PTX3

Summary

PTX3 (pentraxin 3, HGNC:9692) is a protein-coding gene on chromosome 3q25.32, encoding Pentraxin-related protein PTX3 (P26022). Plays a role in the regulation of innate resistance to pathogens, inflammatory reactions, possibly clearance of self-components and female fertility.

This gene encodes a member of the pentraxin protein family. The expression of this protein is induced by inflammatory cytokines in response to inflammatory stimuli in several mesenchymal and epithelial cell types, particularly endothelial cells and mononuclear phagocytes. The protein promotes fibrocyte differentiation and is involved in regulating inflammation and complement activation. It also plays a role in angiogenesis and tissue remodeling. The protein serves as a biomarker for several inflammatory conditions.

Source: NCBI Gene 5806 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 68 total
• MANE Select transcript: NM_002852

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9692
Approved symbol	PTX3
Name	pentraxin 3
Location	3q25.32
Locus type	gene with protein product
Status	Approved
Aliases	TSG-14
Ensembl gene	ENSG00000163661
Ensembl biotype	protein_coding
OMIM	602492
Entrez	5806

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000295927, ENST00000970386

RefSeq mRNA: 1 — MANE Select: NM_002852 NM_002852

CCDS: CCDS3180

Canonical transcript exons

ENST00000295927 — 3 exons

Exon	Start	End
ENSE00001077019	157437513	157437914
ENSE00001157607	157442366	157443633
ENSE00001157616	157436850	157437063

Expression profiles

Bgee: expression breadth ubiquitous, 222 present calls, max score 98.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 228.4901 / max 7782.4514, expressed in 1264 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
39466	228.4901	1264

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cartilage tissue	UBERON:0002418	98.60	gold quality
pericardium	UBERON:0002407	98.57	gold quality
trabecular bone tissue	UBERON:0002483	92.52	gold quality
bone element	UBERON:0001474	91.89	gold quality
bone marrow	UBERON:0002371	91.79	gold quality
tibia	UBERON:0000979	90.72	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.47	gold quality
omental fat pad	UBERON:0010414	89.41	gold quality
peritoneum	UBERON:0002358	89.33	gold quality
mucosa of stomach	UBERON:0001199	89.03	gold quality
lower lobe of lung	UBERON:0008949	88.97	gold quality
adipose tissue of abdominal region	UBERON:0007808	87.39	gold quality
bone marrow cell	CL:0002092	87.01	gold quality
stromal cell of endometrium	CL:0002255	86.48	gold quality
upper lobe of lung	UBERON:0008948	86.45	gold quality
upper lobe of left lung	UBERON:0008952	86.23	gold quality
vena cava	UBERON:0004087	85.59	gold quality
ventricular zone	UBERON:0003053	84.36	gold quality
vermiform appendix	UBERON:0001154	83.87	gold quality
ganglionic eminence	UBERON:0004023	83.61	gold quality
subcutaneous adipose tissue	UBERON:0002190	82.58	gold quality
embryo	UBERON:0000922	82.57	gold quality
left coronary artery	UBERON:0001626	82.30	gold quality
monocyte	CL:0000576	81.88	gold quality
mononuclear cell	CL:0000842	81.31	gold quality
coronary artery	UBERON:0001621	81.19	gold quality
superficial temporal artery	UBERON:0001614	81.17	gold quality
lung	UBERON:0002048	81.02	gold quality
leukocyte	CL:0000738	80.58	gold quality
spleen	UBERON:0002106	80.38	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-8142	yes	2993.14
E-CURD-112	yes	13.24
E-ANND-3	yes	7.49
E-MTAB-10290	no	946.97

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

2 targets.

Target	Regulation
POMC
TH

Upstream regulators (CollecTRI, top): CTNNB1, DDIT3, JUN, NFKB1, NFKB, PITX1, PITX2, PITX3, RELA, SP1, SPI1

miRNA regulators (miRDB)

69 targeting PTX3, 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-3163	100.00	77.23	8605
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-498-3P	99.91	71.27	1114
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-4766-5P	99.75	69.23	2662
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-3660	99.68	67.33	1149
HSA-MIR-4526	99.68	67.07	1136
HSA-MIR-7157-5P	99.66	69.33	1829
HSA-MIR-452-5P	99.65	69.63	1762
HSA-MIR-4676-3P	99.65	69.31	1733

Literature-anchored findings (GeneRIF, showing 40)

• Expression of PTX3 by vIL-6-stimulated Kaposi’s sarcoma cell cultures (PMID:12004288)
• By increasing tissue factor expression, PTX3 plays a potential role in thrombogenesis and ischemic vascular disease. (PMID:12006390)
• PTX3 is produced in advanced atherosclerotic plaques principally by macrophages and endothelial cells and may contribute to the pathogenesis of atherosclerosis. (PMID:12006411)
• Detection of the long pentraxin PTX3 in mesangial cells of patients with IgA glomerulonephritis suggests its potential role in the modulation of glomerular and tubular injury. (PMID:12538709)
• Experiments with recombinant globular head domains of human C1q A, B, and C chains indicated that C1q interacts with PTX3 via its globular head region. Binding of C1q to immobilized PTX3 induced activation of the classical complement pathway. (PMID:12645945)
• The mRNA level of PTX3 was 3.5-fold higher in the melancholic group as compared to that in normal controls and in nonmelancholic depressives (n=8, all groups). (PMID:14603263)
• We provide evidence for expression of PTX3 by vascular smooth muscle cells induced by degraded lipoproteins, which may lead to a vascular acute-phase reaction, contributing to the inflammatory pathogenesis of atherosclerosis. (PMID:15262177)
• serum PTX3 levels appear elevated selectively in response to infection (PMID:15308113)
• Local PTX3 upregulation may modulate vascular smooth muscle cell activation after arterial injury (PMID:16020751)
• PTX3 acts as a third-party agent between microbial stimuli and dying cells, contributing to limit tissue damage under inflammatory conditions and the activation of autoreactive T cells (PMID:16166594)
• TNF-alpha induced PTX3 expression in human lung cell lines and primary epithelial cells; knockdown of either JNK1 or JNK2 with small interfering RNA also significantly reduced the regulated PTX3 expression (PMID:16339571)
• Review discusses clinical significance of different levels of PTX3, its role in induction or protection from autoimmunity, and the presence of specific PTX3 autoantibodies in different autoimmune diseases. (PMID:16380821)
• The coordinated induction by primary, proinflammatory signals of C1q and PTX3 and their reciprocal regulation during inflammation influences the clearance of apoptotic cells by antigen-presenting cells and possibly plays a role in immune homeostasis. (PMID:16617159)
• Significantly higher levels of pentraxin 3 were found in preeclampsia. Intrauterine growth restriction pregnancies showed intermediate levels between normal and preeclamptic patients. (PMID:16647920)
• there is an FGF2-binding domain in the N-terminal extension of PTX3 spanning the PTX3-(97-110) region (PMID:16769728)
• PTX3 could be used as a further marker of disease activity of psoriasis. (PMID:16865225)
• These results provided evidence of an involvement of the PTX3 sugar moiety in C1q recognition and complement activation. (PMID:16981714)
• The levels of plasma PTX3 were increased in patients with arterial inflammation, especially unstable angina pectoris. (PMID:17095712)
• Sources of PTX3 in the lung and the regulatory mechanisms of its expression ni acute injury and infection. (PMID:17277044)
• PTX3 and p66((ShcA)) mRNA levels are significantly more elevated in WBCs and in adipose tissue samples of patients with high levels of LDL compared to those with low levels. (PMID:17380301)
• Innate factors PTX3 and C1q are involved in the homeostasis of nasal mucosa and the pathogenesis of nasal polyposis. (PMID:17424885)
• This study demonstrated a significant association between CSF levels of IL-1beta, Il-6, and IFN-gamma and the severity ot EV71 brain stem encephalitis. (PMID:17441979)
• Cardiac surgical procedures performed with cardiopulmonary bypass are associated with a more pronounced release of PTX3 immediately after operation. (PMID:17487767)
• PTX3 may have a role in atherosclerosis and cardiovascular disease in hemodialysis patients (PMID:17496115)
• findings support previous data showing that VDR SNPs modulate the risk for pulmonary tuberculosis in West Africans and suggest that variation within DC-SIGN and PTX3 also affect the disease outcome (PMID:17611589)
• PTX3 directly interacts with inter-alpha-trypsin inhibitor and has a role in hyaluronan organization and cumulus oophorus expansion (PMID:17675295)
• These data suggest that PTX3 protein may represent an additional and stable marker of inflammation in chronic renal failure. (PMID:17786277)
• PTX3 activates a complement-dependent humoral amplification loop of the innate response to a microbial ligand (PMID:17947708)
• Expression of pentraxin-3 (PTX3) not only in macrophages but also in neutrophils may reflect the role of PTX3 in inflammation. (PMID:18045580)
• Estradiol and progesterone are involved in PTX3 induction and regulation during implantation. Also, of the factors secreted by trophoblast, IL-1beta induces PTX3 in human endometrial stromal cells. (PMID:18048494)
• Human PTX3 binds to influenza A virus and mediates a range of antiviral activities, including inhibition of hemagglutination, neutralization of virus infectivity and inhibition of viral neuraminidase. (PMID:18292565)
• In stage 5 chronic kidney disease and type 2 diabetes with normal renal function, pentraxin 3 was independently associated with proteinuria. Pentraxin 3 and proteinuria were associated with endothelial dysfunction in patients with type 2 diabetes. (PMID:18417746)
• visceral adipose tissue production of PTX3 seems to contribute to the mechanisms underlying the development of atherosclerosis (PMID:18571180)
• PTX3 was an early indicator of shock in patients with severe meningococcal disease that followed a pattern of induction distinct from CRP. (PMID:18650775)
• Emphasis on two new players involved in regulating inflammation at the maternal-fetal interface: the long pentraxin PTX3 and the decoy receptor for inflammatory chemokines D6. (PMID:18676013)
• Human chorionic gonadotropin-induced hormones progesterone and estrogen increase the PTX3 production by human monocytes. (PMID:18685085)
• Cell-specific regulation of PTX3 by glucocorticoid hormones in hematopoietic and nonhematopoietic cells (PMID:18703503)
• Plasma PTX3 levels may not only have laboratory values that differentiate NASH from non-NASH, but be a marker of the severity of hepatic fibrosis in NASH. (PMID:19014569)
• A role is proposed for PTX3 in the localization of complement factor H regulatory activity to surfaces that bind PTX3, thus modulating alternative pathway activation and preventing excessive inflammatory response to tissue injury. (PMID:19050261)
• study shows that intracellular PTX3 translocates at the surface of late apoptotic neutrophils and acts as an ’eat-me’ molecule for their recognition and capture by macrophages (PMID:19079137)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ptx3a	ENSDARG00000068275
danio_rerio	ptx3b	ENSDARG00000079515
mus_musculus	Ptx3	ENSMUSG00000027832
rattus_norvegicus	Ptx3	ENSRNOG00000012280

Paralogs (5): NPTX2 (ENSG00000106236), CRP (ENSG00000132693), APCS (ENSG00000132703), NPTX1 (ENSG00000171246), PTX4 (ENSG00000251692)

Protein

Protein identifiers

Pentraxin-related protein PTX3 — P26022 (reviewed: P26022)

Alternative names: Pentaxin-related protein PTX3, Tumor necrosis factor alpha-induced protein 5, Tumor necrosis factor-inducible gene 14 protein

All UniProt accessions (1): P26022

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in the regulation of innate resistance to pathogens, inflammatory reactions, possibly clearance of self-components and female fertility.

Subunit / interactions. Homooctamer; disulfide-linked. Binds to C1q. (Microbial infection) Interacts with SARS coronavirus-2/SARS-CoV-2 Nucleoprotein and Spike protein homotrimer.

Subcellular location. Secreted.

Post-translational modifications. Glycosylated.

Induction. By IL1B/interleukin-1 beta and TNF.

RefSeq proteins (1): NP_002843* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001759	PTX_dom	Domain
IPR006558	LamG-like	Domain
IPR013320	ConA-like_dom_sf	Homologous_superfamily
IPR030476	Pentaxin_CS	Conserved_site
IPR042837	PTX3	Family
IPR058832	PTX3_N	Domain

Pfam: PF00354, PF26206

UniProt features (43 total): strand 19, disulfide bond 7, sequence variant 4, helix 4, turn 2, coiled-coil region 2, signal peptide 1, chain 1, sequence conflict 1, domain 1, glycosylation site 1

Structure

Experimental structures (PDB)

8 structures.

PDB	Method	Resolution (Å)
8PVQ	X-RAY DIFFRACTION	2.43
7ZL1	ELECTRON MICROSCOPY	2.5
9K6U	ELECTRON MICROSCOPY	2.8
9K6N	ELECTRON MICROSCOPY	3.14
8S50	ELECTRON MICROSCOPY	3.33
9K6V	ELECTRON MICROSCOPY	5.65
9K6W	ELECTRON MICROSCOPY	7.5
9L1U	ELECTRON MICROSCOPY	8.3

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P26022-F1	76.94	0.48

Functional residue map

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

Disulfide bonds (7): 210–271, 317, 318, 47, 49, 103, 179–357

Glycosylation sites (1): 220

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-6798695	Neutrophil degranulation

MSigDB gene sets: 336 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, GSE45365_NK_CELL_VS_CD11B_DC_DN, REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_POSITIVE_REGULATION_OF_ENDOCYTOSIS, DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_DN, MODULE_255, GOBP_INFLAMMATORY_RESPONSE, GOCC_SECRETORY_GRANULE, PEREZ_TP63_TARGETS, GOBP_NEGATIVE_REGULATION_OF_VIRAL_PROCESS, HALMOS_CEBPA_TARGETS_UP, GOBP_GROWTH, GOBP_OOGENESIS, MODULE_317, MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN

GO Biological Process (15): ovarian cumulus expansion (GO:0001550), response to yeast (GO:0001878), inflammatory response (GO:0006954), opsonization (GO:0008228), extracellular matrix organization (GO:0030198), host-mediated suppression of viral proces (GO:0044793), negative regulation by host of viral glycoprotein metabolic process (GO:0044871), innate immune response (GO:0045087), positive regulation of nitric oxide biosynthetic process (GO:0045429), host-mediated suppression of symbiont invasion (GO:0046597), positive regulation of phagocytosis (GO:0050766), negative regulation of glycoprotein metabolic process (GO:1903019), immune system process (GO:0002376), immune response (GO:0006955), response to other organism (GO:0051707)

GO Molecular Function (5): complement component C1q complex binding (GO:0001849), (1->3)-beta-D-glucan binding (GO:0001872), identical protein binding (GO:0042802), virion binding (GO:0046790), protein binding (GO:0005515)

GO Cellular Component (5): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615), extracellular matrix (GO:0031012), specific granule lumen (GO:0035580), tertiary granule lumen (GO:1904724)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Innate Immune System	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
glycoprotein metabolic process	2
protein binding	2
antral ovarian follicle growth	1
ovulation cycle process	1
fused antrum stage	1
developmental growth	1
response to fungus	1
defense response	1
immune effector process	1
phagocytosis, recognition	1
extracellular structure organization	1
external encapsulating structure organization	1
host-mediated perturbation of viral process	1
host-mediated suppression of viral proces	1
modulation by host of viral glycoprotein metabolic process	1
negative regulation of viral process	1
negative regulation of glycoprotein metabolic process	1
immune response	1
defense response to symbiont	1
nitric oxide biosynthetic process	1
positive regulation of biosynthetic process	1
regulation of nitric oxide biosynthetic process	1
innate immune response	1
host-mediated perturbation of symbiont process	1
phagocytosis	1
positive regulation of endocytosis	1
regulation of phagocytosis	1
negative regulation of protein metabolic process	1
regulation of glycoprotein metabolic process	1
biological_process	1
immune system process	1
response to stimulus	1
response to external biotic stimulus	1
biological process involved in interspecies interaction between organisms	1
opsonin binding	1
complement binding	1
protein-containing complex binding	1
polysaccharide binding	1
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1230 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PTX3	MBL2	P11226	965
PTX3	TNFAIP6	P98066	950
PTX3	FCN1	O00602	938
PTX3	SELP	P16109	931
PTX3	FGF2	P09038	920
PTX3	CFHR5	Q9BXR6	916
PTX3	FGF13	Q92913	903
PTX3	FCN2	Q15485	885
PTX3	FGF10	O15520	820
PTX3	FGF17	O60258	816
PTX3	FGF6	P10767	809
PTX3	C1S	P09871	807
PTX3	IL6	P05231	736
PTX3	FGF8	P55075	707
PTX3	MPO	P05164	692

IntAct

133 interactions, top by confidence:

A	B	Type	Score
	MBL2	psi-mi:“MI:0914”(association)	0.940
CFH	PTX3	psi-mi:“MI:0407”(direct interaction)	0.820
PTX3	CFH	psi-mi:“MI:0407”(direct interaction)	0.820
PTX3	CFH	psi-mi:“MI:0914”(association)	0.820
PTX3	CFH	psi-mi:“MI:0210”(hydroxylation reaction)	0.820
PTX3	CFH	psi-mi:“MI:0915”(physical association)	0.820
FGF2	PTX3	psi-mi:“MI:0407”(direct interaction)	0.790
PTX3	FGF2	psi-mi:“MI:0407”(direct interaction)	0.790
FGF2	PTX3	psi-mi:“MI:0915”(physical association)	0.790

BioGRID (65): PTX3 (Affinity Capture-MS), PTX3 (Affinity Capture-MS), PTX3 (Synthetic Growth Defect), PTX3 (Affinity Capture-MS), PTX3 (Affinity Capture-MS), PTX3 (Affinity Capture-MS), PTX3 (Affinity Capture-MS), PTX3 (Affinity Capture-MS), PTX3 (Two-hybrid), FGF2 (Reconstituted Complex), FGF2 (Co-crystal Structure), PTX3 (Reconstituted Complex), PTX3 (Reconstituted Complex), PTX3 (Reconstituted Complex), PTX3 (Reconstituted Complex)

ESM2 similar proteins: A2A699, A2AV25, A2BD09, A5PJQ2, A6H6E2, A8MVW0, O35764, O43278, O55034, O70340, O94901, O95502, O95996, P26022, P47970, P47971, P47972, P48759, P49765, P97738, Q0VCG9, Q15818, Q1RMT9, Q24K15, Q3UMT1, Q496Z2, Q5JTB6, Q62443, Q68BL7, Q6ZMJ2, Q7TQH7, Q7Z4F1, Q86T13, Q86VZ4, Q8CB67, Q8K299, Q8N539, Q8NI99, Q8R0Z6, Q8VCP9

Diamond homologs: A0A1D5NSM8, A2AVA0, D3YXF5, O02839, O19124, O35764, O43405, O62685, O62837, O70340, O76536, O95502, O96530, P00751, P04003, P04186, P06205, P06206, P06207, P06681, P07629, P08174, P08607, P0C6B8, P13944, P14151, P14650, P15529, P17690, P18337, P26022, P32018, P33703, P35419, P42201, P47970, P47971, P47972, P48199, P48759

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
PTX3	“up-regulates activity”	CFH	binding
hsa-miR-101-3p	“down-regulates quantity by destabilization”	PTX3	“post transcriptional regulation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 58 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
Initial triggering of complement	6	85.9×	7e-09
Regulation of Complement cascade	6	33.3×	2e-06

GO biological processes:

GO term	Partners	Fold	FDR
complement activation	7	84.0×	7e-10

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	60
Likely benign	2
Benign	5

Top pathogenic / likely-pathogenic (0)

SpliceAI

250 predictions. Top by Δscore:

Variant	Effect	Δscore
3:157437059:GGACC:G	donor_gain	1.0000
3:157437060:GACC:G	donor_gain	1.0000
3:157437060:GACCG:G	donor_gain	1.0000
3:157437062:CC:C	donor_gain	1.0000
3:157437064:G:GG	donor_gain	1.0000
3:157437912:CAGGT:C	donor_loss	1.0000
3:157437916:T:G	donor_loss	1.0000
3:157437061:ACC:A	donor_gain	0.9900
3:157437062:CCG:C	donor_loss	0.9900
3:157437063:CGTA:C	donor_loss	0.9900
3:157437064:G:A	donor_loss	0.9900
3:157437065:TAAGT:T	donor_loss	0.9900
3:157437511:A:AG	acceptor_gain	0.9900
3:157437512:G:GA	acceptor_gain	0.9900
3:157437512:GC:G	acceptor_gain	0.9900
3:157437512:GCC:G	acceptor_gain	0.9900
3:157437512:GCCAC:G	acceptor_gain	0.9900
3:157442362:CTA:C	acceptor_loss	0.9900
3:157442363:TAG:T	acceptor_loss	0.9900
3:157442364:A:AG	acceptor_gain	0.9900
3:157442364:A:G	acceptor_loss	0.9900
3:157442365:G:GA	acceptor_loss	0.9900
3:157442365:G:GG	acceptor_gain	0.9900
3:157442365:GGTT:G	acceptor_gain	0.9900
3:157437061:A:T	donor_gain	0.9800
3:157437066:AAG:A	donor_loss	0.9800
3:157437508:TCTA:T	acceptor_loss	0.9800
3:157437510:TA:T	acceptor_loss	0.9800
3:157437512:GCCA:G	acceptor_gain	0.9800
3:157437910:GGCAG:G	donor_gain	0.9800

AlphaMissense

2467 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:157442929:T:A	W366R	0.996
3:157442929:T:C	W366R	0.996
3:157442931:G:C	W366C	0.996
3:157442931:G:T	W366C	0.996
3:157442634:G:C	W267C	0.995
3:157442634:G:T	W267C	0.995
3:157442455:A:C	S208R	0.992
3:157442457:T:A	S208R	0.992
3:157442457:T:G	S208R	0.992
3:157442850:G:C	W339C	0.992
3:157442850:G:T	W339C	0.992
3:157442924:T:A	V364D	0.992
3:157442632:T:A	W267R	0.990
3:157442632:T:C	W267R	0.990
3:157442387:T:C	F185S	0.989
3:157442387:T:G	F185C	0.989
3:157442655:G:C	W274C	0.988
3:157442655:G:T	W274C	0.988
3:157442509:T:C	S226P	0.987
3:157442765:G:A	G311D	0.987
3:157442819:T:C	F329S	0.987
3:157442410:T:C	F193L	0.986
3:157442412:T:A	F193L	0.986
3:157442412:T:G	F193L	0.986
3:157442398:T:C	S189P	0.984
3:157442818:T:C	F329L	0.984
3:157442820:C:A	F329L	0.984
3:157442820:C:G	F329L	0.984
3:157442825:G:A	G331E	0.984
3:157442840:T:C	F336S	0.984

dbSNP variants (sampled 300 via entrez): RS1000074101 (3:157437519 C>A,G,T), RS1000807843 (3:157436282 A>C), RS1000872046 (3:157437831 C>A,G), RS1001299836 (3:157437819 G>A,T), RS1001478473 (3:157438983 A>G), RS1001929880 (3:157443353 A>G,T), RS1001982341 (3:157443558 T>C), RS1002005370 (3:157442551 C>G), RS1002544616 (3:157442822 C>T), RS1003542349 (3:157438835 T>A), RS1004045664 (3:157439262 T>C), RS1004225220 (3:157440393 C>G,T), RS1004545508 (3:157439619 C>A,T), RS1004551661 (3:157435740 C>G,T), RS1004662773 (3:157435370 T>C)

Disease associations

OMIM: gene MIM:602492 | 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
GCST005951_143	Body mass index	4.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases expression	8
Benzo(a)pyrene	affects methylation, decreases expression, increases expression	6
Arsenic	decreases expression, affects cotreatment, increases abundance, increases expression, affects expression	4
Particulate Matter	increases abundance, increases expression, decreases expression	4
trichostatin A	increases expression, affects cotreatment, decreases expression	3
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	3
Cisplatin	decreases expression, increases expression, affects cotreatment	3
Silicon Dioxide	decreases expression, increases expression	3
Tretinoin	decreases expression, increases expression	3
Aflatoxin B1	affects expression, decreases methylation, increases expression	3
bisphenol A	decreases expression, increases expression	2
mono-(2-ethylhexyl)phthalate	decreases expression, increases expression	2
cobaltous chloride	decreases expression, increases expression	2
manganese chloride	increases expression, affects cotreatment, increases abundance	2
potassium chromate(VI)	affects cotreatment, decreases expression	2
perfluoro-n-nonanoic acid	decreases expression, increases expression	2
entinostat	decreases expression, affects cotreatment	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases activity, increases expression, decreases expression	2
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	2
(+)-JQ1 compound	decreases expression, affects cotreatment	2
Acetaminophen	affects cotreatment, increases expression	2
Air Pollutants	increases abundance, increases expression, decreases expression	2
Copper	affects binding, increases expression	2
Diethylhexyl Phthalate	affects reaction, increases expression, decreases expression, affects cotreatment	2
Doxorubicin	decreases expression, affects response to substance	2
Manganese	increases expression, affects cotreatment, increases abundance	2
Nickel	increases expression	2
Oxygen	increases expression, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Cyclosporine	increases expression	2

Clinical trials (associated diseases)

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