CLPTM1

Summary

CLPTM1 (CLPTM1 regulator of GABA type A receptor forward trafficking, HGNC:2087) is a protein-coding gene on chromosome 19q13.32, encoding Putative lipid scramblase CLPTM1 (O96005). Involved in GABAergic but not glutamatergic transmission.

Predicted to enable GABA receptor binding activity. Predicted to be involved in regulation of T cell differentiation in thymus. Located in membrane.

Source: NCBI Gene 1209 — RefSeq curated summary.

At a glance

• GWAS associations: 35
• Clinical variants (ClinVar): 143 total
• Druggable target: yes
• MANE Select transcript: NM_001294

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:2087
Approved symbol	CLPTM1
Name	CLPTM1 regulator of GABA type A receptor forward trafficking
Location	19q13.32
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000104853
Ensembl biotype	protein_coding
OMIM	604783
Entrez	1209

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 13 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000337392, ENST00000541297, ENST00000546079, ENST00000585961, ENST00000586915, ENST00000586975, ENST00000587537, ENST00000588274, ENST00000588855, ENST00000589158, ENST00000589347, ENST00000591304, ENST00000870266, ENST00000870267, ENST00000870268, ENST00000870269, ENST00000870270, ENST00000920192, ENST00000969524

RefSeq mRNA: 3 — MANE Select: NM_001294 NM_001282175, NM_001282176, NM_001294

CCDS: CCDS12651, CCDS74394, CCDS74395

Canonical transcript exons

ENST00000337392 — 14 exons

Exon	Start	End
ENSE00000712124	44987179	44987423
ENSE00000712141	44991238	44991373
ENSE00001360300	44992611	44993341
ENSE00002801858	44955380	44955467
ENSE00003475329	44974439	44974597
ENSE00003503615	44988080	44988173
ENSE00003525210	44973087	44973210
ENSE00003560047	44992233	44992400
ENSE00003594667	44990850	44990945
ENSE00003615109	44961963	44962075
ENSE00003635400	44977343	44977460
ENSE00003641953	44986455	44986575
ENSE00003682328	44990395	44990585
ENSE00003784273	44985218	44985303

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 98.34.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 54.8056 / max 695.8460, expressed in 1818 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
176362	52.5070	1817
176359	1.0775	640
176365	0.5631	13
176360	0.2846	123
176366	0.2239	10
176361	0.1217	35
176367	0.0278	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right adrenal gland	UBERON:0001233	98.34	gold quality
right adrenal gland cortex	UBERON:0035827	98.34	gold quality
left adrenal gland	UBERON:0001234	98.33	gold quality
left adrenal gland cortex	UBERON:0035825	98.26	gold quality
right frontal lobe	UBERON:0002810	97.83	gold quality
adrenal cortex	UBERON:0001235	97.66	gold quality
stromal cell of endometrium	CL:0002255	97.63	gold quality
nucleus accumbens	UBERON:0001882	97.63	gold quality
caudate nucleus	UBERON:0001873	97.61	gold quality
adrenal gland	UBERON:0002369	97.50	gold quality
putamen	UBERON:0001874	97.45	gold quality
cingulate cortex	UBERON:0003027	97.29	gold quality
anterior cingulate cortex	UBERON:0009835	97.27	gold quality
amygdala	UBERON:0001876	97.09	gold quality
prefrontal cortex	UBERON:0000451	97.07	gold quality
metanephros cortex	UBERON:0010533	97.00	gold quality
mucosa of transverse colon	UBERON:0004991	96.97	gold quality
skin of leg	UBERON:0001511	96.94	gold quality
right lobe of liver	UBERON:0001114	96.83	gold quality
apex of heart	UBERON:0002098	96.77	gold quality
right hemisphere of cerebellum	UBERON:0014890	96.75	gold quality
body of stomach	UBERON:0001161	96.72	gold quality
skin of abdomen	UBERON:0001416	96.69	gold quality
left testis	UBERON:0004533	96.60	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	96.56	gold quality
right testis	UBERON:0004534	96.55	gold quality
right lobe of thyroid gland	UBERON:0001119	96.45	gold quality
hypothalamus	UBERON:0001898	96.35	gold quality
cerebellar hemisphere	UBERON:0002245	96.29	gold quality
adenohypophysis	UBERON:0002196	96.27	gold quality

Single-cell (SCXA)

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

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

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

25 targeting CLPTM1, 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-4682	100.00	68.89	1258
HSA-MIR-7845-5P	99.88	64.88	771
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-6794-5P	99.76	66.38	1048
HSA-MIR-4716-3P	99.69	66.73	1022
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-892A	99.54	68.16	1141
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-145-3P	99.33	67.66	764
HSA-MIR-8077	99.17	66.67	862
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-5001-5P	99.05	66.76	1972
HSA-MIR-412-3P	98.86	66.89	712
HSA-MIR-6754-3P	98.84	66.60	889
HSA-MIR-605-5P	98.79	68.24	1161
HSA-MIR-7113-5P	97.88	67.33	1735
HSA-MIR-4494	97.86	64.93	850
HSA-MIR-6875-5P	96.87	65.49	958
HSA-MIR-3126-5P	96.87	65.83	912
HSA-MIR-6729-5P	93.02	62.76	138
HSA-MIR-4649-5P	93.02	63.85	141
HSA-MIR-4707-5P	90.95	65.69	110
HSA-MIR-10392-3P	88.79	61.83	122

Literature-anchored findings (GeneRIF, showing 8)

• results identify a critical function of type IV collagens in modulating Dpp in the extracellular space during Drosophila development (PMID:18701888)
• Identification of inactivating mutations in the JAK1, SYNJ2, and CLPTM1 genes in prostate cancer cells (PMID:16102578)
• Results suggest that single nucleotide polymorphism in CLPTM1 influences telomere length and so increases risk of melanoma. (PMID:25457634)
• that the rs401681 polymorphism in the TERT-CLPTM1L locus contributes to lung carcinogenesis only in patients harboring an EGFR mutation (PMID:29033187)
• Non-tumorous oral squamous cells exhibited vague, weak, or little cytoplasmic staining with anti-Clptm1 and CRR9 antibodies. By contrast, robust Clptm1 and CRR9 immunoreactivity was found at the cancer invasion front in 55 and 54 of the 98 OSCC tissue specimens, respectively. (PMID:30635792)
• Authors detected three genome-wide statistically significant single nucleotide polymorphisms mapped to Chromosome 5 CLPTM1L-TERT region. (PMID:31009812)
• a single SNP located at TERT/CLPTM1L multi-cancer risk region as a genetic modifier for risk of pancreatic cancer and melanoma in Dutch CDKN2A mutation carriers (PMID:31203567)
• De novo CLPTM1 variants with reduced GABAA R current response in patients with epilepsy. (PMID:37577761)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	clptm1	ENSDARG00000018973
mus_musculus	Clptm1	ENSMUSG00000002981
rattus_norvegicus	Clptm1	ENSRNOG00000018255
drosophila_melanogaster	CG3702	FBGN0031590
caenorhabditis_elegans		WBGENE00011302
caenorhabditis_elegans		WBGENE00016469

Paralogs (1): CLPTM1L (ENSG00000049656)

Protein

Protein identifiers

Putative lipid scramblase CLPTM1 — O96005 (reviewed: O96005)

Alternative names: Cleft lip and palate transmembrane protein 1

All UniProt accessions (6): O96005, A0A0S2Z3H2, K7EJ16, K7EKQ7, K7EQQ1, K7ERL5

UniProt curated annotations — full annotation on UniProt →

Function. Involved in GABAergic but not glutamatergic transmission. Binds and traps GABAA receptors in the endoplasmic reticulum (ER). Modulates postsynaptic GABAergic transmission, and therefore inhibitory neurotransmission, by reducing the plasma membrane expression of these receptors. Altered GABAergic signaling is one among many causes of cleft palate. Might function as a lipid scramblase, translocating lipids in membranes from one leaflet to the other one. Required for efficient glycosylphosphatidylinositol (GPI) inositol deacylation in the ER, which is a crucial step to switch GPI-anchored proteins (GPI-APs) from protein folding to transport states. May play a role in T-cell development.

Subcellular location. Membrane.

Tissue specificity. Widely expressed.

Polymorphism. A chromosomal translocation involving CLPTM1 is found in a family with cleft lip and palate. However, no etiologic link with the disease is characterized. Translocation t(2;19)(q11.2;q13.3).

Similarity. Belongs to the CLPTM1 family.

Isoforms (3)

UniProt ID	Names	Canonical?
O96005-1	1	yes
O96005-3	2
O96005-4	3

RefSeq proteins (3): NP_001269104, NP_001269105, NP_001285* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008429	CLPTM1	Family

Pfam: PF05602

UniProt features (33 total): topological domain 6, glycosylation site 6, transmembrane region 5, sequence conflict 5, region of interest 2, compositionally biased region 2, modified residue 2, splice variant 2, initiator methionine 1, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O96005-F1	70.90	0.12

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 (2): 2, 601

Glycosylation sites (6): 28, 119, 161, 241, 295, 413

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 151 (showing top): GOBP_REGULATION_OF_CELL_ACTIVATION, ROVERSI_GLIOMA_COPY_NUMBER_UP, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, GOCC_CELL_SURFACE, SP1_Q2_01, PATIL_LIVER_CANCER, GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION, BROWNE_HCMV_INFECTION_24HR_UP, GOBP_REGULATION_OF_HEMOPOIESIS, WANG_LMO4_TARGETS_DN, KOYAMA_SEMA3B_TARGETS_UP, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, GOBP_REGULATION_OF_LYMPHOCYTE_DIFFERENTIATION, TGACATY_UNKNOWN, NOUZOVA_TRETINOIN_AND_H4_ACETYLATION

GO Biological Process (2): cell differentiation (GO:0030154), regulation of T cell differentiation in thymus (GO:0033081)

GO Molecular Function (2): GABA receptor binding (GO:0050811), protein binding (GO:0005515)

GO Cellular Component (4): plasma membrane (GO:0005886), external side of plasma membrane (GO:0009897), endomembrane system (GO:0012505), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
plasma membrane	2
cellular anatomical structure	2
cellular developmental process	1
T cell differentiation in thymus	1
regulation of T cell differentiation	1
signaling receptor binding	1
binding	1
membrane	1
cell periphery	1
cell surface	1
side of membrane	1
vacuole	1

Protein interactions and networks

STRING

1452 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLPTM1	ITM2C	Q9NQX7	611
CLPTM1	MTSS1	O43312	549
CLPTM1	HTRA1	Q92743	540
CLPTM1	GLG1	Q92896	523
CLPTM1	CEACAM19	Q7Z692	506
CLPTM1	UBAC2	Q8NBM4	456
CLPTM1	TERT	O14746	446
CLPTM1	SHISA7	A6NL88	446
CLPTM1	TBX22	Q9Y458	433
CLPTM1	HM13	Q8TCT9	430
CLPTM1	TRAPPC6A	O75865	419
CLPTM1	INSYN1	Q2T9L4	416
CLPTM1	C18orf32	Q8TCD1	414
CLPTM1	SLC6A18	Q96N87	405
CLPTM1	SMYD2	Q9NRG4	404

IntAct

142 interactions, top by confidence:

A	B	Type	Score
TCTN2	CLGN	psi-mi:“MI:0914”(association)	0.780
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
CFTR	HAX1	psi-mi:“MI:0914”(association)	0.610
SLC10A2	CLPTM1	psi-mi:“MI:0915”(physical association)	0.560
SCNN1D	ABHD16A	psi-mi:“MI:0914”(association)	0.530
FBXO2	TMEM131L	psi-mi:“MI:0914”(association)	0.530
CLGN	NPC1	psi-mi:“MI:0914”(association)	0.530
CCR6	PODXL	psi-mi:“MI:0914”(association)	0.530
NCEH1	CLGN	psi-mi:“MI:0914”(association)	0.530
LPAR1	TMEM223	psi-mi:“MI:0914”(association)	0.530
	VAPB	psi-mi:“MI:0914”(association)	0.500
SRD5A2	CLPTM1	psi-mi:“MI:0915”(physical association)	0.500
SRD5A2	CLPTM1	psi-mi:“MI:0914”(association)	0.500
Unc93b1	CLPTM1	psi-mi:“MI:0915”(physical association)	0.500
CLPTM1	AP3S1	psi-mi:“MI:0915”(physical association)	0.400
CLPTM1	CCR2	psi-mi:“MI:0915”(physical association)	0.370
CLPTM1	CCR4	psi-mi:“MI:0915”(physical association)	0.370
CLPTM1	F2RL1	psi-mi:“MI:0915”(physical association)	0.370
CLPTM1	FZD7	psi-mi:“MI:0915”(physical association)	0.370
	CLPTM1	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (198): CLPTM1 (Affinity Capture-MS), CLPTM1 (Affinity Capture-MS), CLPTM1 (Affinity Capture-MS), CLPTM1 (Affinity Capture-MS), CLPTM1 (Affinity Capture-MS), CLPTM1 (Affinity Capture-MS), CLPTM1 (Affinity Capture-MS), CLPTM1 (Affinity Capture-MS), CLPTM1 (Affinity Capture-MS), CLPTM1 (Affinity Capture-MS), CLPTM1 (Affinity Capture-MS), CLPTM1 (Affinity Capture-MS), CLPTM1 (Affinity Capture-MS), CLPTM1 (Affinity Capture-MS), TCTN2 (Affinity Capture-MS)

ESM2 similar proteins: A0A078H868, A0A8I3MKU8, A1C7T5, A1DIF7, A2R616, A6S950, B0XUW3, B2B2N5, B6HJA3, B8N6H2, B9RK42, C0NLX2, C0RZV6, C1G565, C1GZK1, C4JDF8, C5FZ62, C5GN10, C5JCV0, C5PEI5, C6H4B5, C7Z7C3, D1ZIW5, D4AT37, D4DGR3, I6VSD2, O94673, O96005, Q0CVD7, Q0IJ20, Q28FY5, Q29BL9, Q2H0U8, Q2TA63, Q2UDE5, Q3SZR6, Q4WZS1, Q5BBC6, Q5BIY5, Q6DFI2

Diamond homologs: A2VE61, O96005, Q2NL17, Q54RJ1, Q5R7B1, Q5ZKJ0, Q6DEL2, Q6DHU1, Q8BXA5, Q8VBZ3, Q96KA5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 171 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.

GO biological processes:

GO term	Partners	Fold	FDR
ERAD pathway	10	12.6×	7e-06
sodium ion transmembrane transport	7	9.9×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	87
Likely benign	22
Benign	12

Top pathogenic / likely-pathogenic (0)

SpliceAI

2661 predictions. Top by Δscore:

Variant	Effect	Δscore
19:44955464:TCAGG:T	donor_loss	1.0000
19:44955466:AGG:A	donor_loss	1.0000
19:44955467:GGTAC:G	donor_loss	1.0000
19:44961958:CACA:C	acceptor_loss	1.0000
19:44961960:CA:C	acceptor_loss	1.0000
19:44961961:AGG:A	acceptor_loss	1.0000
19:44973085:A:AG	acceptor_gain	1.0000
19:44973085:AG:A	acceptor_gain	1.0000
19:44973086:G:GA	acceptor_gain	1.0000
19:44973086:GG:G	acceptor_gain	1.0000
19:44973211:G:GG	donor_gain	1.0000
19:44974434:A:AG	acceptor_gain	1.0000
19:44974436:CA:C	acceptor_loss	1.0000
19:44974437:A:AG	acceptor_gain	1.0000
19:44974438:G:GT	acceptor_gain	1.0000
19:44974438:GA:G	acceptor_gain	1.0000
19:44974438:GAA:G	acceptor_gain	1.0000
19:44974438:GAAC:G	acceptor_gain	1.0000
19:44974438:GAACC:G	acceptor_gain	1.0000
19:44974560:GCTGC:G	donor_gain	1.0000
19:44974578:C:G	donor_gain	1.0000
19:44974595:CAGG:C	donor_loss	1.0000
19:44974596:AG:A	donor_loss	1.0000
19:44974597:GG:G	donor_loss	1.0000
19:44977340:CAG:C	acceptor_gain	1.0000
19:44977341:A:AG	acceptor_gain	1.0000
19:44977341:AGA:A	acceptor_gain	1.0000
19:44977342:G:A	acceptor_loss	1.0000
19:44977342:G:GG	acceptor_gain	1.0000
19:44977342:GA:G	acceptor_gain	1.0000

AlphaMissense

4410 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:44973107:T:A	I69N	1.000
19:44974443:T:C	L105P	1.000
19:44985263:T:C	L211P	1.000
19:44986491:C:G	H237D	1.000
19:44986494:T:A	W238R	1.000
19:44986494:T:C	W238R	1.000
19:44986497:C:G	H239D	1.000
19:44986539:T:A	W253R	1.000
19:44986539:T:C	W253R	1.000
19:44986541:G:C	W253C	1.000
19:44986541:G:T	W253C	1.000
19:44987187:T:C	F268L	1.000
19:44987189:C:A	F268L	1.000
19:44987189:C:G	F268L	1.000
19:44987215:C:A	P277H	1.000
19:44987238:T:A	W285R	1.000
19:44987238:T:C	W285R	1.000
19:44987240:G:C	W285C	1.000
19:44987240:G:T	W285C	1.000
19:44987328:T:A	W315R	1.000
19:44987328:T:C	W315R	1.000
19:44987340:G:C	A319P	1.000
19:44987344:C:A	A320D	1.000
19:44987423:G:C	K346N	1.000
19:44987423:G:T	K346N	1.000
19:44988084:C:A	A348D	1.000
19:44988087:T:C	L349P	1.000
19:44988111:T:C	L357P	1.000
19:44988140:C:G	H367D	1.000
19:44988143:A:C	S368R	1.000

dbSNP variants (sampled 300 via entrez): RS1000005480 (19:44955400 C>T), RS1000213473 (19:44964977 G>A,C), RS1000326227 (19:44966556 G>T), RS1000332121 (19:44972180 T>C), RS1000419917 (19:44969259 CTGT>C), RS1000483226 (19:44966872 C>T), RS1000488693 (19:44977022 T>C), RS1000493576 (19:44975090 A>G), RS1000592145 (19:44960710 A>T), RS1000665851 (19:44979833 A>AG), RS1000751465 (19:44969584 C>T), RS1000887564 (19:44955362 G>A,C), RS1000959114 (19:44955132 C>A,T), RS1000969252 (19:44956431 G>C), RS1001047978 (19:44971969 C>T)

Disease associations

OMIM: gene MIM:604783 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

35 associations (top):

Study	Trait	p-value
GCST002690_17	Very long-chain saturated fatty acid levels (fatty acid 20:0)	4.000000e-06
GCST005950_15	Body mass index x sex x age interaction (4df test)	2.000000e-10
GCST005951_56	Body mass index	1.000000e-06
GCST005952_8	Body mass index (age>50)	9.000000e-12
GCST005954_4	Body mass index x age interaction	2.000000e-07
GCST006990_2	Cerebrospinal AB1-42 levels in Alzheimer’s disease dementia	3.000000e-07
GCST006993_15	Hippocampal volume in Alzheimer’s disease dementia	8.000000e-07
GCST006996_4	Cerebrospinal AB1-42 levels in mild cognitive impairment	6.000000e-27
GCST006997_3	Cerebrospinal fluid t-tau levels in mild cognitive impairment	1.000000e-13
GCST006998_7	Cerebrospinal fluid p-tau levels in mild cognitive impairment	2.000000e-11
GCST007001_15	Cerebrospinal AB1-42 levels in normal cognition	9.000000e-11
GCST007007_4	Cerebrospinal fluid t-tau levels	1.000000e-20
GCST007008_6	Cerebrospinal fluid p-tau levels	3.000000e-18
GCST007009_7	Hippocampal volume	2.000000e-19
GCST007010_3	Logical memory (delayed recall)	2.000000e-18
GCST007011_3	Logical memory (immediate recall)	2.000000e-13
GCST007012_6	Cerebrospinal fluid AB1-42 levels	1.000000e-51
GCST007320_14	Alzheimer’s disease or family history of Alzheimer’s disease	7.000000e-50
GCST007320_20	Alzheimer’s disease or family history of Alzheimer’s disease	1.000000e-23
GCST007320_76	Alzheimer’s disease or family history of Alzheimer’s disease	2.000000e-11
GCST007320_79	Alzheimer’s disease or family history of Alzheimer’s disease	9.000000e-11
GCST007320_86	Alzheimer’s disease or family history of Alzheimer’s disease	6.000000e-09
GCST007827_13	Alzheimer’s disease or HDL levels (pleiotropy)	7.000000e-22
GCST007827_3	Alzheimer’s disease or HDL levels (pleiotropy)	1.000000e-97
GCST007827_5	Alzheimer’s disease or HDL levels (pleiotropy)	7.000000e-74
GCST007827_6	Alzheimer’s disease or HDL levels (pleiotropy)	7.000000e-54
GCST007827_7	Alzheimer’s disease or HDL levels (pleiotropy)	5.000000e-50
GCST007827_8	Alzheimer’s disease or HDL levels (pleiotropy)	3.000000e-36
GCST008870_74	Keratinocyte cancer (MTAG)	6.000000e-46
GCST008871_46	Basal cell carcinoma	8.000000e-56

EFO canonical traits (14, from GWAS)

EFO ID	Trait name
EFO:0006796	very long-chain saturated fatty acid measurement
EFO:0004340	body mass index
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0004670	beta-amyloid 1-42 measurement
EFO:0005035	hippocampal volume
EFO:0004760	t-tau measurement
EFO:0004763	p-tau measurement
EFO:0004874	memory performance
EFO:0009268	family history of Alzheimer’s disease
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0010176	keratinocyte carcinoma
EFO:0004615	apolipoprotein B measurement
EFO:0004611	low density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066984 (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
7.56	Kd	27.49	nM	CHEMBL5653589
7.56	ED50	27.49	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	2148088: Binding affinity to human CLPTM1 incubated for 45 mins by Kinobead based pull down assay	kd	0.0275	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, increases expression	3
sodium arsenite	increases abundance, increases expression, decreases expression, affects cotreatment	3
Air Pollutants	increases oxidation, increases expression, affects cotreatment, increases abundance	2
Estradiol	decreases expression, increases expression	2
Mercury	decreases expression, increases expression	2
Methotrexate	affects response to substance, decreases expression	2
Smoke	decreases expression, increases abundance, increases expression	2
aristolochic acid I	increases expression	1
bisphenol F	increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	increases abundance, affects cotreatment, increases oxidation	1
deoxynivalenol	decreases expression	1
beta-lapachone	increases expression	1
nickel chloride	decreases expression	1
perfluorooctanoic acid	decreases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
benzo(e)pyrene	affects methylation	1
aflatoxin B2	decreases methylation	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
2,3-dimethoxy-1,4-naphthoquinone	decreases expression	1
bisphenol B	increases expression	1
14-deoxy-11,12-didehydroandrographolide	decreases expression	1
bisphenol S	increases expression	1
bisphenol AF	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
Bortezomib	decreases expression	1
Temozolomide	decreases expression	1
Leflunomide	decreases expression	1
Acetaminophen	increases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	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
CHEMBL5651130	Binding	Binding affinity to human CLPTM1 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

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_E1TY	HAP1 CLPTM1 (-) 3	Cancer cell line	Male
CVCL_E1TZ	HAP1 CLPTM1 (-) 4	Cancer cell line	Male
CVCL_SJ30	HAP1 CLPTM1 (-) 1	Cancer cell line	Male
CVCL_XM86	HAP1 CLPTM1 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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