THY1

Summary

THY1 (Thy-1 cell surface antigen, HGNC:11801) is a protein-coding gene on chromosome 11q23.3, encoding Thy-1 membrane glycoprotein (P04216). May play a role in cell-cell or cell-ligand interactions during synaptogenesis and other events in the brain.

This gene encodes a cell surface glycoprotein and member of the immunoglobulin superfamily of proteins. The encoded protein is involved in cell adhesion and cell communication in numerous cell types, but particularly in cells of the immune and nervous systems. The encoded protein is widely used as a marker for hematopoietic stem cells. This gene may function as a tumor suppressor in nasopharyngeal carcinoma. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 7070 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 32 total
• MANE Select transcript: NM_006288

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11801
Approved symbol	THY1
Name	Thy-1 cell surface antigen
Location	11q23.3
Locus type	gene with protein product
Status	Approved
Aliases	CD90
Ensembl gene	ENSG00000154096
Ensembl biotype	protein_coding
OMIM	188230
Entrez	7070

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 19 protein_coding, 3 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000284240, ENST00000524659, ENST00000524970, ENST00000527590, ENST00000528295, ENST00000528522, ENST00000532974, ENST00000533840, ENST00000580275, ENST00000584021, ENST00000900758, ENST00000900759, ENST00000900760, ENST00000900761, ENST00000900762, ENST00000918468, ENST00000918469, ENST00000918470, ENST00000918471, ENST00000918472, ENST00000918473, ENST00000918474, ENST00000918475, ENST00000956364

RefSeq mRNA: 4 — MANE Select: NM_006288 NM_001311160, NM_001311162, NM_001372050, NM_006288

CCDS: CCDS8424, CCDS91612

Canonical transcript exons

ENST00000284240 — 4 exons

Exon	Start	End
ENSE00001014018	119415476	119419520
ENSE00003529769	119420869	119420929
ENSE00003601322	119420051	119420386
ENSE00003901891	119423113	119423172

Expression profiles

Bgee: expression breadth ubiquitous, 271 present calls, max score 99.48.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 166.4080 / max 2500.2407, expressed in 1203 samples.

FANTOM5 promoters (11 alternative TSS)

Promoter ID	TPM avg	Samples expressed
122741	145.5184	1158
122742	18.2272	1081
122743	0.5055	112
122740	0.4502	248
122727	0.2825	123
122732	0.2682	135
122731	0.2620	135
122730	0.2603	161
122729	0.2506	142
122728	0.2017	106

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
prefrontal cortex	UBERON:0000451	99.48	gold quality
stromal cell of endometrium	CL:0002255	99.07	gold quality
right frontal lobe	UBERON:0002810	98.99	gold quality
gall bladder	UBERON:0002110	98.98	gold quality
frontal cortex	UBERON:0001870	98.94	gold quality
frontal lobe	UBERON:0016525	98.94	gold quality
lateral nuclear group of thalamus	UBERON:0002736	98.89	gold quality
Brodmann (1909) area 9	UBERON:0013540	98.86	gold quality
orbitofrontal cortex	UBERON:0004167	98.71	gold quality
dorsal root ganglion	UBERON:0000044	98.65	gold quality
nucleus accumbens	UBERON:0001882	98.64	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	98.63	gold quality
superior frontal gyrus	UBERON:0002661	98.61	gold quality
neocortex	UBERON:0001950	98.45	gold quality
frontal pole	UBERON:0002795	98.43	gold quality
Brodmann (1909) area 46	UBERON:0006483	98.42	gold quality
parietal lobe	UBERON:0001872	98.24	gold quality
cerebral cortex	UBERON:0000956	98.14	gold quality
postcentral gyrus	UBERON:0002581	98.12	gold quality
Brodmann (1909) area 10	UBERON:0013541	98.05	gold quality
cingulate cortex	UBERON:0003027	98.04	gold quality
anterior cingulate cortex	UBERON:0009835	98.01	gold quality
putamen	UBERON:0001874	98.00	gold quality
cortical plate	UBERON:0005343	97.95	gold quality
substantia nigra pars compacta	UBERON:0001965	97.92	gold quality
smooth muscle tissue	UBERON:0001135	97.90	gold quality
pons	UBERON:0000988	97.88	gold quality
lateral globus pallidus	UBERON:0002476	97.87	gold quality
telencephalon	UBERON:0001893	97.85	gold quality
Ammon’s horn	UBERON:0001954	97.82	gold quality

Single-cell (SCXA)

Detected in 22 experiment(s), a significant marker in 20.

Experiment	Marker?	Max mean expression
E-MTAB-6819	yes	1207.34
E-MTAB-8271	yes	538.25
E-MTAB-10662	yes	458.12
E-MTAB-8530	yes	398.72
E-MTAB-10287	yes	101.88
E-HCAD-35	yes	53.53
E-MTAB-8410	yes	53.39
E-HCAD-5	yes	42.57
E-HCAD-10	yes	40.53
E-MTAB-6678	yes	26.68
E-GEOD-84465	yes	25.81
E-HCAD-31	yes	21.97
E-CURD-46	yes	13.37
E-MTAB-5061	yes	10.92
E-CURD-112	yes	8.44

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): DLX5, EOMES, ETS1, GATA6, HLX, HR, ID2, POU5F1, TBX18, TBXT, ZFP42

miRNA regulators (miRDB)

81 targeting THY1, 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-4533	100.00	69.48	2758
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-6857-5P	99.87	65.32	985
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-6715B-5P	99.64	69.63	1420
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-7152-5P	99.60	69.33	2094
HSA-MIR-548AV-5P	99.60	70.84	2107
HSA-MIR-548K	99.60	70.84	2107
HSA-MIR-12122	99.56	69.33	1672
HSA-MIR-4269	99.55	69.89	1373
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4441	99.49	66.56	3216

Literature-anchored findings (GeneRIF, showing 40)

• Review article on CD90 structure and function. (PMID:11860231)
• Thy-1/Thy-1 ligand interaction may play a role in adhesion of melanoma cells to endothelial cells (PMID:12074634)
• THY1 is a putative tumor suppressor gene for ovarian cancer; and THBS1, SPARC, and FN1 are genes associated with the regulation of in vivo tumor growth rate (PMID:12781446)
• Fibroblast Thy-1 display pre-determines lineage to a contractile or lipid-like phenotype in the human myometrium and orbit. (PMID:14507638)
• The interaction between Thy-1 and Mac-1 is involved in the adhesion of leukocytes to activated endothelial cells as well as in subsequent transendothelial migration of leukocytes into the perivascular tissue. (PMID:15004192)
• THY1 can be designated as a putative tumor suppressor gene for human ovarian cancer. (PMID:15104276)
• IE or E gene products of human cytomegalovirus induce a so far unidentified soluble factor that mediates Thy-1 downregulation. (PMID:15218185)
• results indicate that alphaX-beta2 specifically interacts with Thy-1 (PMID:15850796)
• new pair of adhesion molecules, Thy-1 and alphavbeta3, identified that mediate the interaction of melanoma cells and activated endothelial cells (PMID:15897908)
• THY1 is a good candidate tumour suppressor gene in nasopharyngeal carcinoma, which is significantly associated with lymph node metastases. (PMID:16007174)
• Role of endothelial cell receptor Thy1 in cell adhesion was shown. (PMID:16374458)
• Thy 1 mRNA levels do not reflect the number of RGCs present and extend this to include a parallel decrease in Thy1 protein levels. (PMID:16531284)
• Expression of Thy1 decreased in differentiated ADSC and BMSC. Expression of albumin, CYP2E1, and CYP3A4 increased in differentiated BMSC and ADSC. Hepatic gene activation may involve increased C/EBPbeta and HNF4alpha. (PMID:17007050)
• the distribution and proportion of CD90 positive cells in thyroid associated ophthalmopathy (TAO) and normal orbital tissue (PMID:17243294)
• Thy-1 is not a marker of oval cells but is present on a subpopulation of myofibroblasts/stellate cells. (PMID:17884967)
• Thy1-negative NBL patients have a significantly impaired overall survival compared with Thy1-positive NBL patients. Thus, Thy1 seemed to be a marker with a specific prognostic value in NBL patients. (PMID:17952444)
• All the tumor specimens and 91.6% of blood samples from liver cancer patients bore the CD45(-)CD90+ population, which could generate tumor nodules in immunodeficient mice (PMID:18242515)
• Results support the general concept that the function of ‘adhesion molecules’ in particular of Thy-1, may not only be to provide mechanical support but also regulate neutrophil functions such as extravasation and recruitment of additional neutrophils. (PMID:18389476)
• Epigenetic regulation of Thy-1 is a novel and potentially reversible mechanism in fibrosis that may offer the possibility of new therapeutic options (PMID:18556592)
• increased Thy-1 expression in Graves ophthalmopathy orbital tissues and cultures is likely a consequence of the orbital disease process, reflecting both the presence of increased numbers of Thy-1-positive cells and higher expression on those cells. (PMID:18976167)
• elevated expression of CD90 previously observed in the cancer-associated stroma of the human prostate is biologically significant (PMID:19267366)
• Mitogen-Activated Protein Kinases are essential signalling intermediates for the Antigen CD90 driven proliferation of mouse T-lymphocytes. (PMID:19324083)
• CD90 and CD110 are are useful positive-selection markers for the isolation of cancer stem cells in some cases of T-ALL. (PMID:19341705)
• The decreased level of THY1 expression may be related with the occurrence and development of ovarian serous cystadenocarcinoma. (PMID:19538887)
• Down-regulated/loss expression of THY1 protein in epithelial ovarian cancer is significantly correlated with cancer cell proliferation and metastasis in the epithelial ovarian cancer. (PMID:19615261)
• Data identified three membrane-associated proteins, synaptosomal associated protein 25 (SNAP25), Thy-1 cell surface antigen and zonadhesin, interact with sex hormone binding globulin (SHBG)-ing proteins in the brain. (PMID:19724880)
• The CD90 positive prostate tumor-associated stromal cells showed decreased expression of CXC-chemokines and genes involved in smooth muscle differentiation. (PMID:19737398)
• Loss of expression of THY1 is associated with nasopharyngeal carcinoma. (PMID:19921696)
• down-regulated KLF4, CHGA,GPX3, SST and LIPF, together with up-regulated SERPINH1, THY1 and INHBA is an 8-gene signature for gastric cancer (PMID:20043075)
• Thy-1-integrin alpha(v)beta(5) interactions inhibit contraction-induced latent TGF-beta1 activation, presumably by blocking the binding of extracellular matrix-bound latent TGF-beta1 with integrin alpha(v)beta(5). (PMID:20463011)
• we have identified a stromal cell type (CD90+ fibroblasts) and a molecule (CD90) that distinguishes cancer-associated stroma from ‘benign’ stroma in the prostate (PMID:20562849)
• overexpression of Thy1 may not suppress the development of hepatocellular carcinoma(HCC) Thy1 could provide a clinical prognostic marker for HC (PMID:21272924)
• Loss of Thy-1 in human lung fibroblasts induces a fibrogenic phenotype. (PMID:21577212)
• Data show that a cell population with the CD90 phenotype is enriched in sphere-cultured cells from gastric primary tumors. (PMID:21743497)
• human CD90 identifies a subset of Th17 and Tc17 cells within CD4(+) and CD8(+) T cells, respectively, which are depleted during HIV infection (PMID:22184726)
• CD90 is not only a potential prognostic marker for high-grade gliomas but also a marker for cancer stem cells within gliomas (PMID:22203689)
• binding of leukocytes to activated endothelium mediated by the interaction of CD97 with Thy-1 is involved in firm adhesion of polymorphonuclear cells during inflammation and may play a role in the regulation of leukocyte trafficking to inflammatory sites. (PMID:22210915)
• The researchers demonstrate the role of CD90 as a marker of cancer stem cells within high-grade gliomas (PMID:22426060)
• concentrations were increased in the sera of systemic sclerosis patients, particularly in those with vascular involvement of the lungs (PMID:22807289)
• an increased chondrogenic potential within the CD90+ fraction of human and canine synovial fluid mesenchymal progenitor cells (PMID:22952721)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	thy1	ENSDARG00000035018
danio_rerio	si:dkeyp-69c1.7	ENSDARG00000087165
mus_musculus	Thy1	ENSMUSG00000032011
rattus_norvegicus	Thy1	ENSRNOG00000006604

Protein

Protein identifiers

Thy-1 membrane glycoprotein — P04216 (reviewed: P04216)

Alternative names: CDw90, Thy-1 antigen

All UniProt accessions (6): P04216, B0YJA4, E9PIE1, E9PIM6, E9PNQ8, J3QRJ3

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in cell-cell or cell-ligand interactions during synaptogenesis and other events in the brain.

Subcellular location. Cell membrane.

RefSeq proteins (4): NP_001298089, NP_001298091, NP_001358979, NP_006279* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007110	Ig-like_dom	Domain
IPR013106	Ig_V-set	Domain
IPR013151	Immunoglobulin_dom	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR033292	THY1	Family
IPR036179	Ig-like_dom_sf	Homologous_superfamily

Pfam: PF00047

UniProt features (15 total): glycosylation site 4, disulfide bond 2, sequence conflict 2, modified residue 2, signal peptide 1, chain 1, propeptide 1, domain 1, lipid moiety-binding region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P04216-F1	83.16	0.56

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 (3): 20, 82, 130

Disulfide bonds (2): 28–130, 38–104

Glycosylation sites (4): 139, 42, 79, 119

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-163125	Post-translational modification: synthesis of GPI-anchored proteins
R-HSA-392499	Metabolism of proteins
R-HSA-597592	Post-translational protein modification

MSigDB gene sets: 447 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, GOBP_REGULATION_OF_T_CELL_RECEPTOR_SIGNALING_PATHWAY, GOBP_POSITIVE_REGULATION_OF_CALCIUM_ION_TRANSPORT, GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_REGULATION_OF_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY, TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_UP, GOBP_NEGATIVE_REGULATION_OF_CELL_DEVELOPMENT, GOBP_REGULATION_OF_PHOSPHORYLATION, GOBP_NEGATIVE_REGULATION_OF_KINASE_ACTIVITY, GOBP_FOCAL_ADHESION_ASSEMBLY, GOBP_POSITIVE_REGULATION_OF_CELLULAR_EXTRAVASATION, GOBP_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY, GOBP_REGULATION_OF_GTPASE_ACTIVITY, GOCC_CELL_SURFACE, GOBP_REGENERATION

GO Biological Process (26): angiogenesis (GO:0001525), regulation of cell-matrix adhesion (GO:0001952), positive regulation of cellular extravasation (GO:0002693), negative regulation of protein kinase activity (GO:0006469), cytoskeleton organization (GO:0007010), integrin-mediated signaling pathway (GO:0007229), cell-cell signaling (GO:0007267), negative regulation of cell migration (GO:0030336), heterotypic cell-cell adhesion (GO:0034113), receptor clustering (GO:0043113), positive regulation of GTPase activity (GO:0043547), retinal cone cell development (GO:0046549), focal adhesion assembly (GO:0048041), negative regulation of axonogenesis (GO:0050771), T cell receptor signaling pathway (GO:0050852), negative regulation of T cell receptor signaling pathway (GO:0050860), positive regulation of T cell activation (GO:0050870), positive regulation of release of sequestered calcium ion into cytosol (GO:0051281), positive regulation of focal adhesion assembly (GO:0051894), negative regulation of neuron projection regeneration (GO:0070571), cell-cell adhesion (GO:0098609), regulation of immune system process (GO:0002682), cell adhesion (GO:0007155), cell surface receptor signaling pathway (GO:0007166), regulation of cell migration (GO:0030334), positive regulation of cell adhesion (GO:0045785)

GO Molecular Function (4): GTPase activator activity (GO:0005096), integrin binding (GO:0005178), GPI anchor binding (GO:0034235), protein binding (GO:0005515)

GO Cellular Component (19): extracellular region (GO:0005576), endoplasmic reticulum (GO:0005783), plasma membrane (GO:0005886), focal adhesion (GO:0005925), external side of plasma membrane (GO:0009897), cell surface (GO:0009986), apical plasma membrane (GO:0016324), dendrite (GO:0030425), growth cone (GO:0030426), axolemma (GO:0030673), dendrite membrane (GO:0032590), neuronal cell body membrane (GO:0032809), membrane raft (GO:0045121), extracellular exosome (GO:0070062), presynapse (GO:0098793), postsynapse (GO:0098794), glutamatergic synapse (GO:0098978), membrane (GO:0016020), side of membrane (GO:0098552)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Post-translational protein modification	1
Metabolism of proteins	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	6
synapse	3
cell-matrix adhesion	2
plasma membrane	2
GTPase activity	2
negative regulation of neuron projection development	2
membrane	2
neuron projection membrane	2
blood vessel morphogenesis	1
anatomical structure formation involved in morphogenesis	1
regulation of cell-substrate adhesion	1
positive regulation of leukocyte migration	1
regulation of cellular extravasation	1
cellular extravasation	1
negative regulation of protein phosphorylation	1
protein kinase activity	1
negative regulation of kinase activity	1
regulation of protein kinase activity	1
organelle organization	1
cell surface receptor signaling pathway	1
cell communication	1
signaling	1
cell migration	1
regulation of cell migration	1
negative regulation of cell motility	1
cell-cell adhesion	1
protein localization to membrane	1
regulation of GTPase activity	1
positive regulation of hydrolase activity	1
eye photoreceptor cell development	1
retinal cone cell differentiation	1
cell-substrate junction assembly	1
axonogenesis	1
negative regulation of neurogenesis	1
regulation of axonogenesis	1
antigen receptor-mediated signaling pathway	1
T cell receptor signaling pathway	1
regulation of T cell receptor signaling pathway	1
negative regulation of antigen receptor-mediated signaling pathway	1
T cell activation	1

Protein interactions and networks

STRING

3778 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
THY1	ITGAM	P11215	987
THY1	ENG	P17813	941
THY1	SDC4	P31431	936
THY1	NT5E	P21589	919
THY1	CD34	P28906	915
THY1	PTPRC	P08575	912
THY1	EPHA4	P54764	895
THY1	CD44	P16070	895
THY1	ITGB1	P05556	893
THY1	PECAM1	P16284	876
THY1	ALCAM	Q13740	855
THY1	CD19	P15391	836
THY1	ITGAX	P20702	801
THY1	ITGB2	P05107	798
THY1	CD3E	P07766	792

IntAct

43 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
THY1	APP	psi-mi:“MI:0915”(physical association)	0.560
MCAM	LGALS8	psi-mi:“MI:0914”(association)	0.530
CFTR	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
THY1	CCR8	psi-mi:“MI:0915”(physical association)	0.370
THY1	HTR6	psi-mi:“MI:0915”(physical association)	0.370
TFAP2A	THY1	psi-mi:“MI:0915”(physical association)	0.370
L1TD1	MYO1C	psi-mi:“MI:0914”(association)	0.350
DDR1		psi-mi:“MI:0914”(association)	0.350
TEX101	PSMD12	psi-mi:“MI:0914”(association)	0.350
TEX101	NDUFA4	psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
SYNGAP1	POTEF	psi-mi:“MI:0914”(association)	0.350
CACNA1C	SNRPGP15	psi-mi:“MI:0914”(association)	0.350
SYNGAP1	IGLON5	psi-mi:“MI:0914”(association)	0.350
THY1	GPAA1	psi-mi:“MI:0914”(association)	0.350
CLGN	TMEM131L	psi-mi:“MI:0914”(association)	0.350
DDX28	UBA6	psi-mi:“MI:0914”(association)	0.350
LGALS3	SDCBP	psi-mi:“MI:0914”(association)	0.350
PODXL	TCAF2	psi-mi:“MI:0914”(association)	0.350
SCARB2	SGCE	psi-mi:“MI:0914”(association)	0.350

BioGRID (47): THY1 (Affinity Capture-MS), THY1 (Affinity Capture-Western), THY1 (Biochemical Activity), THY1 (Co-fractionation), SYNJ2BP (Co-fractionation), TOMM22 (Co-fractionation), THY1 (Affinity Capture-MS), THY1 (Two-hybrid), THY1 (Two-hybrid), PIGU (Affinity Capture-MS), GPAA1 (Affinity Capture-MS), STEAP3 (Affinity Capture-MS), PIGK (Affinity Capture-MS), MFN2 (Affinity Capture-MS), GHITM (Affinity Capture-MS)

ESM2 similar proteins: A5D7V5, O62643, O75144, O88875, P01830, P01831, P01909, P04216, P08508, P09793, P12318, P12319, P14778, P15509, P16410, P27645, P27930, P30433, P31994, P31995, P33681, P42069, P42070, P42072, P50283, Q07212, Q0VCS6, Q28110, Q3TEW6, Q58DF9, Q63203, Q6AYT8, Q6Q8B3, Q6XJV4, Q6XJV6, Q75VT8, Q7YR73, Q8BTP3, Q8NC01, Q8SPV8

Diamond homologs: O62643, P01830, P01831, P04216, Q07212

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
POU5F1	“up-regulates quantity by expression”	THY1	“transcriptional regulation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 50 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
positive regulation of cell migration	6	7.9×	6e-03
positive regulation of gene expression	7	5.8×	8e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	25
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

866 predictions. Top by Δscore:

Variant	Effect	Δscore
11:119420131:T:TA	donor_gain	1.0000
11:119421353:A:C	donor_gain	1.0000
11:119421352:AAATT:A	donor_gain	0.9900
11:119423782:AGC:A	donor_gain	0.9900
11:119423007:C:A	donor_gain	0.9800
11:119421352:A:AC	donor_gain	0.9700
11:119420246:T:TA	donor_gain	0.9600
11:119421721:CCAT:C	donor_gain	0.9600
11:119420276:A:AC	donor_gain	0.9500
11:119420277:C:CC	donor_gain	0.9500
11:119423824:CGT:C	donor_gain	0.9500
11:119421348:A:AC	donor_gain	0.9400
11:119421349:C:CC	donor_gain	0.9400
11:119422656:T:TA	donor_gain	0.9300
11:119423006:T:TA	donor_gain	0.9300
11:119423820:A:AC	donor_gain	0.9300
11:119419521:C:CC	acceptor_gain	0.9200
11:119420026:TG:T	donor_gain	0.9200
11:119420929:TCT:T	acceptor_loss	0.9200
11:119420930:C:CC	acceptor_gain	0.9200
11:119420930:CTG:C	acceptor_loss	0.9200
11:119420931:T:C	acceptor_loss	0.9200
11:119423108:CCCA:C	donor_loss	0.9200
11:119423109:CCA:C	donor_loss	0.9200
11:119423110:CAC:C	donor_loss	0.9200
11:119423111:A:AG	donor_loss	0.9200
11:119423112:CC:C	donor_loss	0.9200
11:119423782:AG:A	donor_gain	0.9200
11:119423826:T:TA	donor_gain	0.9200
11:119420165:T:TA	donor_gain	0.9100

AlphaMissense

1036 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:119420269:A:G	F52S	0.998
11:119420120:A:C	Y102D	0.997
11:119420126:C:A	G100C	0.997
11:119420323:A:T	L34H	0.997
11:119420263:A:G	L54P	0.996
11:119420317:A:G	L36P	0.996
11:119420114:A:G	C104R	0.995
11:119420126:C:G	G100R	0.995
11:119420312:A:G	C38R	0.995
11:119420320:C:G	R35P	0.995
11:119420323:A:G	L34P	0.995
11:119420113:C:G	C104S	0.994
11:119420114:A:T	C104S	0.994
11:119420143:A:C	F94C	0.994
11:119420268:G:C	F52L	0.994
11:119420268:G:T	F52L	0.994
11:119420269:A:C	F52C	0.994
11:119420270:A:G	F52L	0.994
11:119420311:C:G	C38S	0.994
11:119420312:A:T	C38S	0.994
11:119420112:A:C	C104W	0.993
11:119420113:C:T	C104Y	0.992
11:119420143:A:G	F94S	0.992
11:119420310:G:C	C38W	0.992
11:119420344:G:T	A27D	0.992
11:119420120:A:T	Y102N	0.991
11:119420142:G:C	F94L	0.991
11:119420142:G:T	F94L	0.991
11:119420144:A:G	F94L	0.991
11:119420158:A:G	L89P	0.991

dbSNP variants (sampled 300 via entrez): RS1000094024 (11:119420751 G>A), RS1000257313 (11:119415046 T>C), RS1000641271 (11:119421637 C>T), RS1000713679 (11:119416033 A>G), RS1000953985 (11:119425655 G>A,C), RS1001205 (11:119422002 T>A,C,G), RS1001206595 (11:119421769 A>G), RS1001230047 (11:119415171 G>A,C), RS1001334552 (11:119415863 C>A), RS1001469967 (11:119415427 C>A,G,T), RS1001912317 (11:119422660 TCTC>T), RS1002041018 (11:119416466 T>C), RS1002113836 (11:119426097 C>A,T), RS1002303194 (11:119419981 A>C), RS1002610108 (11:119420355 G>A,T)

Disease associations

OMIM: gene MIM:188230 | 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
GCST010002_199	Refractive error	3.000000e-34

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression, affects methylation, decreases expression	4
sodium arsenite	affects cotreatment, affects reaction, increases expression, increases reaction, decreases reaction	3
Benzo(a)pyrene	decreases expression, decreases methylation, increases methylation	3
Estradiol	affects expression, affects cotreatment, increases expression, decreases expression	3
(+)-JQ1 compound	increases expression, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tobacco Smoke Pollution	decreases expression	2
Tretinoin	affects cotreatment, increases expression, decreases expression	2
bisphenol F	increases expression	1
propionaldehyde	increases expression	1
tributyltin	decreases expression	1
dimethylselenide	decreases expression, increases oxidation, increases expression	1
arsenite	increases methylation	1
cobaltous chloride	decreases expression	1
butyraldehyde	increases expression	1
tetrabromobisphenol A	decreases expression, increases expression	1
2-bromopalmitate	increases abundance, increases palmitoylation, decreases reaction	1
tobacco tar	decreases expression, decreases reaction	1
ochratoxin A	decreases expression	1
butylbenzyl phthalate	increases expression	1
diallyl disulfide	decreases expression, decreases reaction	1
nickel sulfate	decreases expression	1
methylmercury II	decreases expression	1
allyl sulfide	decreases expression, decreases reaction	1
S-(1,2-dichlorovinyl)cysteine	decreases expression	1
pentanal	increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
ginsenoside Rg3	decreases expression	1
Y 27632	decreases expression	1
entinostat	increases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B0Z3	Abcam U2OS THY1 KO	Cancer cell line	Female
CVCL_B2IJ	Abcam HeLa THY1 KO	Cancer cell line	Female

Clinical trials (associated diseases)

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