GLIPR1

Summary

GLIPR1 (GLI pathogenesis related 1, HGNC:17001) is a protein-coding gene on chromosome 12q21.2, encoding Glioma pathogenesis-related protein 1 (P48060).

This gene encodes a protein with similarity to both the pathogenesis-related protein (PR) superfamily and the cysteine-rich secretory protein (CRISP) family. Increased expression of this gene is associated with myelomocytic differentiation in macrophage and decreased expression of this gene through gene methylation is associated with prostate cancer. The protein has proapoptotic activities in prostate and bladder cancer cells. This gene is a member of a cluster on chromosome 12 containing two other similar genes. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized.

Source: NCBI Gene 11010 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 76 total
• MANE Select transcript: NM_006851

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17001
Approved symbol	GLIPR1
Name	GLI pathogenesis related 1
Location	12q21.2
Locus type	gene with protein product
Status	Approved
Aliases	RTVP1, GliPR
Ensembl gene	ENSG00000139278
Ensembl biotype	protein_coding
OMIM	602692
Entrez	11010

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 nonsense_mediated_decay

ENST00000266659, ENST00000456650, ENST00000536703, ENST00000550491

RefSeq mRNA: 1 — MANE Select: NM_006851 NM_006851

CCDS: CCDS9011

Canonical transcript exons

ENST00000266659 — 6 exons

Exon	Start	End
ENSE00001126768	75480755	75481054
ENSE00001684139	75498824	75503863
ENSE00001727706	75498694	75498720
ENSE00003513501	75481834	75482079
ENSE00003639739	75495577	75495662
ENSE00003645002	75490406	75490518

Expression profiles

Bgee: expression breadth ubiquitous, 273 present calls, max score 98.45.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 135.4238 / max 1969.6068, expressed in 1590 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
126903	85.1932	1526
126905	31.8540	1470
126904	15.9648	1341
126902	0.6115	359
126908	0.6007	207
126909	0.5791	229
126901	0.2407	108
126906	0.2264	127
126907	0.1535	60

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	98.45	gold quality
mononuclear cell	CL:0000842	98.32	gold quality
leukocyte	CL:0000738	98.30	gold quality
secondary oocyte	CL:0000655	97.91	gold quality
stromal cell of endometrium	CL:0002255	97.23	gold quality
pericardium	UBERON:0002407	96.86	gold quality
thoracic aorta	UBERON:0001515	96.84	gold quality
ascending aorta	UBERON:0001496	96.81	gold quality
blood	UBERON:0000178	96.73	gold quality
descending thoracic aorta	UBERON:0002345	96.67	gold quality
granulocyte	CL:0000094	96.65	gold quality
right coronary artery	UBERON:0001625	96.22	gold quality
trabecular bone tissue	UBERON:0002483	95.58	gold quality
smooth muscle tissue	UBERON:0001135	95.53	gold quality
cauda epididymis	UBERON:0004360	95.49	gold quality
blood vessel layer	UBERON:0004797	95.33	gold quality
aorta	UBERON:0000947	95.10	gold quality
synovial joint	UBERON:0002217	94.55	gold quality
left coronary artery	UBERON:0001626	94.00	gold quality
gall bladder	UBERON:0002110	93.91	gold quality
popliteal artery	UBERON:0002250	93.83	gold quality
tibial artery	UBERON:0007610	93.81	gold quality
epithelium of nasopharynx	UBERON:0001951	93.51	gold quality
coronary artery	UBERON:0001621	93.39	gold quality
lymph node	UBERON:0000029	92.86	gold quality
saphenous vein	UBERON:0007318	92.82	gold quality
vermiform appendix	UBERON:0001154	92.67	gold quality
buccal mucosa cell	CL:0002336	92.51	gold quality
mammary duct	UBERON:0001765	92.45	gold quality
bone marrow	UBERON:0002371	92.28	gold quality

Single-cell (SCXA)

Detected in 14 experiment(s), a significant marker in 11.

Experiment	Marker?	Max mean expression
E-MTAB-10287	yes	100.99
E-HCAD-4	yes	67.37
E-HCAD-1	yes	50.39
E-HCAD-10	yes	33.24
E-HCAD-6	yes	31.33
E-CURD-112	yes	26.47
E-MTAB-6701	yes	20.78
E-MTAB-10042	yes	16.87
E-MTAB-8410	yes	15.32
E-ANND-3	yes	11.92
E-MTAB-6678	yes	8.06
E-MTAB-2983	no	2081.19
E-CURD-89	no	635.54
E-MTAB-10290	no	572.64

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): SRF, TP53

miRNA regulators (miRDB)

161 targeting GLIPR1, 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-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488

Literature-anchored findings (GeneRIF, showing 27)

• Expression of the human RTVP-1 gene is down-regulated in human prostate cancer specimens compared with normal human prostate tissue at the mRNA and protein levels. (PMID:14871827)
• In this study we report the identification and characterization of a novel p53 target gene cluster that includes human RTVP1 (hRTVP-1) together with two GLIPR1L genes (GLIPR1L1 and GLIPR1L2) on human chromosome 12q21 and mouse Rtvp1 (PMID:16714093)
• RTVP-1b is a novel splice variant of human RTVP-1, which was isolated from the U87 glioma cell line (PMID:17825796)
• a role for GLIPR1/RTVP-1 deregulation early in Wilms tumorigenesis. (PMID:18030365)
• GLIPR1 is a proapoptotic tumor suppressor acting through the ROS-JNK pathway. (PMID:18199537)
• GLIPR1 expression is downregulated or even lost by promoter methylation in acute myeloid leukemia. (PMID:19483285)
• Induction of GliPR expression by HIV-1 was confirmed in P4-CCR5 cells. (PMID:20356381)
• X-ray data have been collected to beyond 1.9 A resolution from a crystal of GLIPR1 that belonged to the orthorhombic space group P2(1)2(1)2 with average unit-cell parameters a = 85.1, b = 79.5, c = 38.9 A and either a monomer or dimer (PMID:21045302)
• RTVP-1 plays a role in the effect of serum response factor on glioma cell migration (PMID:21777672)
• demonstrate that GLIPR1 is a methylation-silenced gene in the acute myeloid leukemia patients (PMID:21922325)
• GLIPR1 core structure has a conserved central cavity via which CAP proteins are likely to bind to shared ligands. (PMID:21931216)
• Data show that the expression of GLIPR1 and c-Myc were inversely correlated in prostate cancer. (PMID:22025562)
• GLIPR1 interacts with Hsc70, and GLIPR1 overexpression or Hsc70 knockdown leads to transcriptional suppression of AURKA and TPX2. (PMID:23333597)
• Data indicate that combining adenoviral vector-mediated GLIPR1 gene therap (AdGLIPR1) with radiotherapy may achieve additive or synergistic tumor control in selected prostate and bladder tumors. (PMID:23433894)
• miR-137 inhibits Glioblastom stem cell self-renewal and promotes their differentiation by targeting RTVP-1 which down-regulates CXCR4. (PMID:23714687)
• Based on the observed overexpression in AML samples, GliPR1 should be further explored as a potential target for AML (PMID:24008279)
• Overexpression of RTVP-1 in human neural stem cells induced mesenchymal differentiation, whereas silencing of RTVP-1 in glioma stem cells (GSCs) decreased the mesenchymal transformation and stemness of these cells. (PMID:26267319)
• RTVP-1 regulates glioma cell spreading, migration and invasion and that these effects are mediated via interaction with N-WASP and by interfering with the inhibitory effect of hnRNPK on the function of this protein. (PMID:26305187)
• This study reveals a novel pathway that PRMT5/WDR77 regulates GLIPR1 expression to control lung cancer cell growth. (PMID:26988096)
• The present study identified GLIPR1 and miR-16 as key components for regulating the proliferation, migration, invasion and cancer-initiating cells in osteosarcoma (PMID:27460987)
• High GLIPR1 expression is associated with cisplatin resistance in lung cancer. (PMID:28771580)
• Data found that GLIPR1 expression level was low in human bladder cancer tissues. Also, GLIPR1 was shown to inhibit the expression of TPX2. (PMID:28799673)
• Study demonstrates that GLIPR1 expression is frequently reduced in the plasma cells of multiple myeloma (MM)patients. Functional results in MM cell lines and in vivo suggest that GLIPR1 is unlikely to be a potent tumor suppressor in MM. (PMID:31995627)
• GLIPR1 and SPARC expression profile reveals a signature associated with prostate Cancer Brain metastasis. (PMID:33675864)
• Glioma pathogenesis-related protein 1 performs dual functions in tumor cells. (PMID:33742130)
• GLIPR1 promotes proliferation, metastasis and 5-fluorouracil resistance in hepatocellular carcinoma by activating the PI3K/PDK1/ROCK1 pathway. (PMID:35760898)
• Combined therapy of CAR-IL-15/IL-15Ralpha-T cells and GLIPR1 knockdown in cancer cells enhanced anti-tumor effect against gastric cancer. (PMID:38368374)

Cross-species orthologs

46 orthologs

Organism	Symbol	Gene ID
mus_musculus	Glipr1	ENSMUSG00000056888
rattus_norvegicus	Glipr1	ENSRNOG00000026644
drosophila_melanogaster	Ag5r	FBGN0015010
drosophila_melanogaster	Ag5r2	FBGN0020508
drosophila_melanogaster	CG9400	FBGN0030562
drosophila_melanogaster	CG10651	FBGN0032853
drosophila_melanogaster	CG9822	FBGN0034623
drosophila_melanogaster	CG17974	FBGN0034624
drosophila_melanogaster	CG3640	FBGN0035042
drosophila_melanogaster	CG8072	FBGN0036070
drosophila_melanogaster	CG6628	FBGN0036072
drosophila_melanogaster	scpr-C	FBGN0037879
drosophila_melanogaster	scpr-B	FBGN0037888
drosophila_melanogaster	scpr-A	FBGN0037889
drosophila_melanogaster	CG8483	FBGN0038126
drosophila_melanogaster	CG30486	FBGN0050486
drosophila_melanogaster	antr	FBGN0050488
drosophila_melanogaster	CG31286	FBGN0051286
drosophila_melanogaster	CG32313	FBGN0052313
drosophila_melanogaster	CG32679	FBGN0052679
drosophila_melanogaster	CG34002	FBGN0054002
drosophila_melanogaster	CG17575	FBGN0250842
drosophila_melanogaster	CG42564	FBGN0260766
drosophila_melanogaster	CG42780	FBGN0261848
drosophila_melanogaster	CG43775	FBGN0264297
drosophila_melanogaster	CG43776	FBGN0264298
drosophila_melanogaster	CG43777	FBGN0264299
caenorhabditis_elegans		WBGENE00004742
caenorhabditis_elegans		WBGENE00007397
caenorhabditis_elegans		WBGENE00008027
caenorhabditis_elegans		WBGENE00008028
caenorhabditis_elegans		WBGENE00008029
caenorhabditis_elegans		WBGENE00008030
caenorhabditis_elegans		WBGENE00008625
caenorhabditis_elegans		WBGENE00009891
caenorhabditis_elegans		WBGENE00009895
caenorhabditis_elegans		WBGENE00009896
caenorhabditis_elegans		WBGENE00012816
caenorhabditis_elegans		WBGENE00013971
caenorhabditis_elegans		WBGENE00013972
caenorhabditis_elegans		WBGENE00015246
caenorhabditis_elegans		WBGENE00017055
caenorhabditis_elegans		WBGENE00017183
caenorhabditis_elegans		WBGENE00019178
caenorhabditis_elegans		WBGENE00019179
caenorhabditis_elegans		WBGENE00021780

Paralogs (13): CRISP3 (ENSG00000096006), R3HDML (ENSG00000101074), CRISPLD2 (ENSG00000103196), CRISPLD1 (ENSG00000121005), GLIPR2 (ENSG00000122694), CRISP2 (ENSG00000124490), CRISP1 (ENSG00000124812), PI15 (ENSG00000137558), CLEC18B (ENSG00000140839), CLEC18A (ENSG00000157322), CLEC18C (ENSG00000157335), GLIPR1L1 (ENSG00000173401), GLIPR1L2 (ENSG00000180481)

Protein

Protein identifiers

Glioma pathogenesis-related protein 1 — P48060 (reviewed: P48060)

Alternative names: Protein RTVP-1

All UniProt accessions (4): P48060, B4E3S5, F6VVE8, J3QTC9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. According to PubMed:8973356, it is ubiquitously expressed with high levels in lung and kidney and low levels in heart and liver. Highly expressed in cell lines derived from nervous system tumors arising from glia, low or absent in non-glial-derived nervous system tumor cell lines. Also found in fetal kidney. According to PubMed:7607567 it is expressed only in brain tumor glioblastoma multiforme/astrocytoma and not in other nervous system tumors or normal fetal or adult tissues.

Miscellaneous. Highly expressed in glioblastomas.

Similarity. Belongs to the CRISP family.

Isoforms (2)

UniProt ID	Names	Canonical?
P48060-1	1	yes
P48060-2	2, RTVP-1b

RefSeq proteins (1): NP_006842* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001283	CRISP-related	Family
IPR002413	V5_allergen-like	Family
IPR014044	CAP_dom	Domain
IPR018244	Allrgn_V5/Tpx1_CS	Conserved_site
IPR034121	SCP_GLIPR-1-like	Domain
IPR035940	CAP_sf	Homologous_superfamily

Pfam: PF00188

UniProt features (26 total): strand 9, helix 6, turn 3, sequence variant 2, signal peptide 1, chain 1, transmembrane region 1, domain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
3Q2U	X-RAY DIFFRACTION	1.85
3Q2R	X-RAY DIFFRACTION	2.2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P48060-F1	86.65	0.70

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-1989781	PPARA activates gene expression
R-HSA-6798695	Neutrophil degranulation

MSigDB gene sets: 302 (showing top): WALLACE_PROSTATE_CANCER_RACE_UP, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, REACTOME_INNATE_IMMUNE_SYSTEM, GOCC_VACUOLAR_MEMBRANE, GOCC_SECRETORY_GRANULE, MODULE_45, GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN, LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN, WEI_MYCN_TARGETS_WITH_E_BOX, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, WANG_RESPONSE_TO_BEXAROTENE_UP, HUTTMANN_B_CLL_POOR_SURVIVAL_DN, KOYAMA_SEMA3B_TARGETS_UP, RHEIN_ALL_GLUCOCORTICOID_THERAPY_UP, ROZANOV_MMP14_TARGETS_UP

GO Biological Process (0):

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

GO Cellular Component (5): obsolete extracellular space (GO:0005615), plasma membrane (GO:0005886), membrane (GO:0016020), azurophil granule membrane (GO:0035577), extracellular region (GO:0005576)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Regulation of lipid metabolism by PPARalpha	1
Innate Immune System	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
binding	1
membrane	1
cell periphery	1
lysosomal membrane	1
secretory granule membrane	1
azurophil granule	1

Protein interactions and networks

STRING

1144 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GLIPR1	GLIPR2	Q9H4G4	574
GLIPR1	TP53	P04637	553
GLIPR1	LAPTM5	Q13571	520
GLIPR1	HNRNPK	P61978	461
GLIPR1	TNFSF10	P50591	438
GLIPR1	BBS10	Q8TAM1	433
GLIPR1	ASAH1	Q13510	432
GLIPR1	TEX101	Q9BY14	429
GLIPR1	LRRC10	Q5BKY1	425
GLIPR1	MMP2	P08253	423
GLIPR1	ARHGDIB	P52566	416
GLIPR1	IQGAP1	P46940	414
GLIPR1	TSPAN31	Q12999	406
GLIPR1	TMEM37	Q8WXS4	405
GLIPR1	BEST3	Q8N1M1	404

IntAct

17 interactions, top by confidence:

A	B	Type	Score
GLIPR1	ALOXE3	psi-mi:“MI:0915”(physical association)	0.560
HTT	GLIPR1	psi-mi:“MI:0915”(physical association)	0.560
GLIPR1	ALOXE3	psi-mi:“MI:0914”(association)	0.560
CKLF	GLIPR1	psi-mi:“MI:0915”(physical association)	0.400
	ESYT2	psi-mi:“MI:0914”(association)	0.350
E5	ESYT2	psi-mi:“MI:0914”(association)	0.350
	HAX1	psi-mi:“MI:0914”(association)	0.350
ENG	IGKV2-28	psi-mi:“MI:0914”(association)	0.350
GLIPR1	HBB	psi-mi:“MI:0914”(association)	0.350
GLIPR1	queE	psi-mi:“MI:0915”(physical association)	0.000
LCOR	GLIPR1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (32): CMTM6 (Affinity Capture-MS), ALOXE3 (Affinity Capture-MS), ALOXE3 (Affinity Capture-MS), GLIPR1 (Affinity Capture-Western), HSPA8 (Affinity Capture-Western), HSPA8 (Affinity Capture-MS), HSPA5 (Affinity Capture-MS), A1BG (Affinity Capture-MS), DZANK1 (Affinity Capture-MS), SF3B4 (Affinity Capture-MS), RPS29 (Affinity Capture-MS), GLIPR1 (Affinity Capture-MS), GLIPR1 (Affinity Capture-MS), GLIPR1 (Affinity Capture-MS), GLIPR1 (Affinity Capture-MS)

ESM2 similar proteins: A6MFK9, A8S6B6, B0VXV6, B7FDI0, B7FDI1, F8J2D4, F8S0Y4, O19010, P0CB15, P0DMT4, P12020, P16563, P48060, P54108, P60623, P79845, P84805, P84808, Q03401, Q2XXP1, Q2XXP2, Q2XXP4, Q2XXP5, Q2XXQ1, Q2XXQ2, Q2XXQ3, Q2XXQ4, Q2XXQ5, Q2XXQ6, Q32LB5, Q3SB03, Q3SB04, Q3SB05, Q3SB06, Q3SB07, Q60477, Q6UWM5, Q7T1K6, Q7ZT98, Q7ZT99

Diamond homologs: A0A182GL09, A0A1S4EWW7, A0A218QX58, A1BQQ5, A6MFK9, A6QLZ7, A8S6B6, A9QQ26, A9YME1, B2MVK7, B9URJ1, C0ITL3, D4B327, D4P2Y4, F8J2D4, G3CJR9, O19010, O43692, P0CB15, P0DMB9, P0DMT4, P0DPU0, P0DPU1, P0DPU2, P0DPU5, P0DPV2, P0DSI3, P10736, P10737, P12020, P16562, P16563, P35759, P35760, P35778, P35779, P35780, P35781, P35782, P35783

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	55
Likely benign	4
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

907 predictions. Top by Δscore:

Variant	Effect	Δscore
12:75482077:CAGGT:C	donor_loss	1.0000
12:75482078:AGGT:A	donor_loss	1.0000
12:75482079:GGTAA:G	donor_loss	1.0000
12:75482080:GT:G	donor_loss	1.0000
12:75490517:GG:G	donor_gain	1.0000
12:75490518:GG:G	donor_gain	1.0000
12:75495571:TTACA:T	acceptor_loss	1.0000
12:75495572:TACA:T	acceptor_loss	1.0000
12:75495572:TACAG:T	acceptor_gain	1.0000
12:75495573:ACAG:A	acceptor_loss	1.0000
12:75495573:ACAGA:A	acceptor_gain	1.0000
12:75495574:CAG:C	acceptor_gain	1.0000
12:75495574:CAGA:C	acceptor_loss	1.0000
12:75495575:A:AG	acceptor_gain	1.0000
12:75495575:A:C	acceptor_loss	1.0000
12:75495575:AGA:A	acceptor_gain	1.0000
12:75495575:AGAG:A	acceptor_gain	1.0000
12:75495575:AGAGG:A	acceptor_gain	1.0000
12:75495576:G:GA	acceptor_gain	1.0000
12:75495576:GA:G	acceptor_gain	1.0000
12:75495576:GAG:G	acceptor_gain	1.0000
12:75495576:GAGG:G	acceptor_gain	1.0000
12:75495576:GAGGG:G	acceptor_gain	1.0000
12:75495659:TGTGG:T	donor_loss	1.0000
12:75495660:GTG:G	donor_gain	1.0000
12:75495660:GTGGT:G	donor_loss	1.0000
12:75495661:TGGTG:T	donor_loss	1.0000
12:75495663:G:GG	donor_gain	1.0000
12:75495664:T:G	donor_loss	1.0000
12:75495665:G:GT	donor_loss	1.0000

AlphaMissense

1744 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:75481839:G:C	W60C	0.994
12:75481839:G:T	W60C	0.994
12:75490503:G:A	C173Y	0.994
12:75482010:G:C	W117C	0.992
12:75482010:G:T	W117C	0.992
12:75490502:T:A	C173S	0.992
12:75490503:G:C	C173S	0.992
12:75490504:C:G	C173W	0.992
12:75490421:A:C	S146R	0.991
12:75490423:T:A	S146R	0.991
12:75490423:T:G	S146R	0.991
12:75490436:T:A	C151S	0.991
12:75490437:G:C	C151S	0.991
12:75481956:C:A	N99K	0.989
12:75481956:C:G	N99K	0.989
12:75482008:T:A	W117R	0.988
12:75482008:T:C	W117R	0.988
12:75490414:G:C	W143C	0.988
12:75490414:G:T	W143C	0.988
12:75490439:G:C	A152P	0.988
12:75495659:T:A	C206S	0.988
12:75495660:G:C	C206S	0.988
12:75481882:T:A	C75S	0.987
12:75481883:G:C	C75S	0.987
12:75490436:T:C	C151R	0.987
12:75490451:T:A	C156S	0.987
12:75490452:G:C	C156S	0.987
12:75490502:T:C	C173R	0.987
12:75490503:G:T	C173F	0.987
12:75481014:G:C	R45P	0.986

dbSNP variants (sampled 300 via entrez): RS1000012607 (12:75482323 A>G), RS1000111362 (12:75485019 T>C), RS1000394527 (12:75485380 T>C), RS1000708245 (12:75500374 C>CTCAATA), RS1000806805 (12:75497266 T>C), RS1000932057 (12:75490205 A>T), RS1000961804 (12:75480099 C>T), RS1000984369 (12:75503724 C>A,T), RS1001076824 (12:75491034 T>C), RS1001116454 (12:75486202 A>G,T), RS1001321188 (12:75492412 A>G), RS1001359076 (12:75488059 A>C,G), RS1001398925 (12:75486638 G>A,C,T), RS1001826806 (12:75498410 T>G), RS1002205769 (12:75500011 A>G)

Disease associations

OMIM: gene MIM:602692 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST003518_77	Daytime sleep phenotypes	8.000000e-06
GCST012490_435	Femur bone mineral density x serum urate levels interaction	2.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007828	daytime rest measurement
EFO:0004531	urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects expression, decreases methylation, affects cotreatment	6
Benzo(a)pyrene	increases expression	5
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	3
(+)-JQ1 compound	decreases expression	3
Cyclosporine	decreases expression, increases expression	3
Aflatoxin B1	increases expression, increases methylation, affects expression, decreases expression	3
bisphenol A	increases methylation, decreases expression, decreases methylation, affects cotreatment	2
Air Pollutants	increases expression, decreases expression, increases abundance	2
Arsenic	affects methylation, affects cotreatment, increases abundance, increases expression	2
Estradiol	decreases expression, increases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Progesterone	affects cotreatment, decreases expression, increases expression	2
Smoke	increases expression	2
Tobacco Smoke Pollution	increases expression	2
Cadmium Chloride	increases expression	2
Particulate Matter	affects cotreatment, increases expression, decreases expression, increases abundance	2
aristolochic acid I	decreases expression	1
methylmercuric chloride	increases expression	1
methyleugenol	increases expression	1
triphenyl phosphate	affects expression	1
propionaldehyde	increases expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
lead acetate	increases expression	1
quercitrin	decreases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
cobaltous chloride	decreases expression	1
butyraldehyde	increases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
potassium chromate(VI)	decreases expression	1
ferrous chloride	increases expression	1

Clinical trials (associated diseases)

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