PBDC1

Summary

PBDC1 (polysaccharide biosynthesis domain containing 1, HGNC:28790) is a protein-coding gene on chromosome Xq13.3, encoding Protein PBDC1 (Q9BVG4).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 49 total
• Druggable target: yes — 1 molecules with ChEMBL bioactivity
• MANE Select transcript: NM_016500

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28790
Approved symbol	PBDC1
Name	polysaccharide biosynthesis domain containing 1
Location	Xq13.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC874
Ensembl gene	ENSG00000102390
Ensembl biotype	protein_coding
Entrez	51260

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000373357, ENST00000373358, ENST00000718344, ENST00000862784, ENST00000862785, ENST00000862786, ENST00000920256

RefSeq mRNA: 2 — MANE Select: NM_016500 NM_001300888, NM_016500

CCDS: CCDS14432, CCDS75995

Canonical transcript exons

ENST00000373358 — 6 exons

Exon	Start	End
ENSE00000859667	76173585	76173650
ENSE00000859668	76174890	76174949
ENSE00000859669	76175473	76175613
ENSE00000859670	76176881	76176992
ENSE00004034830	76177616	76178314
ENSE00004034831	76173062	76173168

Expression profiles

Bgee: expression breadth ubiquitous, 252 present calls, max score 96.04.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.2798 / max 620.4743, expressed in 1780 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
196766	24.0897	1777
196767	1.1902	856

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
epithelial cell of pancreas	CL:0000083	96.04	gold quality
ileal mucosa	UBERON:0000331	93.74	gold quality
palpebral conjunctiva	UBERON:0001812	93.19	gold quality
duodenum	UBERON:0002114	92.72	gold quality
jejunal mucosa	UBERON:0000399	92.61	gold quality
islet of Langerhans	UBERON:0000006	92.15	gold quality
pancreatic ductal cell	CL:0002079	92.05	gold quality
right adrenal gland cortex	UBERON:0035827	92.03	gold quality
right adrenal gland	UBERON:0001233	91.90	gold quality
mucosa of transverse colon	UBERON:0004991	91.63	gold quality
rectum	UBERON:0001052	91.61	gold quality
mucosa of sigmoid colon	UBERON:0004993	91.61	gold quality
smooth muscle tissue	UBERON:0001135	91.60	gold quality
left adrenal gland	UBERON:0001234	91.56	gold quality
esophagus mucosa	UBERON:0002469	91.44	gold quality
left adrenal gland cortex	UBERON:0035825	91.31	gold quality
adrenal cortex	UBERON:0001235	91.20	gold quality
adrenal gland	UBERON:0002369	91.13	gold quality
esophagus squamous epithelium	UBERON:0006920	91.03	gold quality
small intestine Peyer’s patch	UBERON:0003454	90.86	gold quality
colonic mucosa	UBERON:0000317	90.73	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.67	gold quality
kidney epithelium	UBERON:0004819	90.61	gold quality
esophagus	UBERON:0001043	90.53	gold quality
descending thoracic aorta	UBERON:0002345	90.51	gold quality
small intestine	UBERON:0002108	90.50	gold quality
skin of hip	UBERON:0001554	90.49	gold quality
transverse colon	UBERON:0001157	90.07	gold quality
intestine	UBERON:0000160	90.01	gold quality
large intestine	UBERON:0000059	89.98	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.69

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): YY1

miRNA regulators (miRDB)

13 targeting PBDC1, 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-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-132-3P	99.73	70.56	1424
HSA-MIR-212-3P	99.73	70.65	1424
HSA-MIR-548B-3P	99.38	67.26	1000
HSA-MIR-7702	99.06	65.95	698
HSA-MIR-3936	97.64	64.47	732
HSA-MIR-937-5P	97.43	68.39	667
HSA-MIR-4286	97.20	64.37	1587
HSA-MIR-4474-5P	94.23	67.95	568

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	pbdc1	ENSDARG00000057299
mus_musculus	Pbdc1	ENSMUSG00000031226
rattus_norvegicus	Pbdc1	ENSRNOG00000002662
drosophila_melanogaster	CG7519	FBGN0037087
caenorhabditis_elegans	Y54E5A.5	WBGENE00013200

Protein

Protein identifiers

Protein PBDC1 — Q9BVG4 (reviewed: Q9BVG4)

Alternative names: Polysaccharide biosynthesis domain-containing protein 1

All UniProt accessions (2): Q9BVG4, A6NDF3

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the PBDC1 family.

RefSeq proteins (2): NP_001287817, NP_057584* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008476	PBDC1_metazoa/fungi	Family
IPR021148	Polysacc_synth_dom	Domain
IPR023139	PBDC1-like_dom_sf	Homologous_superfamily

Pfam: PF04669

UniProt features (5 total): modified residue 3, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BVG4-F1	76.66	0.54

Functional residue map

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

Post-translational modifications (3): 126, 181, 197

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 88 (showing top): LI_CISPLATIN_RESISTANCE_DN, HORIUCHI_WTAP_TARGETS_DN, HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_UP, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_PROTEIN_MATURATION, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, GOBP_PROTEIN_FOLDING, GOBP_DE_NOVO_PROTEIN_FOLDING, BENPORATH_OCT4_TARGETS, CEBPB_02, chrXq13, JOHNSTONE_PARVB_TARGETS_3_DN, LEE_BMP2_TARGETS_DN, GCNP_SHH_UP_LATE.V1_UP, GOMF_PROTEIN_FOLDING_CHAPERONE

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

978 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PBDC1	ZDHHC24	Q6UX98	571
PBDC1	SBNO1	A3KN83	531
PBDC1	LRRC42	Q9Y546	497
PBDC1	TIMM17B	O60830	473
PBDC1	SHROOM4	Q9ULL8	449
PBDC1	MYSM1	Q5VVJ2	438
PBDC1	PABIR3	Q6P4D5	433
PBDC1	MPLKIP	Q8TAP9	409
PBDC1	LSM14B	Q9BX40	402
PBDC1	ERICH6	Q7L0X2	392
PBDC1	EFCAB5	A4FU69	376
PBDC1	RIPOR3	Q96MK2	374
PBDC1	TRAPPC13	A5PLN9	373
PBDC1	OR52M1	Q8NGK5	371
PBDC1	AADACL3	Q5VUY0	370

IntAct

26 interactions, top by confidence:

A	B	Type	Score
PBDC1	EEF1A1	psi-mi:“MI:0914”(association)	0.530
EEF1A1	EEF1B2	psi-mi:“MI:0914”(association)	0.530
EEF1A1	ZPR1	psi-mi:“MI:0914”(association)	0.530
CFTR	PBDC1	psi-mi:“MI:0915”(physical association)	0.370
JUN		psi-mi:“MI:0914”(association)	0.350
DLD	NFKBIE	psi-mi:“MI:0914”(association)	0.350
MAPT	POTEF	psi-mi:“MI:0914”(association)	0.350
CUL3	PXDNL	psi-mi:“MI:0914”(association)	0.350
LRRK2		psi-mi:“MI:0914”(association)	0.350
BABAM1	PYCR3	psi-mi:“MI:0914”(association)	0.350
RIN3		psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
PBDC1	POTEF	psi-mi:“MI:0914”(association)	0.350
EEF1A2	IGLL5	psi-mi:“MI:0914”(association)	0.350
GPKOW	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
PBDC1	CTNNB1	psi-mi:“MI:0915”(physical association)	0.000
PBDC1	PHB1	psi-mi:“MI:0915”(physical association)	0.000
PBDC1	SMAD2	psi-mi:“MI:0915”(physical association)	0.000
PPP1R16A	PBDC1	psi-mi:“MI:0915”(physical association)	0.000
STRN4	PBDC1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (59): EEF1A1 (Affinity Capture-MS), EEF1A2 (Affinity Capture-MS), TTLL12 (Affinity Capture-MS), PBDC1 (Co-fractionation), EEF1A2 (Affinity Capture-MS), EEF1A1 (Affinity Capture-MS), TTLL12 (Affinity Capture-MS), PBDC1 (Affinity Capture-MS), PBDC1 (Affinity Capture-MS), PBDC1 (Affinity Capture-MS), PBDC1 (Affinity Capture-MS), PBDC1 (Affinity Capture-MS), PBDC1 (Affinity Capture-MS), PBDC1 (Two-hybrid), PBDC1 (Affinity Capture-MS)

ESM2 similar proteins: A8MQG7, B0Y8Z0, F4HPN2, F4HXQ7, F4I8S3, F4INW9, F4K487, M4C367, O22829, O60158, O64571, O74792, P0C759, P24813, P25370, Q08AX9, Q10180, Q3TTP0, Q3UZB0, Q4WWA0, Q5BB76, Q5R675, Q5RDG2, Q66H38, Q6GPE9, Q6P1M9, Q6PB60, Q6PI77, Q71HP2, Q794H2, Q7T2B3, Q7X9V2, Q7XWS7, Q924R9, Q96D09, Q99457, Q99MX1, Q9BE11, Q9BVG4, Q9BZQ2

Diamond homologs: O59727, Q08971, Q9BVG4, Q9D0B6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	15
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

731 predictions. Top by Δscore:

Variant	Effect	Δscore
X:76173165:GCCG:G	donor_gain	1.0000
X:76173166:CCGG:C	donor_loss	1.0000
X:76173651:G:GG	donor_gain	1.0000
X:76174888:A:AG	acceptor_gain	1.0000
X:76174889:G:GA	acceptor_gain	1.0000
X:76174947:AAGGT:A	donor_loss	1.0000
X:76174948:AGGT:A	donor_loss	1.0000
X:76174950:G:GG	donor_gain	1.0000
X:76174951:T:A	donor_loss	1.0000
X:76175461:ACT:A	acceptor_gain	1.0000
X:76175463:T:TA	acceptor_gain	1.0000
X:76175468:C:CA	acceptor_gain	1.0000
X:76175468:CGCA:C	acceptor_loss	1.0000
X:76175470:CA:C	acceptor_loss	1.0000
X:76175471:A:AG	acceptor_gain	1.0000
X:76175471:A:AT	acceptor_loss	1.0000
X:76175471:AGCT:A	acceptor_gain	1.0000
X:76175472:G:GT	acceptor_gain	1.0000
X:76175472:GC:G	acceptor_gain	1.0000
X:76175472:GCT:G	acceptor_gain	1.0000
X:76175472:GCTG:G	acceptor_gain	1.0000
X:76175472:GCTGA:G	acceptor_gain	1.0000
X:76175610:AGAG:A	donor_gain	1.0000
X:76175611:G:GT	donor_gain	1.0000
X:76175611:GAG:G	donor_gain	1.0000
X:76175611:GAGGT:G	donor_loss	1.0000
X:76175612:AGG:A	donor_loss	1.0000
X:76175613:GGTAA:G	donor_loss	1.0000
X:76175614:G:GG	donor_gain	1.0000
X:76176876:TATA:T	acceptor_loss	1.0000

AlphaMissense

1542 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:76174908:T:A	W39R	0.999
X:76174908:T:C	W39R	0.999
X:76174910:G:C	W39C	0.999
X:76174910:G:T	W39C	0.999
X:76176884:T:A	W101R	0.999
X:76176884:T:C	W101R	0.999
X:76176886:G:C	W101C	0.999
X:76176886:G:T	W101C	0.999
X:76174932:G:C	A47P	0.998
X:76174933:C:A	A47D	0.998
X:76175474:T:C	L53P	0.998
X:76176936:G:A	G118D	0.998
X:76176945:T:C	L121P	0.998
X:76177630:T:C	F142L	0.998
X:76177632:C:A	F142L	0.998
X:76177632:C:G	F142L	0.998
X:76177652:G:C	R149P	0.998
X:76177658:G:C	R151P	0.998
X:76174911:G:C	A40P	0.997
X:76174920:G:C	A43P	0.997
X:76175595:G:C	K93N	0.997
X:76175595:G:T	K93N	0.997
X:76176942:T:C	L120S	0.997
X:76177637:C:A	A144D	0.997
X:76177643:A:T	E146V	0.997
X:76174912:C:A	A40D	0.996
X:76175610:A:C	K98N	0.996
X:76175610:A:T	K98N	0.996
X:76176885:G:C	W101S	0.996
X:76176947:C:G	R122G	0.996

dbSNP variants (sampled 300 via entrez): RS1002272324 (X:76174794 C>T), RS1002404383 (X:76175234 G>A), RS1003687312 (X:76176740 T>C), RS1004180213 (X:76174898 T>C,G), RS1004289685 (X:76175791 T>C), RS1004320689 (X:76175295 G>A), RS1004652541 (X:76173089 T>A,C), RS1007412834 (X:76176349 T>A,G), RS1008955168 (X:76171181 G>A,C), RS1009502616 (X:76176602 A>G), RS1009778716 (X:76176370 G>A), RS1013788050 (X:76174285 G>A), RS1014176505 (X:76172527 C>T), RS1014271261 (X:76174634 A>G), RS1014539402 (X:76172033 T>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST006031_14	Potassium levels	3.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009283	potassium measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5725172 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,538 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

Molecule	Name	Phase	Patents
CHEMBL1232461	MOLIBRESIB	2	1,538

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

ChEMBL bioactivities

3 potent at pChembl≥5 of 3 total, top 3 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.31	Kd	48.58	nM	CHEMBL5653589
7.14	ED50	72.95	nM	CHEMBL5653589
5.00	IC50	1e+04	nM	MOLIBRESIB

PubChem BioAssay actives

2 with measured affinity, of 8 total; 2 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2148940: Binding affinity to human PBDC1 incubated for 45 mins by Kinobead based pull down assay	kd	0.0486	uM
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide	2178950: Inhibition of CXORF26 (unknown origin) incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysis	ic50	10.0000	uM

CTD chemical–gene interactions

37 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	3
Particulate Matter	decreases expression, increases abundance, affects cotreatment, increases expression	3
aristolochic acid I	increases expression	1
FR900359	increases phosphorylation	1
dicrotophos	decreases expression	1
2,4,6-tribromophenol	decreases expression	1
bisphenol A	decreases expression	1
decabromobiphenyl ether	decreases expression	1
arsenite	affects binding, increases reaction	1
sodium arsenite	increases abundance, decreases expression	1
tetrabromobisphenol A	decreases expression	1
isobutyl alcohol	affects cotreatment, increases abundance, increases expression	1
nutlin 3	affects cotreatment, increases secretion	1
abrine	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
pentabrominated diphenyl ether 100	decreases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases abundance, decreases expression	1
Benzene	increases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Catechin	affects cotreatment, decreases expression	1
Dactinomycin	affects cotreatment, increases secretion	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Ivermectin	decreases expression	1
Lead	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5651982	Binding	Binding affinity to human PBDC1 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

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