PTMS

Summary

PTMS (parathymosin, HGNC:9629) is a protein-coding gene on chromosome 12p13.31, encoding Parathymosin (P20962). Parathymosin may mediate immune function by blocking the effect of prothymosin alpha which confers resistance to certain opportunistic infections.

Predicted to enable histone binding activity. Predicted to be involved in negative regulation of apoptotic process and positive regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 5763 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 18 total
• Druggable target: yes
• MANE Select transcript: NM_002824

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9629
Approved symbol	PTMS
Name	parathymosin
Location	12p13.31
Locus type	gene with protein product
Status	Approved
Aliases	ParaT
Ensembl gene	ENSG00000159335
Ensembl biotype	protein_coding
OMIM	168440
Entrez	5763

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000309083, ENST00000389462, ENST00000538057, ENST00000540667, ENST00000710358

RefSeq mRNA: 2 — MANE Select: NM_002824 NM_001330333, NM_002824

CCDS: CCDS81656, CCDS8560

Canonical transcript exons

ENST00000309083 — 5 exons

Exon	Start	End
ENSE00002265104	6770392	6770952
ENSE00003544822	6769603	6769674
ENSE00003621358	6769921	6769999
ENSE00003622130	6770157	6770218
ENSE00004011638	6766363	6766750

Expression profiles

Bgee: expression breadth ubiquitous, 258 present calls, max score 99.96.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 539.0801 / max 4883.5893, expressed in 1824 samples.

FANTOM5 promoters (21 alternative TSS)

Promoter ID	TPM avg	Samples expressed
123721	413.9223	1820
123725	53.1120	1803
123736	13.0866	1640
123719	11.5472	1652
123723	11.0011	1663
123735	8.7057	1601
123720	6.5985	1708
123737	3.1657	1150
123724	3.1014	1422
123722	3.0520	1290

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tendon of biceps brachii	UBERON:0008188	99.96	gold quality
right hemisphere of cerebellum	UBERON:0014890	99.71	gold quality
right lobe of liver	UBERON:0001114	99.67	gold quality
cerebellar hemisphere	UBERON:0002245	99.65	gold quality
body of uterus	UBERON:0009853	99.63	gold quality
cerebellar cortex	UBERON:0002129	99.59	gold quality
lower esophagus	UBERON:0013473	99.59	gold quality
lower esophagus muscularis layer	UBERON:0035833	99.59	gold quality
ganglionic eminence	UBERON:0004023	99.58	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	99.57	gold quality
muscle layer of sigmoid colon	UBERON:0035805	99.54	gold quality
right ovary	UBERON:0002118	99.53	gold quality
popliteal artery	UBERON:0002250	99.53	gold quality
tibial artery	UBERON:0007610	99.53	gold quality
left ovary	UBERON:0002119	99.52	gold quality
left uterine tube	UBERON:0001303	99.51	gold quality
left coronary artery	UBERON:0001626	99.50	gold quality
descending thoracic aorta	UBERON:0002345	99.50	gold quality
cortical plate	UBERON:0005343	99.50	gold quality
ascending aorta	UBERON:0001496	99.48	gold quality
thoracic aorta	UBERON:0001515	99.48	gold quality
right coronary artery	UBERON:0001625	99.47	gold quality
ventricular zone	UBERON:0003053	99.47	gold quality
aorta	UBERON:0000947	99.43	gold quality
mucosa of stomach	UBERON:0001199	99.43	gold quality
right lung	UBERON:0002167	99.43	gold quality
metanephros cortex	UBERON:0010533	99.42	gold quality
endocervix	UBERON:0000458	99.41	gold quality
nerve	UBERON:0001021	99.37	gold quality
tibial nerve	UBERON:0001323	99.37	gold quality

Single-cell (SCXA)

Detected in 17 experiment(s), a significant marker in 11.

Experiment	Marker?	Max mean expression
E-MTAB-8495	yes	524.30
E-MTAB-5061	yes	265.05
E-HCAD-1	yes	77.98
E-MTAB-6701	yes	45.54
E-GEOD-134144	yes	36.33
E-MTAB-10553	yes	29.19
E-CURD-122	yes	21.21
E-CURD-88	yes	12.00
E-ANND-3	yes	11.21
E-GEOD-125970	yes	10.31
E-CURD-46	yes	9.98
E-MTAB-10662	no	2316.75
E-MTAB-10485	no	1839.86
E-MTAB-10018	no	1508.24
E-MTAB-10283	no	673.49

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
NR3C1	Activation

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Parathymosin — P20962 (reviewed: P20962)

All UniProt accessions (4): P20962, A0A158RFU3, A0AA34QVV1, F5GXR3

UniProt curated annotations — full annotation on UniProt →

Function. Parathymosin may mediate immune function by blocking the effect of prothymosin alpha which confers resistance to certain opportunistic infections.

Similarity. Belongs to the pro/parathymosin family.

RefSeq proteins (2): NP_001317262, NP_002815* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004931	Pro/parathymosin	Family

Pfam: PF03247

UniProt features (13 total): modified residue 8, compositionally biased region 2, initiator methionine 1, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P20962-F1	62.03	0.00

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 (8): 15, 52, 92, 2, 2, 4, 5, 13

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 225 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, GGGTGGRR_PAX4_03, COUP_01, NFKB_C, IRF7_01, MODULE_75, HNF4_DR1_Q3, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, HNF4_01, TGANTCA_AP1_C, GATA1_03, PU1_Q6, MYB_Q3, LXR_Q3

GO Biological Process (4): immune system process (GO:0002376), DNA replication (GO:0006260), negative regulation of apoptotic process (GO:0043066), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (1): histone binding (GO:0042393)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
biological_process	1
DNA metabolic process	1
DNA biosynthetic process	1
apoptotic process	1
regulation of apoptotic process	1
negative regulation of programmed cell death	1
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
protein binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

25 interactions, top by confidence:

A	B	Type	Score
BRAF	NRAS	psi-mi:“MI:0914”(association)	0.860
PARP2	PTMS	psi-mi:“MI:0557”(adp ribosylation reaction)	0.440
Plk4		psi-mi:“MI:0915”(physical association)	0.400
Pds5a		psi-mi:“MI:0915”(physical association)	0.400
Ccdc15		psi-mi:“MI:0915”(physical association)	0.400
Haus6	HAUS5	psi-mi:“MI:0915”(physical association)	0.400
PTMS	SDCBP2	psi-mi:“MI:0915”(physical association)	0.370
SOD1	NPEPPSL1	psi-mi:“MI:0914”(association)	0.350
cfp17	AP3B1	psi-mi:“MI:0914”(association)	0.350
NEDD4	HMGB1P1	psi-mi:“MI:0914”(association)	0.350
TRIM24	DDTL	psi-mi:“MI:0914”(association)	0.350
AKT3	COL1A1	psi-mi:“MI:0914”(association)	0.350
KLF15		psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
FOXQ1	ZNF609	psi-mi:“MI:2364”(proximity)	0.270
TAL1	TNPO2	psi-mi:“MI:2364”(proximity)	0.270
PTMS	SCHIP1	psi-mi:“MI:0915”(physical association)	0.000
PTMS	SMAD2	psi-mi:“MI:0915”(physical association)	0.000
MYB	PTMS	psi-mi:“MI:0915”(physical association)	0.000
PTMS	ZNF24	psi-mi:“MI:0915”(physical association)	0.000
RXRB	PTMS	psi-mi:“MI:0915”(physical association)	0.000
GET4	PTMS	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (95): SDCBP2 (Two-hybrid), PTMS (Affinity Capture-MS), PTMS (Affinity Capture-RNA), PTMS (Affinity Capture-MS), PTMS (Affinity Capture-MS), PTMS (Proximity Label-MS), PTMS (Proximity Label-MS), NEDD4 (Affinity Capture-MS), SUMO2 (Affinity Capture-MS), BASP1 (Affinity Capture-MS), PTMS (Affinity Capture-MS), PTMS (Affinity Capture-MS), PDIA4 (Affinity Capture-MS), MARCKS (Affinity Capture-MS), PGAM1 (Affinity Capture-MS)

ESM2 similar proteins: A1CQS5, A1D3N8, A2QPM6, A3LXX5, A4QYF9, A5DLG8, A5E145, A5PLC8, A6SMQ7, A6ZQX9, A7ER98, A7TR90, A8N7N4, B0D1Q8, O45181, P01252, P04550, P06302, P06454, P08814, P20962, P26350, P34618, P40019, P91753, Q0C807, Q0V3E0, Q10020, Q10239, Q1E4L8, Q2GNS7, Q2UBH8, Q4WJ31, Q56WH4, Q59RN6, Q59VR3, Q5B2V2, Q5R790, Q5U274, Q68F55

Diamond homologs: P04550, P08814, P20962, Q9D0J8

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
PTMS	“up-regulates quantity by expression”	NR3C1	“transcriptional regulation”
PTMS	“up-regulates activity”	EP300	binding
PTMS	“up-regulates activity”	NCOA1	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 32 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
Diseases of signal transduction by growth factor receptors and second messengers	5	14.9×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	5
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

784 predictions. Top by Δscore:

Variant	Effect	Δscore
12:6766747:CAAGG:C	donor_loss	1.0000
12:6766749:AGGT:A	donor_loss	1.0000
12:6766750:GGTA:G	donor_loss	1.0000
12:6766751:GTAC:G	donor_loss	1.0000
12:6769599:GCA:G	acceptor_loss	1.0000
12:6769601:A:AC	acceptor_loss	1.0000
12:6769601:A:AG	acceptor_gain	1.0000
12:6769601:AG:A	acceptor_gain	1.0000
12:6769602:G:A	acceptor_loss	1.0000
12:6769602:G:GA	acceptor_gain	1.0000
12:6769602:GG:G	acceptor_gain	1.0000
12:6769648:A:T	donor_gain	1.0000
12:6769660:A:T	donor_gain	1.0000
12:6769663:G:GT	donor_gain	1.0000
12:6769663:GAA:G	donor_gain	1.0000
12:6769670:TGGAG:T	donor_loss	1.0000
12:6769672:G:GT	donor_gain	1.0000
12:6769672:GAGGT:G	donor_loss	1.0000
12:6769673:AGGT:A	donor_loss	1.0000
12:6769674:GGTG:G	donor_loss	1.0000
12:6769675:G:C	donor_loss	1.0000
12:6769909:T:TA	acceptor_gain	1.0000
12:6769919:A:AC	acceptor_loss	1.0000
12:6769966:G:GT	donor_gain	1.0000
12:6769975:G:GT	donor_gain	1.0000
12:6769978:G:GT	donor_gain	1.0000
12:6769984:G:GT	donor_gain	1.0000
12:6769989:G:T	donor_gain	1.0000
12:6769990:G:GT	donor_gain	1.0000
12:6769990:G:T	donor_gain	1.0000

AlphaMissense

676 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:6770428:G:T	G99W	0.987
12:6770418:G:C	K95N	0.979
12:6770418:G:T	K95N	0.979
12:6770409:A:C	K92N	0.977
12:6770409:A:T	K92N	0.977
12:6770420:C:T	T96I	0.975
12:6770416:A:G	K95E	0.974
12:6770429:G:A	G99E	0.966
12:6769611:G:C	K18N	0.965
12:6769611:G:T	K18N	0.965
12:6770428:G:A	G99R	0.964
12:6770428:G:C	G99R	0.964
12:6769932:C:A	N43K	0.962
12:6769932:C:G	N43K	0.962
12:6770417:A:T	K95M	0.959
12:6770427:T:A	N98K	0.954
12:6770427:T:G	N98K	0.954
12:6770200:G:C	K80N	0.953
12:6770200:G:T	K80N	0.953
12:6770417:A:C	K95T	0.953
12:6770411:G:C	R93P	0.951
12:6769933:G:T	G44W	0.950
12:6769617:G:C	K20N	0.949
12:6769617:G:T	K20N	0.949
12:6769620:G:C	K21N	0.948
12:6769620:G:T	K21N	0.948
12:6770408:A:T	K92I	0.944
12:6770407:A:G	K92E	0.941
12:6769607:T:C	L17P	0.932
12:6770203:A:C	R81S	0.932

dbSNP variants (sampled 300 via entrez): RS1001276040 (12:6766275 C>A), RS1001362615 (12:6766775 C>G,T), RS1001373825 (12:6766539 G>A,C,T), RS1001438853 (12:6769437 G>C), RS1001644715 (12:6769798 T>C), RS1003580236 (12:6771452 T>C), RS1004186096 (12:6771123 G>C), RS1004916570 (12:6764381 G>C), RS1005287761 (12:6764658 A>C), RS1005583543 (12:6768370 C>A,T), RS1005771456 (12:6768302 C>G,T), RS1006062732 (12:6767090 G>A,C), RS1006198876 (12:6767950 C>T), RS1006328089 (12:6766127 C>T), RS1006527867 (12:6766824 C>T)

Disease associations

OMIM: gene MIM:168440 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066490 (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
7.41	Kd	39.4	nM	CHEMBL3752910
7.41	ED50	39.4	nM	CHEMBL3752910

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-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149920: Binding affinity to human PTMS incubated for 45 mins by Kinobead based pull down assay	kd	0.0394	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
methylmercuric chloride	increases expression, affects cotreatment	3
Benzo(a)pyrene	increases methylation, decreases expression	3
Particulate Matter	increases abundance, increases expression, affects cotreatment, decreases expression	3
bisphenol A	affects expression, decreases expression	2
sodium arsenite	affects methylation, increases expression	2
Air Pollutants	increases expression, decreases expression, increases abundance	2
Valproic Acid	affects expression, decreases expression	2
Cyclosporine	decreases expression	2
Cadmium Chloride	increases expression	2
UF010 compound	increases acetylation	1
FR900359	increases phosphorylation	1
bisphenol F	increases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	decreases expression, increases activity, affects binding	1
lead acetate	increases expression	1
beta-lapachone	decreases expression	1
cobaltous chloride	decreases expression	1
butyraldehyde	decreases expression	1
cupric chloride	increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluoro-n-nonanoic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
ICG 001	decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	increases expression	1
(+)-JQ1 compound	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
Resveratrol	affects cotreatment, decreases expression	1
Temozolomide	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
CHEMBL5652962	Binding	Binding affinity to human PTMS 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.