YPEL5

gene
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Also known as CGI-127

Summary

YPEL5 (yippee like 5, HGNC:18329) is a protein-coding gene on chromosome 2p23.1, encoding Protein yippee-like 5 (P62699). Component of the CTLH E3 ubiquitin-protein ligase complex that selectively accepts ubiquitin from UBE2H and mediates ubiquitination and subsequent proteasomal degradation of the transcription factor HBP1. It is a selective cancer dependency (DepMap: 74.8% of cell lines).

Predicted to enable metal ion binding activity. Predicted to be involved in cell population proliferation. Part of ubiquitin ligase complex.

Source: NCBI Gene 51646 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 13 total
  • Cancer dependency (DepMap): dependent in 74.8% of screened cell lines
  • MANE Select transcript: NM_016061

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18329
Approved symbolYPEL5
Nameyippee like 5
Location2p23.1
Locus typegene with protein product
StatusApproved
AliasesCGI-127
Ensembl geneENSG00000119801
Ensembl biotypeprotein_coding
OMIM609726
Entrez51646

Gene structure

Transcript identifiers

Ensembl transcripts: 40 — 35 protein_coding, 5 protein_coding_CDS_not_defined

ENST00000261353, ENST00000379519, ENST00000379520, ENST00000402003, ENST00000402708, ENST00000470120, ENST00000482474, ENST00000490211, ENST00000492439, ENST00000495673, ENST00000871629, ENST00000871630, ENST00000871631, ENST00000871632, ENST00000871633, ENST00000871634, ENST00000871635, ENST00000871636, ENST00000871637, ENST00000871638, ENST00000871639, ENST00000871640, ENST00000871641, ENST00000921992, ENST00000921993, ENST00000921994, ENST00000921995, ENST00000921996, ENST00000921997, ENST00000956321, ENST00000956322, ENST00000956323, ENST00000956324, ENST00000956325, ENST00000956326, ENST00000956327, ENST00000956328, ENST00000956329, ENST00000956330, ENST00000956331

RefSeq mRNA: 4 — MANE Select: NM_016061 NM_001127399, NM_001127400, NM_001127401, NM_016061

CCDS: CCDS1771

Canonical transcript exons

ENST00000261353 — 3 exons

ExonStartEnd
ENSE000010785583015861930160533
ENSE000018757163014700730147062
ENSE000035574353015662830156792

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 99.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 135.8607 / max 4732.9545, expressed in 1821 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
1955381.35011797
1955253.79821815
2021460.209084
195560.101329
195540.081720
195570.080331
195580.076430
2021470.064828
195550.058115
195620.040915

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065599.93gold quality
oocyteCL:000002399.88gold quality
endothelial cellCL:000011599.52gold quality
amniotic fluidUBERON:000017399.34gold quality
middle temporal gyrusUBERON:000277199.10gold quality
spermCL:000001999.04gold quality
palpebral conjunctivaUBERON:000181298.95gold quality
Brodmann (1909) area 23UBERON:001355498.76gold quality
bone marrowUBERON:000237198.75gold quality
eyeUBERON:000097098.72gold quality
renal glomerulusUBERON:000007498.66gold quality
monocyteCL:000057698.62gold quality
mononuclear cellCL:000084298.62gold quality
metanephric glomerulusUBERON:000473698.60gold quality
male germ cellCL:000001598.56gold quality
leukocyteCL:000073898.48gold quality
ponsUBERON:000098898.23gold quality
upper leg skinUBERON:000426298.13gold quality
bone marrow cellCL:000209298.11gold quality
germinal epithelium of ovaryUBERON:000130498.10gold quality
pigmented layer of retinaUBERON:000178298.07gold quality
nephron tubuleUBERON:000123198.06gold quality
retinaUBERON:000096698.04gold quality
hair follicleUBERON:000207398.01gold quality
superior frontal gyrusUBERON:000266198.00gold quality
parietal pleuraUBERON:000240097.97gold quality
visceral pleuraUBERON:000240197.92gold quality
kidney epitheliumUBERON:000481997.91gold quality
pleuraUBERON:000097797.90gold quality
postcentral gyrusUBERON:000258197.89gold quality

Single-cell (SCXA)

Detected in 9 experiment(s), a significant marker in 7.

ExperimentMarker?Max mean expression
E-GEOD-111727yes3152.59
E-MTAB-9467yes1893.49
E-MTAB-6678yes1432.07
E-GEOD-135922yes35.32
E-CURD-88yes32.51
E-MTAB-9067yes11.97
E-CURD-89no4383.84
E-MTAB-7606no641.69
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

134 targeting YPEL5, 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-432-3P100.0067.86705
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-1193100.0065.93529
HSA-MIR-3646100.0073.565283
HSA-MIR-656-3P100.0072.152788
HSA-MIR-3134100.0066.43777
HSA-MIR-428299.9975.366408
HSA-MIR-569699.9872.364487
HSA-MIR-1213699.9872.815713
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-512-3P99.9767.351049
HSA-MIR-314899.9775.066478
HSA-MIR-60799.9773.625593
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-391099.9571.132227
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-141-3P99.9472.792421
HSA-MIR-200A-3P99.9472.682420
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-6768-5P99.9267.361942

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 74.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 5)

  • YPEL5 protein of the YPEL gene family is involved in the cell cycle progression by interacting with two distinct proteins RanBPM and RanBP10. (PMID:20580816)
  • results indicate that SCN-iPS cells provide a useful disease model for SCN, and the activation of the Wnt3a/beta-catenin pathway may offer a novel therapy for SCN with ELANE mutation (PMID:23382248)
  • YPEL5 silencing enhanced the induction of IFNB1 by pattern recognition receptors and phosphorylation of TBK1/IKBKE kinases, whereas co-immunoprecipitation experiments revealed that YPEL5 interacted physically with IKBKE. (PMID:27705791)
  • results demonstrate the functional conservation between yeast Moh1 and human YPEL5, and their involvement in mitochondria-dependent apoptosis induced by DNA damage (PMID:28173693)
  • METTL3/YTHDF2 m6A axis accelerates colorectal carcinogenesis through epigenetically suppressing YPEL5. (PMID:33411363)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioypel5ENSDARG00000088929
mus_musculusYpel5ENSMUSG00000039770
rattus_norvegicusYpel5ENSRNOG00000026742
drosophila_melanogasterYpeFBGN0288857
caenorhabditis_elegansWBGENE00015250
caenorhabditis_elegansWBGENE00015251

Paralogs (10): L2HGDH (ENSG00000087299), YPEL3 (ENSG00000090238), PDPR (ENSG00000090857), YPEL1 (ENSG00000100027), FOXRED1 (ENSG00000110074), SARDH (ENSG00000123453), DMGDH (ENSG00000132837), AMT (ENSG00000145020), YPEL4 (ENSG00000166793), YPEL2 (ENSG00000175155)

Protein

Protein identifiers

Protein yippee-like 5P62699 (reviewed: P62699)

All UniProt accessions (1): P62699

UniProt curated annotations — full annotation on UniProt →

Function. Component of the CTLH E3 ubiquitin-protein ligase complex that selectively accepts ubiquitin from UBE2H and mediates ubiquitination and subsequent proteasomal degradation of the transcription factor HBP1. Required for normal cell proliferation.

Subunit / interactions. Identified in the CTLH complex that contains GID4, RANBP9 and/or RANBP10, MKLN1, MAEA, RMND5A (or alternatively its paralog RMND5B), GID8, ARMC8, WDR26 and YPEL5. Within this complex, MAEA, RMND5A (or alternatively its paralog RMND5B), GID8, WDR26, and RANBP9 and/or RANBP10 form the catalytic core, while GID4, MKLN1, ARMC8 and YPEL5 have ancillary roles. Interacts with RANBP9 and RANBP10.

Subcellular location. Nucleus. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Spindle pole. Midbody.

Similarity. Belongs to the yippee family.

RefSeq proteins (4): NP_001120871, NP_001120872, NP_001120873, NP_057145* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004910Yippee/Mis18/CereblonDomain
IPR034751YippeeDomain
IPR039058Yippee_famFamily

Pfam: PF03226

UniProt features (22 total): strand 9, binding site 4, helix 3, turn 3, chain 1, domain 1, modified residue 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
8QBNELECTRON MICROSCOPY3.2
9RSDELECTRON MICROSCOPY3.38
9RSCELECTRON MICROSCOPY3.42

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P62699-F193.240.85

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 (4): 17; 20; 73; 76

Post-translational modifications (1): 118

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-6798695Neutrophil degranulation

MSigDB gene sets: 316 (showing top): KOBAYASHI_EGFR_SIGNALING_24HR_UP, REACTOME_INNATE_IMMUNE_SYSTEM, GOCC_SECRETORY_GRANULE, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, IVANOVA_HEMATOPOIESIS_MATURE_CELL, CAGCTG_AP4_Q5, CCATCCA_MIR432, GOCC_MICROTUBULE_ORGANIZING_CENTER, MISSIAGLIA_REGULATED_BY_METHYLATION_UP, GTGTTGA_MIR505, ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP, BACH2_01, GOCC_CENTROSOME, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5

GO Biological Process (1): cell population proliferation (GO:0008283)

GO Molecular Function (2): metal ion binding (GO:0046872), protein binding (GO:0005515)

GO Cellular Component (11): ubiquitin ligase complex (GO:0000151), extracellular region (GO:0005576), nucleus (GO:0005634), centrosome (GO:0005813), midbody (GO:0030496), mitotic spindle pole (GO:0097431), tertiary granule lumen (GO:1904724), ficolin-1-rich granule lumen (GO:1904813), spindle pole (GO:0000922), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Innate Immune System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
intracellular organelle lumen2
cellular process1
cation binding1
binding1
intracellular protein-containing complex1
transferase complex1
intracellular membrane-bounded organelle1
centriole1
microtubule organizing center1
spindle pole1
mitotic spindle1
tertiary granule1
ficolin-1-rich granule1
spindle1
intracellular anatomical structure1
intracellular membraneless organelle1

Protein interactions and networks

STRING

1254 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
YPEL5RANBP10Q6VN20839
YPEL5WDR26Q9H7D7760
YPEL5RANBP9Q96S59721
YPEL5MKLN1Q9UL63719
YPEL5MAEAQ7L5Y9697
YPEL5GID8Q9NWU2691
YPEL5GID4Q8IVV7689
YPEL5RMND5BQ96G75676
YPEL5ARMC8Q8IUR7674
YPEL5RMND5AQ9H871608
YPEL5FAM162BQ5T6X4542
YPEL5TMEM167AQ8TBQ9502
YPEL5HEXDQ8WVB3462
YPEL5UBE2HP37286460
YPEL5LCLAT1Q6UWP7447

IntAct

125 interactions, top by confidence:

ABTypeScore
ARMC8HTRA2psi-mi:“MI:0914”(association)0.750
RANBP9YPEL5psi-mi:“MI:0914”(association)0.640
PRG2YPEL5psi-mi:“MI:0914”(association)0.640
CCDC120AIPpsi-mi:“MI:0914”(association)0.640
GID8HTRA2psi-mi:“MI:0914”(association)0.610
YPEL5PSMA1psi-mi:“MI:0915”(physical association)0.560
TRAF5YPEL5psi-mi:“MI:0915”(physical association)0.560
YPEL5SHC3psi-mi:“MI:0915”(physical association)0.560
MAPKBP1YPEL5psi-mi:“MI:0915”(physical association)0.560
YPEL5DDIT4Lpsi-mi:“MI:0915”(physical association)0.560
GSC2YPEL5psi-mi:“MI:0915”(physical association)0.560
YPEL5PFDN5psi-mi:“MI:0915”(physical association)0.560
YPEL5CTDSP1psi-mi:“MI:0915”(physical association)0.560
YPEL5PLAGL2psi-mi:“MI:0915”(physical association)0.560
YPEL5ZNF655psi-mi:“MI:0915”(physical association)0.560
PSMA1YPEL5psi-mi:“MI:0915”(physical association)0.560
JPH4ZSWIM8psi-mi:“MI:0914”(association)0.530
EMILIN3ZZEF1psi-mi:“MI:0914”(association)0.530
CBFA2T3CBFA2T2psi-mi:“MI:0914”(association)0.530
MRPL18GTPBP10psi-mi:“MI:0914”(association)0.530
GNLYYPEL5psi-mi:“MI:0914”(association)0.530
PIGTZNF609psi-mi:“MI:0914”(association)0.530
EFHC2YPEL5psi-mi:“MI:0914”(association)0.510
RANBP10HTRA2psi-mi:“MI:0914”(association)0.510
RANBP9DDX5psi-mi:“MI:0914”(association)0.510
RMND5BPSMA7psi-mi:“MI:0914”(association)0.510
WDR26HTRA2psi-mi:“MI:0914”(association)0.510

BioGRID (112): YPEL5 (Affinity Capture-MS), YPEL5 (Affinity Capture-MS), YPEL5 (Affinity Capture-MS), YPEL5 (Affinity Capture-MS), YPEL5 (Affinity Capture-MS), YPEL5 (Affinity Capture-MS), YPEL5 (Affinity Capture-MS), YPEL5 (Affinity Capture-MS), YPEL5 (Affinity Capture-MS), YPEL5 (Affinity Capture-MS), YPEL5 (Affinity Capture-MS), RANBP10 (Affinity Capture-MS), WDR26 (Affinity Capture-MS), YPEL5 (Affinity Capture-MS), ARMC8 (Affinity Capture-MS)

ESM2 similar proteins: A7ZMP8, A8A0X0, A9MFH4, A9N292, B1IPF3, B1LDV3, B1XGN8, B4T3Y1, B4TGC8, B4TUA8, B5F860, B5FJF9, B5YQ71, B6IBJ9, B7L6Q3, B7LQ21, B7M1J2, B7MAY9, B7MVQ9, B7N5B4, B7NSZ8, B7USF8, C4ZZD4, C5BR54, P0A746, P0A747, P0A748, P38191, P59234, P62699, P62700, P65449, P65450, Q0T4Y5, Q0TH50, Q2V3E2, Q321R4, Q3Z2B6, Q3ZBE7, Q4R4Q6

Diamond homologs: A6QPH8, O44440, O60688, P38191, P59234, P61236, P61237, P62699, P62700, Q2V3E2, Q2YDI3, Q3ZBE7, Q4R4Q6, Q5RDN9, Q5RDU7, Q5XID5, Q65Z54, Q65Z55, Q65Z56, Q65Z57, Q65Z58, Q65Z59, Q65Z93, Q65Z95, Q6NWI4, Q8S5M8, Q96NS1, Q96QA6, Q9C777, Q9DG42, Q9ESC7, Q9FN32, Q9LY56, Q9SR97, Q9T096, Q9U3G6, Q9URW3, Q9W2X7, Q9XZF0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 110 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
Regulation of pyruvate metabolism864.3×8e-11
Pyruvate metabolism528.7×2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance9
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

540 predictions. Top by Δscore:

VariantEffectΔscore
2:30147059:CAGGG:Cdonor_loss1.0000
2:30147060:AGGGT:Adonor_loss1.0000
2:30147061:GG:Gdonor_gain1.0000
2:30147062:GG:Gdonor_gain1.0000
2:30147062:GGT:Gdonor_loss1.0000
2:30147063:G:GGdonor_gain1.0000
2:30148303:G:GTdonor_gain1.0000
2:30158615:TTA:Tacceptor_loss1.0000
2:30158618:G:Aacceptor_loss1.0000
2:30158618:GGTA:Gacceptor_gain1.0000
2:30147059:CAGG:Cdonor_gain0.9900
2:30147060:AGG:Adonor_gain0.9900
2:30147061:GGG:Gdonor_gain0.9900
2:30156626:A:AGacceptor_gain0.9900
2:30156627:G:GGacceptor_gain0.9900
2:30156790:AAGG:Adonor_loss0.9900
2:30156793:G:GGdonor_loss0.9900
2:30158617:AG:Aacceptor_gain0.9900
2:30158618:GG:Gacceptor_gain0.9900
2:30158618:GGT:Gacceptor_gain0.9900
2:30147058:TCAGG:Tdonor_gain0.9800
2:30147063:G:Tdonor_gain0.9800
2:30147064:T:Adonor_loss0.9800
2:30155849:GCCTT:Gacceptor_gain0.9800
2:30156622:TCCTA:Tacceptor_gain0.9800
2:30156623:CCTAG:Cacceptor_gain0.9800
2:30156624:CTAGG:Cacceptor_gain0.9800
2:30156625:TAGG:Tacceptor_gain0.9800
2:30156626:AG:Aacceptor_gain0.9800
2:30156626:AGG:Aacceptor_gain0.9800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000094465 (2:30147199 C>A), RS1000136868 (2:30158240 A>G), RS1000474197 (2:30154044 A>G), RS1000525914 (2:30153878 A>C), RS1001031987 (2:30160712 A>G), RS1001072368 (2:30159515 A>C), RS1001216701 (2:30150148 T>A,C), RS1001475870 (2:30155224 A>G), RS1001528294 (2:30154939 A>G), RS1001746933 (2:30149636 C>G,T), RS1002333913 (2:30155159 A>C), RS1002519634 (2:30156245 A>T), RS1002585840 (2:30150675 C>T), RS1003077466 (2:30146662 C>T), RS1003108679 (2:30146836 C>G,T)

Disease associations

OMIM: gene MIM:609726 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST008644_20Celiac disease and Rheumatoid arthritis2.000000e-08
GCST009363_55Triglyceride levels x short total sleep time interaction (2df test)1.000000e-08
GCST011346_12Total cholesterol levels4.000000e-09
GCST011347_14Low density lipoprotein cholesterol levels4.000000e-08

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004530triglyceride measurement
EFO:0004574total cholesterol measurement
EFO:0004611low density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression, decreases expression, increases abundance5
(+)-JQ1 compounddecreases expression, increases expression3
Air Pollutantsaffects cotreatment, increases abundance, increases expression, affects expression, decreases expression3
Estradioldecreases expression3
Valproic Acidaffects expression, decreases expression, increases expression3
bisphenol Faffects cotreatment, increases methylation, increases expression2
cobaltous chlorideincreases expression2
Ozoneaffects cotreatment, increases expression, increases abundance, affects expression2
Tetrachlorodibenzodioxinincreases expression2
Tobacco Smoke Pollutionincreases expression2
Tretinoinincreases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression, increases expression2
Cadmium Chlorideincreases expression2
Genisteindecreases expression2
GSK-J4increases expression1
afuresertibincreases expression1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases expression, increases abundance1
bisphenol Adecreases expression1
hydroxyhydroquinoneincreases expression1
arseniteaffects binding, increases reaction1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, decreases expression1
4-aminophenylarsenoxideaffects binding, decreases reaction1
methacrylaldehydeaffects cotreatment, increases expression, increases abundance1
di-n-butylphosphoric acidaffects expression1
chloropicrinincreases expression1
monomethylarsonous acidincreases expression1
K 7174increases expression1
erucylphospho-N,N,N-trimethylpropylammoniumincreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): celiac disease