B3GALT9

Summary

B3GALT9 (beta-1,3-galactosyltransferase 9, HGNC:53652) is a protein-coding gene on chromosome 9q33.2, encoding Beta-1,3-galactosyltransferase 9 (A8MXE2). Putative glycosyltransferase that could catalyze the transfer of galactose residues from UDP-alpha-D-galactose.

Predicted to enable glycosyltransferase activity. Predicted to be involved in protein O-linked glycosylation. Predicted to be located in Golgi apparatus and membrane. Predicted to be active in Golgi membrane.

Source: NCBI Gene 100288842 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001386823

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53652
Approved symbol	B3GALT9
Name	beta-1,3-galactosyltransferase 9
Location	9q33.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000214654
Ensembl biotype	protein_coding
OMIM	620239
Entrez	100288842

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000437707, ENST00000464488, ENST00000645473, ENST00000689072

RefSeq mRNA: 1 — MANE Select: NM_001386823 NM_001386823

CCDS: CCDS94472

Canonical transcript exons

ENST00000689072 — 3 exons

Exon	Start	End
ENSE00003805456	120796423	120796609
ENSE00003924593	120793467	120793922
ENSE00003938585	120798575	120801787

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 86.72.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.72	gold quality
islet of Langerhans	UBERON:0000006	81.12	gold quality
calcaneal tendon	UBERON:0003701	78.59	gold quality
bone marrow cell	CL:0002092	78.29	gold quality
bone marrow	UBERON:0002371	76.55	gold quality
rectum	UBERON:0001052	75.34	gold quality
tonsil	UBERON:0002372	75.08	gold quality
monocyte	CL:0000576	74.39	gold quality
lymph node	UBERON:0000029	74.39	gold quality
leukocyte	CL:0000738	74.25	gold quality
corpus callosum	UBERON:0002336	73.77	gold quality
ventricular zone	UBERON:0003053	73.28	gold quality
endometrium	UBERON:0001295	73.18	gold quality
right adrenal gland cortex	UBERON:0035827	73.09	gold quality
stromal cell of endometrium	CL:0002255	72.98	gold quality
vermiform appendix	UBERON:0001154	72.08	gold quality
right adrenal gland	UBERON:0001233	71.98	gold quality
adrenal tissue	UBERON:0018303	71.85	gold quality
pancreas	UBERON:0001264	71.81	gold quality
gall bladder	UBERON:0002110	71.78	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	71.57	gold quality
smooth muscle tissue	UBERON:0001135	71.29	gold quality
urinary bladder	UBERON:0001255	71.24	gold quality
duodenum	UBERON:0002114	70.98	gold quality
left adrenal gland	UBERON:0001234	70.95	gold quality
adrenal gland	UBERON:0002369	70.90	gold quality
fallopian tube	UBERON:0003889	70.49	gold quality
placenta	UBERON:0001987	70.21	gold quality
skeletal muscle tissue	UBERON:0001134	69.60	gold quality
left adrenal gland cortex	UBERON:0035825	68.98	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.79

Regulation

Is transcription factor: no

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	b3galt9	ENSDARG00000094253
mus_musculus	B3galt9	ENSMUSG00000107167
rattus_norvegicus	B3galt9	ENSRNOG00000069270
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), B3GALT4 (ENSG00000235863), B3GNT9 (ENSG00000237172)

Protein

Protein identifiers

Beta-1,3-galactosyltransferase 9 — A8MXE2 (reviewed: A8MXE2)

Alternative names: UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 10

All UniProt accessions (3): A8MXE2, A0A2R8YCE0, A0A8I5KVM7

UniProt curated annotations — full annotation on UniProt →

Function. Putative glycosyltransferase that could catalyze the transfer of galactose residues from UDP-alpha-D-galactose.

Subcellular location. Golgi apparatus membrane.

Similarity. Belongs to the glycosyltransferase 31 family.

RefSeq proteins (1): NP_001373752* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002659	Glyco_trans_31	Family

Pfam: PF01762

UniProt features (7 total): glycosylation site 3, topological domain 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A8MXE2-F1	87.78	0.64

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (3): 66, 96, 109

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 18 (showing top): GOMF_HEXOSYLTRANSFERASE_ACTIVITY, GOMF_GLYCOSYLTRANSFERASE_ACTIVITY, DIDO1_TARGET_GENES, HMG20B_TARGET_GENES, RBM34_TARGET_GENES, SETD7_TARGET_GENES, ZBTB12_TARGET_GENES, ZNF711_TARGET_GENES, ZSCAN30_TARGET_GENES, ZC3H11A_TARGET_GENES, ZSCAN5DP_TARGET_GENES, EWSR1_TARGET_GENES, ZBTB44_TARGET_GENES, AUTS2_TARGET_GENES, ADA2_TARGET_GENES

GO Biological Process (4): protein O-linked glycosylation (GO:0006493), obsolete protein glycosylation (GO:0006486), lipid metabolic process (GO:0006629), carbohydrate derivative biosynthetic process (GO:1901137)

GO Molecular Function (3): glycosyltransferase activity (GO:0016757), hexosyltransferase activity (GO:0016758), transferase activity (GO:0016740)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
glycoprotein biosynthetic process	1
primary metabolic process	1
biosynthetic process	1
carbohydrate derivative metabolic process	1
transferase activity	1
glycosyltransferase activity	1
catalytic 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

120 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
B3GALT9	RFNG	Q9Y644	506
B3GALT9	B3GALNT2	Q8NCR0	476
B3GALT9	B3GLCT	Q6Y288	424
B3GALT9	CHPF	Q8IZ52	420
B3GALT9	Q6GMV1	Q6GMV1	387
B3GALT9	C1GALT1C1	Q96EU7	383
B3GALT9	CHSY1	Q86X52	382
B3GALT9	CSGALNACT1	Q8TDX6	370
B3GALT9	C1GALT1	Q9NS00	364
B3GALT9	LFNG	Q8NES3	341
B3GALT9	A4GALT	Q9NPC4	322
B3GALT9	B4GALNT2	Q8NHY0	311
B3GALT9	ST3GAL2	Q16842	309
B3GALT9	A3GALT2	U3KPV4	295
B3GALT9	GBGT1	Q8N5D6	279

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A2AIR5, A5D7I4, A8MXE2, A9X1C8, B4F753, B9EKX1, O60242, O60656, O75077, O77485, O77486, O77487, O95803, P16442, P23945, P25291, P97464, Q10981, Q14246, Q16394, Q4R766, Q5GJ04, Q5IGR7, Q5IGR8, Q5M7U7, Q5RBC3, Q5VYY2, Q62452, Q64633, Q64634, Q6AYT7, Q6ZQM8, Q704V6, Q7ZTV5, Q80ZF8, Q8TCU5, Q99LR1, Q9D4Y8, Q9D806, Q9DGB6

Diamond homologs: A8MXE2, O43825, O54904, O54905, O75752, O88178, O96024, Q1RLK6, Q5HZL5, Q5JCS9, Q5R5Y3, Q5RAL7, Q66H69, Q6AY39, Q6DE15, Q6P3P5, Q793U7, Q7JK24, Q7JK25, Q7JK26, Q7T3S5, Q864U6, Q864U8, Q8BGY6, Q8R3I9, Q920V1, Q95US5, Q99NB2, Q9BYG0, Q9C0J1, Q9JI67, Q9MYM7, Q9N293, Q9N294, Q9N295, Q9Y2A9, Q9Y2C3, Q9Y5Z6, Q9Z0F0, Q24157

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

238 predictions. Top by Δscore:

Variant	Effect	Δscore
9:120793144:CTGA:C	donor_loss	0.9900
9:120793145:TGA:T	donor_loss	0.9900
9:120793146:GAC:G	donor_loss	0.9900
9:120793147:A:AT	donor_loss	0.9900
9:120793148:C:CG	donor_loss	0.9900
9:120793349:CAGA:C	donor_gain	0.9700
9:120793354:CCGGA:C	donor_loss	0.9500
9:120793355:CGGAC:C	donor_loss	0.9500
9:120793356:GGAC:G	donor_loss	0.9500
9:120793357:GA:G	donor_loss	0.9500
9:120793359:C:A	donor_loss	0.9500
9:120793255:CGC:C	acceptor_gain	0.9400
9:120793258:C:CC	acceptor_gain	0.9400
9:120793360:C:G	donor_loss	0.9400
9:120793258:C:CA	acceptor_loss	0.9200
9:120793259:T:A	acceptor_loss	0.9200
9:120793348:A:AC	donor_gain	0.9200
9:120793349:C:CC	donor_gain	0.9200
9:120793254:GCGC:G	acceptor_gain	0.9100
9:120793255:CGCC:C	acceptor_gain	0.9100
9:120793256:GC:G	acceptor_gain	0.9100
9:120793257:CC:C	acceptor_gain	0.9100
9:120793374:C:CA	donor_gain	0.9100
9:120793253:GGCGC:G	acceptor_gain	0.9000
9:120793105:C:CA	donor_gain	0.8900
9:120793352:A:AC	donor_gain	0.8800
9:120793353:C:CC	donor_gain	0.8800
9:120793350:AGACC:A	donor_loss	0.8700
9:120793351:GA:G	donor_loss	0.8700
9:120793352:ACC:A	donor_loss	0.8700

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000689644 (9:120799709 A>G), RS1000746828 (9:120798871 C>A,T), RS1001134074 (9:120792580 ATTTT>A,ATTT,ATTTTT), RS1001205969 (9:120792819 T>C), RS1001577364 (9:120799295 A>C), RS1001851544 (9:120800610 T>C), RS1002139423 (9:120793236 G>A,C), RS1002353655 (9:120793544 G>C), RS1002359278 (9:120801257 C>A,T), RS1002366388 (9:120800948 A>G), RS1002471791 (9:120793853 G>A), RS1002687226 (9:120795165 G>A,T), RS1003181013 (9:120795420 C>G), RS1003203188 (9:120801355 G>A), RS1003233647 (9:120793828 A>AT)

Disease associations

OMIM: gene MIM:620239 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Esketamine	decreases expression	1
ferrous chloride	decreases expression	1

Clinical trials (associated diseases)

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