YLPM1

gene
On this page

Also known as ZAPPPP1R169

Summary

YLPM1 (YLP motif containing 1, HGNC:17798) is a protein-coding gene on chromosome 14q24.3, encoding YLP motif-containing protein 1 (P49750). Plays a role in the reduction of telomerase activity during differentiation of embryonic stem cells by binding to the core promoter of TERT and controlling its down-regulation.

Enables RNA binding activity. Predicted to be involved in regulation of telomere maintenance. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Located in nuclear speck.

Source: NCBI Gene 56252 — RefSeq curated summary.

At a glance

  • GWAS associations: 10
  • Clinical variants (ClinVar): 396 total
  • MANE Select transcript: NM_019589

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17798
Approved symbolYLPM1
NameYLP motif containing 1
Location14q24.3
Locus typegene with protein product
StatusApproved
AliasesZAP, PPP1R169
Ensembl geneENSG00000119596
Ensembl biotypeprotein_coding
OMIM619766
Entrez56252

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 5 protein_coding, 2 protein_coding_CDS_not_defined, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000325680, ENST00000546901, ENST00000547879, ENST00000549197, ENST00000549293, ENST00000550021, ENST00000552421, ENST00000553381, ENST00000554107, ENST00000930604

RefSeq mRNA: 2 — MANE Select: NM_019589 NM_001411052, NM_019589

CCDS: CCDS45135, CCDS91906

Canonical transcript exons

ENST00000325680 — 21 exons

ExonStartEnd
ENSE000008082287477844774778683
ENSE000008082327480255674802676
ENSE000008082347480991074810002
ENSE000008082357481022574810420
ENSE000008082377481262874812782
ENSE000008082387481620374816265
ENSE000008082407481693174817107
ENSE000008082417481719474817277
ENSE000009411517479758074799697
ENSE000009411527480938074809797
ENSE000011962047481657174816690
ENSE000011962497481162074811738
ENSE000015985977478040574780584
ENSE000016695227478133474782325
ENSE000035034877483526574835447
ENSE000036004277482921374829343
ENSE000036148947482425674824307
ENSE000037015367481823174818314
ENSE000037016147482105774821137
ENSE000037175127483577574837318
ENSE000038480557476331674764362

Expression profiles

Bgee: expression breadth ubiquitous, 290 present calls, max score 96.47.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 41.0216 / max 434.1932, expressed in 1817 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
14058039.85821816
1405790.7700442
1405840.3933164

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ganglionic eminenceUBERON:000402396.47gold quality
cortical plateUBERON:000534396.34gold quality
tendon of biceps brachiiUBERON:000818895.95gold quality
sural nerveUBERON:001548895.90gold quality
spermCL:000001995.62gold quality
ventricular zoneUBERON:000305395.60gold quality
right uterine tubeUBERON:000130295.44gold quality
male germ cellCL:000001595.39gold quality
left ovaryUBERON:000211995.31gold quality
right ovaryUBERON:000211895.17gold quality
medial globus pallidusUBERON:000247794.76gold quality
adrenal tissueUBERON:001830394.71gold quality
right hemisphere of cerebellumUBERON:001489094.53gold quality
tibial nerveUBERON:000132394.29gold quality
cerebellar hemisphereUBERON:000224594.27gold quality
body of uterusUBERON:000985394.18gold quality
endocervixUBERON:000045894.14gold quality
cerebellar cortexUBERON:000212994.09gold quality
globus pallidusUBERON:000187594.02gold quality
corpus callosumUBERON:000233694.02gold quality
tendonUBERON:000004394.00gold quality
stromal cell of endometriumCL:000225593.94gold quality
ovaryUBERON:000099293.94gold quality
calcaneal tendonUBERON:000370193.87gold quality
colonic epitheliumUBERON:000039793.81gold quality
embryoUBERON:000092293.79gold quality
endothelial cellCL:000011593.71gold quality
mucosa of stomachUBERON:000119993.62gold quality
ectocervixUBERON:001224993.47gold quality
right frontal lobeUBERON:000281093.42gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes9.25
E-MTAB-9801yes5.79

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

104 targeting YLPM1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4262100.0073.263931
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-3163100.0077.238605
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4533100.0069.482758
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-8485100.0077.574731
HSA-MIR-5692A100.0074.406850
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-548N99.9871.944170
HSA-MIR-569699.9872.364487
HSA-MIR-314899.9775.066478
HSA-MIR-60799.9773.625593
HSA-MIR-548AN99.9770.912817
HSA-MIR-570-3P99.9672.414910
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-101-3P99.9475.032230
HSA-MIR-144-3P99.9473.982698
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-548AE-3P99.9372.664867

Literature-anchored findings (GeneRIF, showing 1)

  • ZAP3 is a putative nucleoside kinase that targets protein phosphatase-1 through its highly conserved carboxy-terminal RVRW sequence. (PMID:17890166)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioylpm1ENSDARG00000043680
mus_musculusYlpm1ENSMUSG00000021244
rattus_norvegicusYlpm1ENSRNOG00000027317
drosophila_melanogasterZAP3FBGN0052685

Protein

Protein identifiers

YLP motif-containing protein 1P49750 (reviewed: P49750)

Alternative names: Nuclear protein ZAP3, ZAP113

All UniProt accessions (5): P49750, F8VU51, H0YI23, H0YIQ2, U3KQT9

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in the reduction of telomerase activity during differentiation of embryonic stem cells by binding to the core promoter of TERT and controlling its down-regulation.

Subunit / interactions. Interacts with PPP1CA and NCOA5. Forms a complex with ILF2, ILF3, KHDRBS1, RBMX, NCOA5 and PPP1CA.

Subcellular location. Nucleus. Nucleus speckle.

Tissue specificity. Expressed in neuronal, neuroblastoma and embryonic kidney cell lines (at protein level).

Isoforms (3)

UniProt IDNamesCanonical?
P49750-44yes
P49750-33
P49750-11

RefSeq proteins (2): NP_001397981, NP_062535* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR026314YLP_motif_con_p1Family
IPR027417P-loop_NTPaseHomologous_superfamily
IPR058903Spectrin_YLPM1-likeDomain

Pfam: PF13671, PF26583

UniProt features (73 total): compositionally biased region 41, region of interest 8, modified residue 8, cross-link 7, sequence conflict 5, splice variant 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P49750-F143.790.02

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 (15): 735, 756, 814, 829, 831, 1100, 1119, 1402, 891, 983, 983, 1053, 1053, 1652, 1710

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 112 (showing top): GOBP_CHROMOSOME_ORGANIZATION, BROWNE_HCMV_INFECTION_6HR_DN, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOBP_TELOMERE_ORGANIZATION, GOBP_REGULATION_OF_TELOMERE_MAINTENANCE, chr14q24, BROWNE_HCMV_INFECTION_24HR_DN, GOBP_REGULATION_OF_CHROMOSOME_ORGANIZATION, MARKEY_RB1_ACUTE_LOF_UP, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, GOCC_NUCLEAR_SPECK, GOCC_NUCLEAR_BODY, GOCC_RIBONUCLEOPROTEIN_GRANULE, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, MARSON_BOUND_BY_E2F4_UNSTIMULATED

GO Biological Process (1): regulation of telomere maintenance (GO:0032204)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), nuclear speck (GO:0016607)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
telomere maintenance1
regulation of chromosome organization1
regulation of DNA metabolic process1
nucleic acid binding1
binding1
intracellular membrane-bounded organelle1
nuclear ribonucleoprotein granule1

Protein interactions and networks

STRING

1054 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
YLPM1RBMXP38159581
YLPM1ZNF318Q5VUA4557
YLPM1AREL1O15033548
YLPM1PROX2Q3B8N5521
YLPM1BPIFB2Q8N4F0486
YLPM1DVL3Q92997485
YLPM1RBM12BQ8IXT5473
YLPM1KHDRBS1Q07666469
YLPM1RAPH1Q70E73468
YLPM1GPHNQ9NQX3462
YLPM1WDR3Q9UNX4441
YLPM1RPS6KL1Q9Y6S9437
YLPM1VRTNQ9H8Y1430
YLPM1LUC7L3O95232427
YLPM1HEATR1Q9H583425

IntAct

137 interactions, top by confidence:

ABTypeScore
PPP1CBCCDC85Cpsi-mi:“MI:0914”(association)0.750
PPP1CBCCDC85Cpsi-mi:“MI:2364”(proximity)0.750
PPP1CCCCDC85Cpsi-mi:“MI:0914”(association)0.740
PPP1CCCCDC85Cpsi-mi:“MI:2364”(proximity)0.740
PPP1CAYLPM1psi-mi:“MI:0915”(physical association)0.690
PPP1CACCDC85Cpsi-mi:“MI:0914”(association)0.670
PPP1CACCDC85Cpsi-mi:“MI:2364”(proximity)0.670
MAGEE1MCCpsi-mi:“MI:0914”(association)0.670
NCK2SH3PXD2Bpsi-mi:“MI:0914”(association)0.640
P4HA3FAM171A2psi-mi:“MI:0914”(association)0.640
KPNA1TCERG1psi-mi:“MI:0914”(association)0.640
NCKIPSDGEMIN2psi-mi:“MI:0914”(association)0.640
HNRNPDHNRNPDLpsi-mi:“MI:0914”(association)0.560
YLPM1PPP1CCpsi-mi:“MI:0915”(physical association)0.550
PCGF1CBX4psi-mi:“MI:0914”(association)0.530
NAGKZBTB43psi-mi:“MI:0914”(association)0.530
ZFC3H1HNRNPCL1psi-mi:“MI:0914”(association)0.530
NONOYLPM1psi-mi:“MI:0915”(physical association)0.520
YLPM1CACNA1Apsi-mi:“MI:0915”(physical association)0.510
CACNA1AYLPM1psi-mi:“MI:0915”(physical association)0.510
CPSF6DDX39Apsi-mi:“MI:0914”(association)0.480
SRGAP2YLPM1psi-mi:“MI:0407”(direct interaction)0.440

BioGRID (223): YLPM1 (Affinity Capture-MS), YLPM1 (Affinity Capture-MS), YLPM1 (Affinity Capture-MS), YLPM1 (Affinity Capture-MS), YLPM1 (Affinity Capture-MS), SMARCC1 (Co-fractionation), SMARCC2 (Co-fractionation), YLPM1 (Co-fractionation), YLPM1 (Proximity Label-MS), YLPM1 (Affinity Capture-MS), YLPM1 (Affinity Capture-MS), YLPM1 (Affinity Capture-MS), YLPM1 (Affinity Capture-MS), YLPM1 (Affinity Capture-MS), YLPM1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GVQ3, A0A1W2PPK0, A0A1W2PPM1, A2A9I7, A6NCI8, A6QQS3, A7XCE8, E9PI22, E9PXT9, O15016, O91083, P09414, P0DMB1, P17923, P18804, P20879, P35965, P49750, Q0P670, Q12857, Q1RMX6, Q32LN6, Q32MG2, Q3B8N5, Q3T016, Q3V0A6, Q4JK59, Q5BI31, Q5T035, Q5ZKH6, Q642A3, Q6AXV6, Q6IMN6, Q6P1W5, Q6PEX7, Q6X4T0, Q80YD3, Q86UF4, Q8BII1, Q8C5V0

Diamond homologs: P0CB49, P49750, Q9R0I7

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.

Reactome pathways:

PathwayPartnersFoldFDR
mRNA Polyadenylation2316.4×2e-19
Dengue Virus Genome Translation and Replication512.9×3e-03
mRNA Splicing - Minor Pathway712.7×1e-04
Processing of Capped Intron-Containing Pre-mRNA1912.7×9e-14
mRNA Splicing - Major Pathway2712.0×2e-19
mRNA Splicing1311.6×1e-08
RHOU GTPase cycle511.3×5e-03
mRNA 3’-end processing711.2×2e-04

GO biological processes:

GO termPartnersFoldFDR
negative regulation of mRNA splicing, via spliceosome629.8×8e-06
U2-type prespliceosome assembly520.3×5e-04
mRNA splicing, via spliceosome2313.7×8e-17
autophagosome maturation613.7×5e-04
regulation of circadian rhythm813.5×2e-05
regulation of alternative mRNA splicing, via spliceosome812.7×3e-05
mitophagy612.4×8e-04
RNA processing79.9×6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance343
Likely benign12
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

3125 predictions. Top by Δscore:

VariantEffectΔscore
14:74778439:T:Aacceptor_gain1.0000
14:74778443:GTA:Gacceptor_loss1.0000
14:74778445:A:AGacceptor_gain1.0000
14:74778445:A:Cacceptor_loss1.0000
14:74778445:AG:Aacceptor_gain1.0000
14:74778446:G:GGacceptor_gain1.0000
14:74778446:GG:Gacceptor_gain1.0000
14:74778446:GGA:Gacceptor_gain1.0000
14:74778648:G:GTdonor_gain1.0000
14:74778681:CAGG:Cdonor_loss1.0000
14:74778682:AGGT:Adonor_loss1.0000
14:74778684:G:GAdonor_loss1.0000
14:74778685:T:Gdonor_loss1.0000
14:74780397:A:AGacceptor_gain1.0000
14:74780398:T:Gacceptor_gain1.0000
14:74780400:TTTA:Tacceptor_loss1.0000
14:74780400:TTTAG:Tacceptor_gain1.0000
14:74780401:TTAGT:Tacceptor_gain1.0000
14:74780402:TAG:Tacceptor_gain1.0000
14:74780403:A:AGacceptor_gain1.0000
14:74780403:A:Tacceptor_loss1.0000
14:74780403:AG:Aacceptor_gain1.0000
14:74780403:AGTCT:Aacceptor_gain1.0000
14:74780404:G:GGacceptor_gain1.0000
14:74780404:G:Tacceptor_gain1.0000
14:74780404:GT:Gacceptor_gain1.0000
14:74780404:GTC:Gacceptor_gain1.0000
14:74780404:GTCT:Gacceptor_gain1.0000
14:74780404:GTCTG:Gacceptor_gain1.0000
14:74780405:TCTG:Tacceptor_gain1.0000

AlphaMissense

13992 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
14:74763680:T:CL64P1.000
14:74799640:T:AL1448H1.000
14:74799655:A:CH1453P1.000
14:74799661:T:GI1455S1.000
14:74799664:T:AI1456N1.000
14:74799664:T:CI1456T1.000
14:74799664:T:GI1456S1.000
14:74799667:T:CL1457S1.000
14:74799672:G:CA1459P1.000
14:74799673:C:AA1459D1.000
14:74799675:G:CA1460P1.000
14:74799685:T:CL1463P1.000
14:74799697:G:CR1467P1.000
14:74816207:T:AV1836D1.000
14:74816210:T:AV1837D1.000
14:74816213:T:AI1838K1.000
14:74816213:T:GI1838R1.000
14:74816221:G:AG1841R1.000
14:74816221:G:CG1841R1.000
14:74816222:G:AG1841E1.000
14:74816222:G:TG1841V1.000
14:74816230:G:CG1844R1.000
14:74816231:G:AG1844D1.000
14:74816237:G:AG1846E1.000
14:74816249:T:AV1850D1.000
14:74816258:T:CL1853P1.000
14:74816264:G:CR1855P1.000
14:74816602:C:AP1866H1.000
14:74816611:T:CL1869P1.000
14:74816620:A:TD1872V1.000

dbSNP variants (sampled 300 via entrez): RS1000047216 (14:74762751 A>G), RS1000173073 (14:74814632 T>C,G), RS1000179794 (14:74810932 T>G), RS1000205600 (14:74765952 C>A), RS1000219731 (14:74773039 G>A), RS1000250282 (14:74775908 A>C,T), RS1000318046 (14:74765670 C>T), RS1000322946 (14:74775565 A>T), RS1000405714 (14:74813582 T>C), RS1000444212 (14:74779002 G>A), RS1000480305 (14:74769251 A>C,G,T), RS1000547361 (14:74771666 A>G), RS1000581507 (14:74774336 G>A,T), RS1000615630 (14:74808779 G>A), RS1000654880 (14:74773967 C>T)

Disease associations

OMIM: gene MIM:619766 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): myoepithelial tumor (MONDO:0002380)

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

StudyTraitp-value
GCST004603_139Platelet count5.000000e-09
GCST005237_3Mood instability1.000000e-06
GCST005238_3Mood instability3.000000e-09
GCST006976_18Macular thickness4.000000e-25
GCST007709_128General factor of neuroticism2.000000e-11
GCST007709_130General factor of neuroticism1.000000e-09
GCST010241_69Apolipoprotein A1 levels5.000000e-14
GCST90000514_22Gastroesophageal reflux disease2.000000e-09
GCST90002400_138Plateletcrit2.000000e-13
GCST90002402_192Platelet count2.000000e-12

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0004309platelet count
EFO:0008475mood instability measurement
EFO:0007660neuroticism measurement
EFO:0004614apolipoprotein A 1 measurement
EFO:0007985platelet crit

MeSH disease descriptors (1)

DescriptorNameTree numbers
D009208MyoepitheliomaC04.557.435.585

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression3
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression, decreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
FR900359affects phosphorylation1
TAK-243decreases sumoylation1
dicrotophosincreases expression1
triphenyl phosphateaffects expression1
sodium arsenatedecreases expression1
titanium dioxidedecreases methylation1
arsenitedecreases reaction, affects binding1
sodium arseniteaffects cotreatment, decreases expression, increases abundance1
cobaltous chloridedecreases expression1
butyraldehydedecreases expression1
manganese chloridedecreases expression, increases abundance, affects cotreatment1
di-n-butylphosphoric acidaffects expression1
dorsomorphinaffects cotreatment, decreases expression1
bisphenol Saffects expression1
LDN 193189affects cotreatment, increases expression1
Arsenic Trioxideincreases expression1
Vorinostatdecreases expression1
Arsenicaffects cotreatment, decreases expression, increases abundance1
Caffeinedecreases phosphorylation1
Cisplatindecreases expression1
Doxorubicindecreases expression1
Enzyme Inhibitorsincreases O-linked glycosylation, decreases activity1
Ivermectindecreases expression1
Manganesedecreases expression, increases abundance, affects cotreatment1
Mercuric Chloridedecreases expression1
Ribonucleotidesaffects binding1
Seleniumdecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03600649PHASE1UNKNOWNClinical Trial of SP-2577 (Seclidemstat) in Patients With Relapsed or Refractory Ewing or Ewing-related Sarcomas
NCT05266196PHASE1/PHASE2UNKNOWNA Rollover Protocol to Allow for Continued Access to the LSD1 Inhibitor Seclidemstat (SP-2577)
NCT06239272PHASE1/PHASE2RECRUITINGNRSTS2021, A Risk Adapted Study Evaluating Maintenance Pazopanib, Limited Margin, Dose-Escalated Radiation Therapy and Selinexor in Non-Rhabdomyosarcoma Soft Tissue Sarcoma (NRSTS)
NCT06625190PHASE1/PHASE2RECRUITINGAlpha/Beta T and B Cell Depletion With Zoledronic Acid for Solid Tumors
NCT06244420Not specifiedCOMPLETEDMalignant Myoepithelioma of Bone and Soft Tissues: Diagnostic Imaging and Histology in Relation to Prognosis