PDCL3

Summary

PDCL3 (phosducin like 3, HGNC:28860) is a protein-coding gene on chromosome 2q11.2, encoding Phosducin-like protein 3 (Q9H2J4). Acts as a chaperone for the angiogenic VEGF receptor KDR/VEGFR2, increasing its abundance by inhibiting its ubiquitination and degradation.

This gene encodes a member of the phosducin-like protein family and is a putative modulator of heterotrimeric G proteins. The protein shares extensive amino acid sequence homology with phosducin. Members of the phosducin-like protein family have been shown to bind to the beta-gamma subunits of G proteins.

Source: NCBI Gene 79031 — RefSeq curated summary.

At a glance

• Gene–disease (curated): megacystis-microcolon-intestinal hypoperistalsis syndrome (Moderate, GenCC)
• GWAS associations: 2
• Clinical variants (ClinVar): 40 total
• MANE Select transcript: NM_024065

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28860
Approved symbol	PDCL3
Name	phosducin like 3
Location	2q11.2
Locus type	gene with protein product
Status	Approved
Aliases	VIAF1
Ensembl gene	ENSG00000115539
Ensembl biotype	protein_coding
OMIM	611678
Entrez	79031

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000264254, ENST00000416255, ENST00000450127, ENST00000718278, ENST00000928050, ENST00000928051, ENST00000928052

RefSeq mRNA: 1 — MANE Select: NM_024065 NM_024065

CCDS: CCDS33261

Canonical transcript exons

ENST00000264254 — 6 exons

Exon	Start	End
ENSE00000771909	100569578	100569721
ENSE00000771916	100571590	100571798
ENSE00001072179	100562993	100563073
ENSE00001872699	100576354	100576739
ENSE00003572811	100566503	100566629
ENSE00003681994	100568931	100569021

Expression profiles

Bgee: expression breadth ubiquitous, 141 present calls, max score 93.68.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.9683 / max 952.8712, expressed in 1806 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
21594	20.2558	1799
21595	2.2217	1178
21590	0.7273	386
21593	0.3584	159
21591	0.3210	133
21592	0.0841	24

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
gastrocnemius	UBERON:0001388	93.68	gold quality
muscle of leg	UBERON:0001383	93.41	gold quality
skeletal muscle organ	UBERON:0014892	93.34	gold quality
smooth muscle tissue	UBERON:0001135	92.95	gold quality
urinary bladder	UBERON:0001255	92.12	gold quality
lower esophagus muscularis layer	UBERON:0035833	91.97	gold quality
popliteal artery	UBERON:0002250	91.96	gold quality
tibial artery	UBERON:0007610	91.96	gold quality
lower esophagus	UBERON:0013473	91.94	gold quality
ganglionic eminence	UBERON:0004023	91.86	gold quality
substantia nigra	UBERON:0002038	91.78	gold quality
right coronary artery	UBERON:0001625	91.65	gold quality
hindlimb stylopod muscle	UBERON:0004252	91.55	gold quality
islet of Langerhans	UBERON:0000006	91.52	gold quality
rectum	UBERON:0001052	91.52	gold quality
skeletal muscle tissue	UBERON:0001134	91.36	gold quality
left coronary artery	UBERON:0001626	91.24	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	91.18	gold quality
aorta	UBERON:0000947	91.01	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	90.92	gold quality
esophagus	UBERON:0001043	90.91	gold quality
monocyte	CL:0000576	90.79	gold quality
ventricular zone	UBERON:0003053	90.63	gold quality
leukocyte	CL:0000738	90.62	gold quality
heart left ventricle	UBERON:0002084	90.47	gold quality
muscle layer of sigmoid colon	UBERON:0035805	90.47	gold quality
placenta	UBERON:0001987	90.46	gold quality
vermiform appendix	UBERON:0001154	90.42	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.31	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	90.30	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-89	no	519.86
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

35 targeting PDCL3, 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-4776-3P	100.00	68.73	1340
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-1323	99.83	69.89	2471
HSA-MIR-548O-3P	99.74	69.30	2228
HSA-MIR-8084	99.73	69.57	1760
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-497-3P	99.61	69.71	1990
HSA-MIR-510-3P	99.54	70.06	2965
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-580-5P	99.28	70.94	1776
HSA-MIR-3125	99.14	68.49	2269
HSA-MIR-3916	98.99	68.04	2155

Literature-anchored findings (GeneRIF, showing 8)

• Data support a model in which Plp2p modulates the biogenesis of several CCT substrates relating to cell cycle and cytoskeletal function, which together contribute to the essential function of PLP2. (PMID:17429077)
• Data support a model in which Plp2p modulates the biogenesis of several CCT substrates relating to cell cycle and cytoskeletal function, which together contribute to the essential function of PLP2. (PMID:17429077)
• data provide strong evidence for the role of PDCL3 in angiogenesis and establishes the molecular mechanism by which it regulates VEGFR-2 expression and function. (PMID:23792958)
• The data provide new insights for the chaperone function of PDCL3 in angiogenesis and the roles of hypoxia and N-terminal methionine acetylation in PDCL3 expression and its effect on VEGFR-2. (PMID:26059764)
• family-based GWAS of imputed SNPs revealed novel genomic variants in (or near) PTPRG, OSBPL6, and PDCL3 that influence risk for Alzheimer’s Disease. rs7609954 in the gene PTPRG, rs1347297 in the gene OSBPL6, and rs1513625 near PDCL3. In addition, rs72953347 in OSBPL6 and two SNPs in the gene CDKAL1 showed marginally significant association with LOAD (rs10456232, P-value=4.76 x 10-7; rs62400067, P-value=3.54 x 10-7). (PMID:26830138)
• results have shown that PhLP2A interacts with Hsp90 and exhibits molecular chaperone activity toward denatured proteins. (PMID:27496612)
• Fetal megacystis-microcolon: Genetic mutational spectrum and identification of PDCL3 as a novel candidate gene. (PMID:32621347)
• PDCL3 as a prognostic factor and associated with the VEGF signaling pathway in glioma. (PMID:39107869)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
		ENSDARG00000100651
mus_musculus	Pdcl3	ENSMUSG00000026078
rattus_norvegicus	Pdcl3	ENSRNOG00000013286

Paralogs (4): TXNDC9 (ENSG00000115514), PDC (ENSG00000116703), PDCL (ENSG00000136940), PDCL2 (ENSG00000163440)

Protein

Protein identifiers

Phosducin-like protein 3 — Q9H2J4 (reviewed: Q9H2J4)

Alternative names: HTPHLP, PhPL3, Viral IAP-associated factor 1

All UniProt accessions (3): C9JST4, Q9H2J4, H7BZP2

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a chaperone for the angiogenic VEGF receptor KDR/VEGFR2, increasing its abundance by inhibiting its ubiquitination and degradation. Inhibits the folding activity of the chaperonin-containing T-complex (CCT) which leads to inhibition of cytoskeletal actin folding. Acts as a chaperone during heat shock alongside HSP90 and HSP40/70 chaperone complexes. Modulates the activation of caspases during apoptosis.

Subunit / interactions. Interacts (via thioredoxin fold region) with KDR/VEGFR2 (via juxtamembrane domain). Forms ternary complexes with the chaperonin CCT complex and actin substrate, leading to inhibition of actin folding. Interacts with XIAP (via BIR 3 and RING domain). Interacts with HSP90AA1 and HSP90AB1.

Subcellular location. Cytoplasm. Perinuclear region. Endoplasmic reticulum.

Tissue specificity. Expressed in endothelial cells (at protein level). Expressed in all tissues examined including spleen, thymus, prostate, testis, ovary, small intestine and colon.

Post-translational modifications. N-terminal methionine acetylation destabilizes the protein.

Similarity. Belongs to the phosducin family.

RefSeq proteins (1): NP_076970* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR024253	Phosducin_thioredoxin-like_dom	Domain
IPR036249	Thioredoxin-like_sf	Homologous_superfamily
IPR051498	Phosducin-like_chap/apop_reg	Family

Pfam: PF02114

UniProt features (31 total): helix 10, strand 8, modified residue 4, turn 3, region of interest 3, chain 1, domain 1, mutagenesis site 1

Structure

Experimental structures (PDB)

6 structures.

PDB	Method	Resolution (Å)
7NVM	ELECTRON MICROSCOPY	3.1
8I9U	ELECTRON MICROSCOPY	3.1
8I1U	ELECTRON MICROSCOPY	3.24
8I6J	ELECTRON MICROSCOPY	3.82
8I9Q	ELECTRON MICROSCOPY	4.22
8IB8	ELECTRON MICROSCOPY	4.42

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H2J4-F1	79.69	0.34

Antibody-complex structures (SAbDab): 1 — 7NVM

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 (4): 1, 43, 234, 236

Mutagenesis-validated functional residues (1):

Position	Phenotype
1	loss of acetylation. increases protein stability.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 136 (showing top): GOBP_NEGATIVE_REGULATION_OF_PROTEOLYSIS, GOBP_REGULATION_OF_PHOSPHORYLATION, GOBP_POSITIVE_REGULATION_OF_VASCULATURE_DEVELOPMENT, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_PROTEIN_MATURATION, GOBP_REGULATION_OF_CATABOLIC_PROCESS, CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_DN, GOBP_PROTEIN_STABILIZATION, GOBP_BLOOD_VESSEL_MORPHOGENESIS, GOBP_PROTEIN_FOLDING, GOBP_REGULATION_OF_PROTEIN_STABILITY, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS, GOBP_EPITHELIAL_CELL_PROLIFERATION, GOMF_SIGNALING_RECEPTOR_BINDING

GO Biological Process (11): angiogenesis (GO:0001525), positive regulation of endothelial cell proliferation (GO:0001938), protein folding (GO:0006457), apoptotic process (GO:0006915), positive regulation of gene expression (GO:0010628), actin cytoskeleton organization (GO:0030036), positive regulation of angiogenesis (GO:0045766), regulation of peptidyl-tyrosine phosphorylation (GO:0050730), protein stabilization (GO:0050821), negative regulation of protein folding (GO:1903333), negative regulation of ubiquitin-dependent protein catabolic process (GO:2000059)

GO Molecular Function (3): vascular endothelial growth factor receptor 2 binding (GO:0043184), protein folding chaperone (GO:0044183), protein binding (GO:0005515)

GO Cellular Component (7): nucleoplasm (GO:0005654), cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), cytosol (GO:0005829), protein-containing complex (GO:0032991), perinuclear region of cytoplasm (GO:0048471), perinucleolar compartment (GO:0097356)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
cytoplasm	3
protein folding	2
nuclear lumen	2
blood vessel morphogenesis	1
anatomical structure formation involved in morphogenesis	1
endothelial cell proliferation	1
regulation of endothelial cell proliferation	1
positive regulation of epithelial cell proliferation	1
cellular process	1
protein maturation	1
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
gene expression	1
regulation of gene expression	1
positive regulation of macromolecule biosynthetic process	1
cytoskeleton organization	1
actin filament-based process	1
angiogenesis	1
regulation of angiogenesis	1
positive regulation of vasculature development	1
regulation of protein phosphorylation	1
peptidyl-tyrosine phosphorylation	1
regulation of protein stability	1
negative regulation of cellular process	1
regulation of protein folding	1
ubiquitin-dependent protein catabolic process	1
negative regulation of protein catabolic process	1
regulation of ubiquitin-dependent protein catabolic process	1
vascular endothelial growth factor receptor binding	1
molecular_function	1
binding	1
intracellular anatomical structure	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular_component	1

Protein interactions and networks

STRING

1030 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PDCL3	PLP2	Q04941	840
PDCL3	TCP1	P17987	756
PDCL3	TUBB	P05218	676
PDCL3	TUBB2A	Q13885	650
PDCL3	TXN	P10599	618
PDCL3	KDR	P35968	471
PDCL3	HSP90AA1	P07900	447
PDCL3	HSP90AB1	P08238	439
PDCL3	ZNF496	Q96IT1	412
PDCL3	TXNDC9	O14530	394
PDCL3	EHD2	Q9NZN4	392
PDCL3	PPP4C	P33172	385
PDCL3	ACTB	P02570	384
PDCL3	EHD3	Q9NZN3	382
PDCL3	CPED1	A4D0V7	371
PDCL3	ANKRD23	Q86SG2	371

IntAct

90 interactions, top by confidence:

A	B	Type	Score
ACTR1A	DCTN2	psi-mi:“MI:0914”(association)	0.790
TUBG1	TUBG1	psi-mi:“MI:2364”(proximity)	0.760
CCT2	TXNDC9	psi-mi:“MI:0914”(association)	0.730
DCAF7	DIAPH1	psi-mi:“MI:0914”(association)	0.730
CCT2	PPP6C	psi-mi:“MI:0914”(association)	0.640
PDCL3	PEX7	psi-mi:“MI:0914”(association)	0.640
CCT3	TXNDC9	psi-mi:“MI:0914”(association)	0.640
CCT5	TXNDC9	psi-mi:“MI:0914”(association)	0.640
CCT7	TXNDC9	psi-mi:“MI:0914”(association)	0.640
DCAF12L2	CETN3	psi-mi:“MI:0914”(association)	0.640
MPPED1	TXNDC9	psi-mi:“MI:0914”(association)	0.640
Cct3	PDCD5	psi-mi:“MI:0915”(physical association)	0.560
Cct7	PDCD5	psi-mi:“MI:0915”(physical association)	0.560
ACTBL2	POTEF	psi-mi:“MI:0914”(association)	0.530
FBXW4	TXNDC9	psi-mi:“MI:0914”(association)	0.530
PEX7	TCP1	psi-mi:“MI:0914”(association)	0.530
CCT3	PDCD5	psi-mi:“MI:0914”(association)	0.530
CCT6A	TXNDC9	psi-mi:“MI:0914”(association)	0.530
DTL	DNAJA2	psi-mi:“MI:0914”(association)	0.530
CCT7	PEX7	psi-mi:“MI:0914”(association)	0.530
DCAF5	PFDN6	psi-mi:“MI:0914”(association)	0.530
FBXW4	TCP1	psi-mi:“MI:0914”(association)	0.530
TLE2	HSPA8	psi-mi:“MI:0914”(association)	0.530

BioGRID (165): PDCL3 (Affinity Capture-RNA), PDCL3 (Affinity Capture-MS), PDCL3 (Affinity Capture-MS), PDCL3 (Affinity Capture-MS), PDCL3 (Affinity Capture-MS), CCT3 (Co-fractionation), CCT6A (Co-fractionation), CCT7 (Co-fractionation), CCT8 (Co-fractionation), PDCL3 (Co-fractionation), PDCL3 (Biochemical Activity), PDCL3 (Proximity Label-MS), PDCL3 (Proximity Label-MS), PDCL3 (Proximity Label-MS), PDCL3 (Affinity Capture-MS)

ESM2 similar proteins: A0A7U2QYM2, A0FKG7, A0JN39, D2SW95, O55236, O60508, O60942, P23514, P36954, P36958, P53618, P60898, P60899, P97789, Q32P66, Q32P73, Q5BJZ6, Q5R4A0, Q5R4J9, Q5R8R4, Q5R922, Q5RB77, Q5VQ78, Q5XK67, Q5ZIA5, Q66HV4, Q6H8D5, Q6H8D6, Q6NLH0, Q7ZVX6, Q80UM3, Q80UY1, Q8C878, Q8IZH2, Q8L5V0, Q8L828, Q8TBC4, Q99MI7, Q9BXJ9, Q9C827

Diamond homologs: O77560, P19632, P20941, P20942, P41686, Q0VCW8, Q13371, Q2HJA9, Q4KLJ8, Q5RB77, Q63737, Q6P268, Q71A38, Q71A39, Q8BVF2, Q9DBX2, Q9H2J4, Q9QW08, Q9VUR7, Q9XS39, Q12017, Q32LN3, Q78Y63, Q8MR62, Q8N4E4, Q9Y7L1, O14530, O18883, O64628, Q6NPL9, Q8K581, Q8LCV1, Q9CQ79, Q71A37

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 93 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Prefoldin mediated transfer of substrate to CCT/TriC	12	84.4×	1e-18
Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding	10	72.8×	5e-15
Formation of tubulin folding intermediates by CCT/TriC	9	68.0×	2e-13
Chaperonin-mediated protein folding	10	53.7×	1e-13
BBSome-mediated cargo-targeting to cilium	6	53.2×	3e-08
Association of TriC/CCT with target proteins during biosynthesis	10	52.3×	1e-13
Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding	9	48.3×	5e-12
Protein folding	10	46.4×	4e-13

GO biological processes:

GO term	Partners	Fold	FDR
positive regulation of telomere maintenance via telomerase	8	81.4×	5e-12
binding of sperm to zona pellucida	7	41.0×	3e-08
protein folding	12	17.2×	4e-10
protein stabilization	11	10.2×	6e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	32
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

966 predictions. Top by Δscore:

Variant	Effect	Δscore
2:100566499:CTAG:C	acceptor_loss	1.0000
2:100566500:TAGGA:T	acceptor_gain	1.0000
2:100566501:A:AG	acceptor_gain	1.0000
2:100566501:A:AT	acceptor_loss	1.0000
2:100566501:AG:A	acceptor_gain	1.0000
2:100566502:G:GG	acceptor_gain	1.0000
2:100566502:G:GT	acceptor_loss	1.0000
2:100566502:GG:G	acceptor_gain	1.0000
2:100566622:GTCA:G	donor_gain	1.0000
2:100566626:G:GG	donor_gain	1.0000
2:100566626:GTGG:G	donor_loss	1.0000
2:100566627:TGG:T	donor_gain	1.0000
2:100566627:TGGG:T	donor_loss	1.0000
2:100566628:GG:G	donor_gain	1.0000
2:100566628:GGG:G	donor_gain	1.0000
2:100566629:GG:G	donor_gain	1.0000
2:100566630:G:GG	donor_gain	1.0000
2:100568897:A:G	acceptor_gain	1.0000
2:100568903:T:A	acceptor_gain	1.0000
2:100568910:T:TA	acceptor_gain	1.0000
2:100568914:A:AG	acceptor_gain	1.0000
2:100568914:AAT:A	acceptor_gain	1.0000
2:100568915:A:G	acceptor_gain	1.0000
2:100568915:AT:A	acceptor_gain	1.0000
2:100568916:T:G	acceptor_gain	1.0000
2:100568916:T:TA	acceptor_gain	1.0000
2:100568919:A:AG	acceptor_gain	1.0000
2:100568920:A:G	acceptor_gain	1.0000
2:100568923:A:AG	acceptor_gain	1.0000
2:100568929:A:AG	acceptor_gain	1.0000

AlphaMissense

1576 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:100566526:G:C	W10C	0.996
2:100566526:G:T	W10C	0.996
2:100571602:T:G	C127W	0.996
2:100571666:G:C	A149P	0.996
2:100571709:T:C	L163P	0.996
2:100571712:C:A	P164H	0.996
2:100571600:T:C	C127R	0.995
2:100571634:C:A	A138D	0.995
2:100571724:T:A	V168D	0.995
2:100566524:T:A	W10R	0.994
2:100566524:T:C	W10R	0.994
2:100571601:G:A	C127Y	0.994
2:100569670:T:A	V106D	0.993
2:100569705:C:G	H118D	0.993
2:100569709:T:C	L119P	0.993
2:100571711:C:T	P164S	0.993
2:100571712:C:G	P164R	0.993
2:100571667:C:A	A149D	0.992
2:100571718:T:A	I166K	0.992
2:100566537:T:C	L14S	0.991
2:100576369:T:C	L198P	0.991
2:100569624:T:C	F91L	0.990
2:100569626:C:A	F91L	0.990
2:100569626:C:G	F91L	0.990
2:100569709:T:A	L119H	0.990
2:100571601:G:T	C127F	0.990
2:100571622:T:C	L134P	0.990
2:100571683:C:G	C154W	0.990
2:100571658:T:C	F146S	0.989
2:100571685:T:A	I155K	0.989

dbSNP variants (sampled 300 via entrez): RS1000008672 (2:100573740 T>C), RS1000171589 (2:100565560 C>G), RS1000259992 (2:100572526 AT>A,ATT), RS1000356312 (2:100567438 C>A,G), RS1000486414 (2:100562512 G>C), RS1000577459 (2:100576913 T>C,G), RS1000963400 (2:100566140 T>C), RS1001018299 (2:100572324 G>T), RS1001117958 (2:100576470 A>T), RS1001183570 (2:100576173 C>A), RS1001219402 (2:100568391 C>T), RS1001250013 (2:100566277 C>T), RS1001292867 (2:100568063 C>T), RS1001453536 (2:100574233 C>T), RS1001494515 (2:100565457 G>A)

Disease associations

OMIM: gene MIM:611678 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
megacystis-microcolon-intestinal hypoperistalsis syndrome	Moderate	Autosomal recessive

Mondo (1): megacystis-microcolon-intestinal hypoperistalsis syndrome (MONDO:0025986)

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST007155_1	Household income	2.000000e-08
GCST008181_14	Spontaneous preterm birth without premature rupture of membranes	5.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0009695	household income
EFO:0006917	spontaneous preterm birth

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Binding affinities (BindingDB)

1 measured of 7 human assays (7 total across all organisms); most potent 1 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value
2-(1-keto-7,8-dihydro-6H-cyclopenta[2,3]thieno[2,4-d]pyrimidin-2-yl)acetic acid ethyl ester	IC50	106000 nM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	2
Tretinoin	decreases expression	2
dicrotophos	decreases expression	1
bisphenol A	decreases expression	1
cobaltous chloride	decreases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
phenethyl isothiocyanate	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
ICG 001	decreases expression	1
abrine	decreases expression	1
LDN 193189	decreases expression, affects cotreatment	1
Arsenic Trioxide	decreases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Atrazine	decreases expression	1
Benztropine	decreases expression	1
Cannabidiol	decreases expression	1
Cisplatin	increases expression	1
Hydrogen Peroxide	affects expression	1
Ivermectin	decreases expression	1
Lead	affects expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Progesterone	decreases expression	1
Smoke	decreases expression	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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