0.9200
16:67150862:CACGC:C	donor_loss	0.9200
16:67150863:ACG:A	donor_gain	0.9100
16:67150864:CGC:C	donor_gain	0.9100
16:67150863:ACGCT:A	donor_gain	0.8300
16:67150864:CGCTC:C	donor_gain	0.8300
16:67150672:C:CC	acceptor_gain	0.8100
16:67150898:C:CA	donor_gain	0.7800
16:67150668:CAGC:C	acceptor_gain	0.7700
16:67150669:AGCCT:A	acceptor_loss	0.7600
16:67150670:GCCT:G	acceptor_loss	0.7600
16:67150671:CCTG:C	acceptor_loss	0.7600
16:67150672:C:CG	acceptor_loss	0.7600
16:67150673:T:A	acceptor_loss	0.7600
16:67150816:TCC:T	donor_gain	0.7600
16:67150670:GC:G	acceptor_gain	0.7400
16:67150671:CC:C	acceptor_gain	0.7400
16:67150855:CGACA:C	donor_loss	0.7300
16:67150830:C:A	donor_gain	0.7200
16:67150682:A:T	acceptor_loss	0.7100
16:67150681:C:CT	acceptor_loss	0.7000

AlphaMissense

2555 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:67149539:T:A	D316V	0.999
16:67149865:C:A	K207N	0.999
16:67149865:C:G	K207N	0.999
16:67149914:T:A	D191V	0.999
16:67149538:G:C	D316E	0.998
16:67149538:G:T	D316E	0.998
16:67149539:T:C	D316G	0.998
16:67149539:T:G	D316A	0.998
16:67149540:C:G	D316H	0.998
16:67149542:T:A	D315V	0.998
16:67149674:T:C	Y271C	0.998
16:67149800:T:A	D229V	0.998
16:67150024:G:C	F154L	0.998
16:67150024:G:T	F154L	0.998
16:67150025:A:C	F154C	0.998
16:67150026:A:G	F154L	0.998
16:67150069:C:A	W139C	0.998
16:67150069:C:G	W139C	0.998
16:67150092:G:T	R132S	0.998
16:67149543:C:G	D315H	0.997
16:67149675:A:G	Y271H	0.997
16:67149844:C:A	W214C	0.997
16:67149844:C:G	W214C	0.997
16:67149895:G:C	F197L	0.997
16:67149895:G:T	F197L	0.997
16:67149897:A:G	F197L	0.997
16:67149915:C:G	D191H	0.997
16:67150025:A:G	F154S	0.997
16:67150071:A:G	W139R	0.997
16:67150071:A:T	W139R	0.997

dbSNP variants (sampled 300 via entrez): RS1000042696 (16:67151387 CT>C), RS1000114051 (16:67152868 A>T), RS1000531733 (16:67148098 A>G), RS1000562328 (16:67151202 C>G), RS1000963083 (16:67148559 T>A), RS1001360337 (16:67150684 G>C,T), RS1001729621 (16:67150940 T>A,G), RS1001730703 (16:67150356 T>C,G), RS1001991444 (16:67150578 G>A), RS1002462735 (16:67148980 C>T), RS1002586247 (16:67151543 T>C,G), RS1002995156 (16:67149843 C>T), RS1003435761 (16:67149511 G>A), RS1003996201 (16:67149433 G>A,C), RS1004027306 (16:67149641 G>A)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:116800

GenCC curated gene-disease

Mondo (1): cataract 5 multiple types (MONDO:0007290)

Orphanet (1): Early onset non-syndromic cataract (Orphanet:91492)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C535342	Cataract, zonular (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
aminomethylphosphonic acid (AMPA)	decreases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	affects binding, increases activity, increases expression	1
bisphenol A	affects cotreatment, increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
entinostat	increases expression	1
jinfukang	increases expression	1
Acetaminophen	decreases expression	1
Benzo(a)pyrene	increases methylation, affects methylation	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Lead	affects expression	1
Methotrexate	increases expression	1
Niclosamide	increases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Tretinoin	increases expression	1
Valproic Acid	increases methylation, decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
2,4-Dichlorophenoxyacetic Acid	decreases expression	1
Cyclosporine	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.