CLINT1

Summary

CLINT1 (clathrin interactor 1, HGNC:23186) is a protein-coding gene on chromosome 5q33.3, encoding Clathrin interactor 1 (Q14677). Binds to membranes enriched in phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2).

This gene encodes a protein with similarity to the epsin family of endocytic adapter proteins. The encoded protein interacts with clathrin, the adapter protein AP-1 and phosphoinositides. This protein may be involved in the formation of clathrin coated vesicles and trafficking between the trans-Golgi network and endosomes. Mutations in this gene are associated with a susceptibility to schizophrenia and psychotic disorders. Alternate splicing results in multiple transcript variants.

Source: NCBI Gene 9685 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 101 total
• Druggable target: yes
• MANE Select transcript: NM_014666

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23186
Approved symbol	CLINT1
Name	clathrin interactor 1
Location	5q33.3
Locus type	gene with protein product
Status	Approved
Aliases	ENTH, KIAA0171, EPNR, CLINT
Ensembl gene	ENSG00000113282
Ensembl biotype	protein_coding
OMIM	607265
Entrez	9685

Gene structure

Transcript identifiers

Ensembl transcripts: 35 — 31 protein_coding, 3 retained_intron, 1 nonsense_mediated_decay

ENST00000411809, ENST00000518855, ENST00000521047, ENST00000521615, ENST00000522381, ENST00000523094, ENST00000523908, ENST00000524306, ENST00000530302, ENST00000530742, ENST00000904376, ENST00000904377, ENST00000904378, ENST00000904379, ENST00000904380, ENST00000904381, ENST00000904382, ENST00000904383, ENST00000904384, ENST00000904385, ENST00000930851, ENST00000930852, ENST00000930853, ENST00000930854, ENST00000930855, ENST00000930856, ENST00000930857, ENST00000930858, ENST00000930859, ENST00000930860, ENST00000930861, ENST00000930862, ENST00000960219, ENST00000960220, ENST00000960221

RefSeq mRNA: 3 — MANE Select: NM_014666 NM_001195555, NM_001195556, NM_014666

CCDS: CCDS47330, CCDS56388, CCDS56389

Canonical transcript exons

ENST00000411809 — 12 exons

Exon	Start	End
ENSE00000768573	157816734	157816830
ENSE00001084563	157814185	157814293
ENSE00001084564	157785747	157787992
ENSE00001120766	157805866	157806112
ENSE00001120773	157809628	157809805
ENSE00001120777	157813063	157813227
ENSE00002101605	157858930	157859145
ENSE00003467363	157791703	157791995
ENSE00003485758	157803650	157803719
ENSE00003534725	157817443	157817547
ENSE00003538550	157789363	157789513
ENSE00003619311	157794898	157794972

Expression profiles

Bgee: expression breadth ubiquitous, 294 present calls, max score 98.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 70.5455 / max 1784.9772, expressed in 1826 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
64547	68.9075	1826
64546	1.6379	938

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
palpebral conjunctiva	UBERON:0001812	98.93	gold quality
esophagus squamous epithelium	UBERON:0006920	98.18	gold quality
corpus epididymis	UBERON:0004359	98.14	gold quality
bronchial epithelial cell	CL:0002328	98.08	gold quality
epithelium of nasopharynx	UBERON:0001951	98.08	gold quality
gingival epithelium	UBERON:0001949	97.96	gold quality
choroid plexus epithelium	UBERON:0003911	97.91	gold quality
gall bladder	UBERON:0002110	97.75	gold quality
epithelium of bronchus	UBERON:0002031	97.73	gold quality
bronchus	UBERON:0002185	97.70	gold quality
caput epididymis	UBERON:0004358	97.64	gold quality
gingiva	UBERON:0001828	97.50	gold quality
penis	UBERON:0000989	97.49	gold quality
tibia	UBERON:0000979	97.48	gold quality
rectum	UBERON:0001052	97.48	gold quality
pylorus	UBERON:0001166	97.46	gold quality
tonsil	UBERON:0002372	97.39	gold quality
esophagus mucosa	UBERON:0002469	97.37	gold quality
pharyngeal mucosa	UBERON:0000355	97.36	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	97.33	gold quality
mucosa of sigmoid colon	UBERON:0004993	97.32	gold quality
oral cavity	UBERON:0000167	97.26	gold quality
cauda epididymis	UBERON:0004360	97.22	gold quality
minor salivary gland	UBERON:0001830	97.20	gold quality
bone marrow cell	CL:0002092	97.12	gold quality
mouth mucosa	UBERON:0003729	97.09	gold quality
nephron tubule	UBERON:0001231	97.05	gold quality
bone marrow	UBERON:0002371	97.00	gold quality
colonic mucosa	UBERON:0000317	96.95	gold quality
mucosa of paranasal sinus	UBERON:0005030	96.93	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-9801	yes	5.44
E-MTAB-6678	no	3.93
E-CURD-112	no	2.71
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MYC

miRNA regulators (miRDB)

104 targeting CLINT1, 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-5692A	100.00	74.40	6850
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-6755-5P	99.95	65.59	464
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-95-5P	99.89	72.17	3973

Literature-anchored findings (GeneRIF, showing 13)

• a novel clathrin-associated protein identified through subcellular proteomics; data suggest a role in clathrin-mediated budding on internal membranes (PMID:12213833)
• might participate in the formation of clathrin-coated vesicles at the level of the trans-Golgi network and remains associated with the vesicles longer than clathrin and adaptors (PMID:12429846)
• EpsinR is an ENTH domain-containing protein that interacts with AP-1 (PMID:12589059)
• Our work reveals the existence of clathrin-independent and -dependent transport steps in the retrograde route, and establishes a function for clathrin and epsinR at the endosome-TGN interface. (PMID:15068792)
• epsinR is an adaptor for vesicle-associated soluble NSF attachment protein receptor (PMID:15371541)
• Four adjacent markers at the 5’ end of the Epsin 4 gene showed significant evidence of linkage disequilibrium with schizophrenia. (PMID:15793701)
• Results indicate the presence of a locus near the 5’ end of Epsin 4 conferring susceptibility to the disease and provide further support for Epsin 4 as an important potential contributor to genetic risk in schizophrenia. (PMID:16402136)
• characterization of the molecular details governing the sorting of a SNARE into clathrin-coated vesicles, namely the direct recognition of the three-helical bundle H(abc) domain of the mouse SNARE Vti1b by the human clathrin adaptor epsinR (PMID:18033301)
• Our results suggest that the examined region of Epsin 4 does not have a major influence on susceptibility to schizophrenia in Japanese. (PMID:18696005)
• Variation in the Epsin 4 gene is significantly associated with psychotic disorder in this Latino population (PMID:18929466)
• These results do not support a significant role of GRIA1 or CLINT1 in the development of schizophrenia in the German population. (PMID:21116212)
• Although epsinR has been shown to be a cargo adaptor, the present study indicates that it is an order of magnitude more abundant in CCVs than its known cargo protein, vti1b, suggesting that it may have other functions as well. (PMID:26179914)
• The cargo adapter protein CLINT1 is phosphorylated by the Numb-associated kinase BIKE and mediates dengue virus infection. (PMID:35452674)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	clint1a	ENSDARG00000025535
danio_rerio	clint1b	ENSDARG00000089914
mus_musculus	Clint1	ENSMUSG00000006169
rattus_norvegicus	Clint1	ENSRNOG00000005406
drosophila_melanogaster	lqfR	FBGN0261279

Paralogs (5): EPN3 (ENSG00000049283), EPN1 (ENSG00000063245), EPN2 (ENSG00000072134), MYCBPAP (ENSG00000136449), ENTHD1 (ENSG00000176177)

Protein

Protein identifiers

Clathrin interactor 1 — Q14677 (reviewed: Q14677)

Alternative names: Clathrin-interacting protein localized in the trans-Golgi region, Enthoprotin, Epsin-4, Epsin-related protein

All UniProt accessions (6): A0A0S2Z4Y4, A0A0S2Z5H3, Q14677, H0YCL3, H0YD52, H0YDU9

UniProt curated annotations — full annotation on UniProt →

Function. Binds to membranes enriched in phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2). May have a role in transport via clathrin-coated vesicles from the trans-Golgi network to endosomes. Stimulates clathrin assembly.

Subunit / interactions. Binds clathrin heavy chain and AP-2. Interacts with VTI1B. Interacts with GGA2 (via GAE domain). Interacts with AP1G1 (via GAE domain). Interacts with AP1G2 (via GAE domain).

Subcellular location. Cytoplasm. Perinuclear region. Membrane. Cytoplasmic vesicle. Clathrin-coated vesicle.

Tissue specificity. Ubiquitously expressed at low to intermediate levels.

Polymorphism. Genetic variations in CLINT1 may contribute to susceptibility to schizophrenia (SCZD1) and psychotic disorders in some populations.

Similarity. Belongs to the epsin family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q14677-1	1	yes
Q14677-2	2
Q14677-3	3

RefSeq proteins (3): NP_001182484, NP_001182485, NP_055481* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008942	ENTH_VHS	Homologous_superfamily
IPR013809	ENTH	Domain

Pfam: PF01417

UniProt features (53 total): mutagenesis site 15, modified residue 11, helix 9, region of interest 6, splice variant 3, binding site 2, compositionally biased region 2, chain 1, domain 1, sequence conflict 1, strand 1, turn 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
1XGW	X-RAY DIFFRACTION	1.9
2QY7	X-RAY DIFFRACTION	2
2V8S	X-RAY DIFFRACTION	2.22

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q14677-F1	58.15	0.21

Functional residue map

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

Ligand- & substrate-binding residues (2): 29; 67

Post-translational modifications (11): 163, 166, 173, 205, 210, 227, 245, 299, 308, 312, 624

Mutagenesis-validated functional residues (15):

Position	Phenotype
29	reduces lipid binding. abolishes lipid binding; when associated with g-34.
34	abolishes lipid binding; when associated with l-29.
41	normal binding to vti1b.
46	normal binding to vti1b.
52	abolished binding to vti1b.
53–54	abolished binding to vti1b.
95	normal binding to vti1b.
96	abolished binding to vti1b.
146	abolished binding to vti1b. rescued binding to vti1b r-23 mutant.
153	normal binding to vti1b.
159	normal binding to vti1b.
349	decreases ap-1 and ap-2 binding.
371	slightly decreases ap-1 binding.
422	strongly decreases clathrin binding.
423–426	strongly reduces clathrin binding.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-432722	Golgi Associated Vesicle Biogenesis
R-HSA-9918476	Assembly and Release of Dengue Virus Virions

MSigDB gene sets: 197 (showing top): IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_CLATHRIN_COAT_ASSEMBLY, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, ONKEN_UVEAL_MELANOMA_UP, GOCC_COATED_VESICLE, HEN1_01, GENTILE_UV_HIGH_DOSE_DN, GOCC_VESICLE_COAT, SCHLOSSER_SERUM_RESPONSE_DN, RYTTCCTG_ETS2_B, SESTO_RESPONSE_TO_UV_C5, FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN, ATCATGA_MIR433, BASAKI_YBX1_TARGETS_DN

GO Biological Process (2): endocytosis (GO:0006897), clathrin coat assembly (GO:0048268)

GO Molecular Function (5): phospholipid binding (GO:0005543), clathrin binding (GO:0030276), cadherin binding (GO:0045296), protein binding (GO:0005515), lipid binding (GO:0008289)

GO Cellular Component (12): nucleoplasm (GO:0005654), endosome (GO:0005768), Golgi apparatus (GO:0005794), cytosol (GO:0005829), plasma membrane (GO:0005886), membrane (GO:0016020), clathrin vesicle coat (GO:0030125), perinuclear region of cytoplasm (GO:0048471), cytoplasm (GO:0005737), endomembrane system (GO:0012505), clathrin-coated vesicle (GO:0030136), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
trans-Golgi Network Vesicle Budding	1
Dengue Virus Infection	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	6
cytoplasm	4
binding	2
endomembrane system	2
vesicle budding from membrane	1
membrane invagination	1
vesicle-mediated transport	1
import into cell	1
protein-containing complex assembly	1
lipid binding	1
protein binding	1
cell adhesion molecule binding	1
nuclear lumen	1
cytoplasmic vesicle	1
intracellular membrane-bounded organelle	1
membrane	1
cell periphery	1
clathrin coat	1
vesicle coat	1
clathrin-coated vesicle membrane	1
intracellular anatomical structure	1
vacuole	1
plasma membrane	1
coated vesicle	1
intracellular vesicle	1

Protein interactions and networks

STRING

1678 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLINT1	VTI1B	Q9UEU0	987
CLINT1	CLTCL1	P53675	866
CLINT1	CLTC	Q00610	859
CLINT1	PICALM	Q13492	829
CLINT1	GGA2	Q9UJY4	798
CLINT1	VAMP7	P51809	738
CLINT1	SNAP91	O60641	720
CLINT1	CLTB	P09497	674
CLINT1	STX16	O14662	661
CLINT1	OCRL	Q01968	656
CLINT1	AP2A1	O95782	642
CLINT1	GABRP	O00591	639
CLINT1	CLTA	P09496	623
CLINT1	EPS15	P42566	603
CLINT1	AMPH	P49418	602

IntAct

190 interactions, top by confidence:

A	B	Type	Score
MED4	MED19	psi-mi:“MI:2364”(proximity)	0.900
STAMBP	PIK3C2A	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
BMP2K	CLINT1	psi-mi:“MI:0915”(physical association)	0.710
BMP2K	CLINT1	psi-mi:“MI:0217”(phosphorylation reaction)	0.710
AP1S2	AP1G1	psi-mi:“MI:0914”(association)	0.660
CLINT1	Vti1b	psi-mi:“MI:0407”(direct interaction)	0.650
SEC16A	SEC13	psi-mi:“MI:0914”(association)	0.640
STAMBPL1	PIK3C2A	psi-mi:“MI:0914”(association)	0.640
CLINT1	VTI1B	psi-mi:“MI:2364”(proximity)	0.610
GABARAPL1	IPO5	psi-mi:“MI:0914”(association)	0.590
YWHAH	BLTP3B	psi-mi:“MI:2364”(proximity)	0.570
CLINT1	GDPD5	psi-mi:“MI:0915”(physical association)	0.560
CLINT1	WFS1	psi-mi:“MI:0915”(physical association)	0.560
CLINT1	KIF1B	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (324): CLINT1 (Affinity Capture-MS), AP2B1 (Co-fractionation), CLINT1 (Affinity Capture-MS), CLINT1 (Proximity Label-MS), CLINT1 (Proximity Label-MS), CLINT1 (Proximity Label-MS), CLINT1 (Proximity Label-MS), CLINT1 (Affinity Capture-MS), CLINT1 (Affinity Capture-MS), CLINT1 (Affinity Capture-MS), CLINT1 (Affinity Capture-MS), CLINT1 (Affinity Capture-MS), CLINT1 (Affinity Capture-MS), CLINT1 (Affinity Capture-MS), CLINT1 (Affinity Capture-MS)

ESM2 similar proteins: A7Z035, O08719, O14964, O55012, O60641, O75061, O75553, O88339, O88797, O95208, P47160, P52594, P70429, P78813, P97318, P98078, P98082, Q05140, Q0V8S0, Q13492, Q14677, Q27974, Q2TA45, Q4KLH5, Q5EA00, Q5F413, Q5R896, Q61548, Q67YI9, Q6CHN0, Q7M6Y3, Q7TN29, Q80TZ3, Q80VP1, Q8CHU3, Q8CJH2, Q8IYB5, Q8K2K6, Q8L860, Q8WU79

Diamond homologs: A7Z035, O74423, O88339, O95208, P47160, P78813, Q05785, Q12518, Q14677, Q4V882, Q54EH1, Q67YI9, Q80VP1, Q8CHU3, Q8IYW4, Q8VY07, Q91W69, Q93YP4, Q99KN9, Q9H201, Q9Y6I3, Q9Z1Z3, Q07872

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 184 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
WNT5A-dependent internalization of FZD4	5	30.9×	3e-05
Lysosome Vesicle Biogenesis	7	18.6×	9e-06
Golgi Associated Vesicle Biogenesis	11	17.9×	4e-09
Host Interactions of HIV factors	5	13.7×	9e-04
RHO GTPases activate PKNs	5	12.9×	1e-03
TBC/RABGAPs	6	12.7×	3e-04
EPH-ephrin mediated repulsion of cells	7	12.5×	7e-05
Clathrin-mediated endocytosis	16	11.1×	5e-10

GO biological processes:

GO term	Partners	Fold	FDR
clathrin coat assembly	7	41.4×	8e-08
clathrin-dependent endocytosis	9	34.9×	3e-09
negative regulation of protein localization to plasma membrane	5	20.8×	6e-04
mitophagy	7	14.8×	1e-04
synaptic vesicle endocytosis	5	14.4×	3e-03
autophagosome maturation	6	14.0×	6e-04
positive regulation of protein import into nucleus	5	14.0×	3e-03
autophagosome assembly	7	10.5×	6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	83
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2035 predictions. Top by Δscore:

Variant	Effect	Δscore
5:157794895:TACC:T	donor_loss	1.0000
5:157794897:CCT:C	donor_loss	1.0000
5:157805870:A:C	donor_gain	1.0000
5:157806108:TGTCG:T	acceptor_gain	1.0000
5:157806110:TCG:T	acceptor_gain	1.0000
5:157806111:CG:C	acceptor_gain	1.0000
5:157806111:CGC:C	acceptor_gain	1.0000
5:157806112:GC:G	acceptor_loss	1.0000
5:157806113:C:CC	acceptor_gain	1.0000
5:157806113:CT:C	acceptor_loss	1.0000
5:157806120:A:C	acceptor_gain	1.0000
5:157806122:A:C	acceptor_gain	1.0000
5:157806123:T:C	acceptor_gain	1.0000
5:157806123:T:TC	acceptor_gain	1.0000
5:157809623:AATAC:A	donor_loss	1.0000
5:157809624:ATAC:A	donor_loss	1.0000
5:157809625:TAC:T	donor_loss	1.0000
5:157809626:A:AT	donor_loss	1.0000
5:157809806:C:CC	acceptor_gain	1.0000
5:157809806:C:CG	acceptor_loss	1.0000
5:157809807:T:C	acceptor_loss	1.0000
5:157809816:CAT:C	acceptor_gain	1.0000
5:157813105:A:AC	donor_gain	1.0000
5:157813106:C:CC	donor_gain	1.0000
5:157813106:CTTGT:C	donor_gain	1.0000
5:157813223:CTCAT:C	acceptor_gain	1.0000
5:157813225:CAT:C	acceptor_gain	1.0000
5:157813228:C:CC	acceptor_gain	1.0000
5:157813230:A:AC	acceptor_gain	1.0000
5:157813230:A:C	acceptor_gain	1.0000

AlphaMissense

4168 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:157813126:C:G	A152P	1.000
5:157813134:C:G	R149P	1.000
5:157813143:C:G	R146P	1.000
5:157813146:A:G	L145P	1.000
5:157813146:A:T	L145H	1.000
5:157813194:C:A	R129L	1.000
5:157813194:C:G	R129P	1.000
5:157813195:G:C	R129G	1.000
5:157813199:A:C	N127K	1.000
5:157813199:A:T	N127K	1.000
5:157813206:C:A	G125V	1.000
5:157813206:C:T	G125D	1.000
5:157813207:C:A	G125C	1.000
5:157813207:C:G	G125R	1.000
5:157813207:C:T	G125S	1.000
5:157813212:T:C	D123G	1.000
5:157813212:T:G	D123A	1.000
5:157813213:C:G	D123H	1.000
5:157814205:A:G	L111P	1.000
5:157814211:C:G	R109P	1.000
5:157814214:A:G	L108S	1.000
5:157814226:T:G	H104P	1.000
5:157814227:G:C	H104D	1.000
5:157814229:T:A	E103V	1.000
5:157814230:C:T	E103K	1.000
5:157814231:T:A	R102S	1.000
5:157814231:T:G	R102S	1.000
5:157814232:C:G	R102T	1.000
5:157814235:G:T	A101D	1.000
5:157814236:C:G	A101P	1.000

dbSNP variants (sampled 300 via entrez): RS1000006570 (5:157851299 G>C), RS1000024134 (5:157840633 T>C), RS1000036771 (5:157823739 A>C,G), RS1000062608 (5:157857254 G>T), RS1000145384 (5:157809138 A>G), RS1000204416 (5:157803388 A>G), RS1000230513 (5:157860854 T>C), RS1000259218 (5:157804736 C>A,T), RS1000290624 (5:157848113 AT>A,ATT), RS1000298433 (5:157835426 A>C), RS1000350277 (5:157835727 C>A), RS1000389574 (5:157854043 A>G), RS1000433456 (5:157824596 G>C,T), RS1000450005 (5:157829295 C>CT), RS1000494274 (5:157816320 A>T)

Disease associations

OMIM: gene MIM:607265 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST007094_152	Diastolic blood pressure	3.000000e-19
GCST007095_53	Systolic blood pressure	6.000000e-08
GCST007095_54	Systolic blood pressure	2.000000e-07
GCST007096_164	Pulse pressure	1.000000e-07
GCST007098_104	Diastolic blood pressure	7.000000e-08
GCST007098_105	Diastolic blood pressure	2.000000e-07
GCST007099_29	Systolic blood pressure	1.000000e-19

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0006336	diastolic blood pressure
EFO:0006335	systolic blood pressure
EFO:0005763	pulse pressure measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066453 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.78	Kd	164.3	nM	CHEMBL5653589
6.78	ED50	164.3	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 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	2148082: Binding affinity to human CLINT1 incubated for 45 mins by Kinobead based pull down assay	kd	0.1643	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression, affects binding, increases reaction	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
uranyl acetate	affects expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, affects localization, increases expression	1
beta-lapachone	decreases expression	1
methylparaben	increases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
ICG 001	decreases expression	1
bisphenol B	increases expression	1
LDN 193189	decreases expression, affects cotreatment	1
NSC 689534	affects binding, increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Caffeine	affects phosphorylation	1
Copper	affects binding, increases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Formaldehyde	decreases expression	1
Furaldehyde	affects cotreatment, affects localization, increases expression	1
Ivermectin	decreases expression	1
Lead	decreases expression	1
Ozone	affects expression, increases abundance	1
Sodium Chloride	affects cotreatment, affects localization, increases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	increases expression	1
Uranium	affects expression	1
Valproic Acid	affects expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5651124	Binding	Binding affinity to human CLINT1 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.