YPEL1

Summary

YPEL1 (yippee like 1, HGNC:12845) is a protein-coding gene on chromosome 22q11.21-q11.22, encoding Protein yippee-like 1 (O60688). May play a role in epithelioid conversion of fibroblasts. It is a selective cancer dependency (DepMap: 13.6% of cell lines).

This gene is located in the region associated with DiGeorge syndrome on chromosome 22. The encoded protein localizes to the centrosome and nucleolus and may play a role in the regulation of cell division.

Source: NCBI Gene 29799 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 11 total
• Cancer dependency (DepMap): dependent in 13.6% of screened cell lines
• MANE Select transcript: NM_013313

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12845
Approved symbol	YPEL1
Name	yippee like 1
Location	22q11.21-q11.22
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000100027
Ensembl biotype	protein_coding
OMIM	608082
Entrez	29799

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 retained_intron

ENST00000339468, ENST00000403503, ENST00000477675, ENST00000672036

RefSeq mRNA: 1 — MANE Select: NM_013313 NM_013313

CCDS: CCDS13794

Canonical transcript exons

ENST00000339468 — 5 exons

Exon	Start	End
ENSE00001364652	21710628	21710908
ENSE00001368304	21697536	21701218
ENSE00001734685	21703839	21703882
ENSE00001892965	21735615	21735794
ENSE00003613170	21703370	21703478

Expression profiles

Bgee: expression breadth ubiquitous, 217 present calls, max score 98.27.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.2380 / max 172.3687, expressed in 995 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
193241	3.4219	930
193240	0.5683	277
193237	0.1186	17
193238	0.0733	24
193239	0.0431	11
193236	0.0127	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	98.27	gold quality
right testis	UBERON:0004534	97.97	gold quality
sperm	CL:0000019	96.75	gold quality
testis	UBERON:0000473	96.39	gold quality
male germ cell	CL:0000015	95.80	gold quality
adult organism	UBERON:0007023	94.38	gold quality
cortical plate	UBERON:0005343	93.93	gold quality
oocyte	CL:0000023	91.91	gold quality
ganglionic eminence	UBERON:0004023	91.39	gold quality
secondary oocyte	CL:0000655	90.72	gold quality
nucleus accumbens	UBERON:0001882	89.05	gold quality
caudate nucleus	UBERON:0001873	87.87	gold quality
buccal mucosa cell	CL:0002336	87.84	silver quality
putamen	UBERON:0001874	86.70	gold quality
gastrocnemius	UBERON:0001388	85.95	gold quality
granulocyte	CL:0000094	85.67	gold quality
muscle of leg	UBERON:0001383	84.67	gold quality
prefrontal cortex	UBERON:0000451	84.16	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.05	gold quality
ventricular zone	UBERON:0003053	83.88	gold quality
mucosa of stomach	UBERON:0001199	82.74	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.67	gold quality
cingulate cortex	UBERON:0003027	81.92	gold quality
telencephalon	UBERON:0001893	81.70	gold quality
anterior cingulate cortex	UBERON:0009835	81.70	gold quality
right frontal lobe	UBERON:0002810	81.09	gold quality
neocortex	UBERON:0001950	81.08	gold quality
embryo	UBERON:0000922	81.04	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	80.92	gold quality
frontal cortex	UBERON:0001870	80.84	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.93

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

132 targeting YPEL1, 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-3613-3P	100.00	76.36	7965
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-548BB-3P	99.86	70.58	4354

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 13.6% of screened cell lines.

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	ypel1	ENSDARG00000035630
mus_musculus	Ypel1	ENSMUSG00000022773
rattus_norvegicus		ENSRNOG00000077135
drosophila_melanogaster	l(2)37Bb	FBGN0002021
drosophila_melanogaster	CG3270	FBGN0033093
caenorhabditis_elegans		WBGENE00010847

Paralogs (10): L2HGDH (ENSG00000087299), YPEL3 (ENSG00000090238), PDPR (ENSG00000090857), FOXRED1 (ENSG00000110074), YPEL5 (ENSG00000119801), SARDH (ENSG00000123453), DMGDH (ENSG00000132837), AMT (ENSG00000145020), YPEL4 (ENSG00000166793), YPEL2 (ENSG00000175155)

Protein

Protein identifiers

Protein yippee-like 1 — O60688 (reviewed: O60688)

All UniProt accessions (3): O60688, A0A5F9ZHD1, B5MCX2

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in epithelioid conversion of fibroblasts.

Subcellular location. Nucleus.

Similarity. Belongs to the yippee family.

RefSeq proteins (1): NP_037445* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004910	Yippee/Mis18/Cereblon	Domain
IPR034751	Yippee	Domain
IPR039058	Yippee_fam	Family

Pfam: PF03226

UniProt features (8 total): binding site 4, chain 1, domain 1, short sequence motif 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O60688-F1	90.56	0.80

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): 23; 26; 79; 82

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 141 (showing top): VERHAAK_AML_WITH_NPM1_MUTATED_DN, GCANCTGNY_MYOD_Q6, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, MARTINEZ_RB1_TARGETS_UP, DOANE_RESPONSE_TO_ANDROGEN_DN, MODULE_88, WANG_CISPLATIN_RESPONSE_AND_XPC_DN, CUI_TCF21_TARGETS_2_UP, CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, MODULE_55, MODULE_13, MYB_Q6, SMAD4_Q6, GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN

GO Biological Process (0):

GO Molecular Function (1): metal ion binding (GO:0046872)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

520 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
YPEL1	C1QL4	Q86Z23	498
YPEL1	WDR26	Q9H7D7	480
YPEL1	ZNF564	Q8TBZ8	432
YPEL1	C1QL2	Q7Z5L3	413
YPEL1	VANGL2	Q9ULK5	398
YPEL1	NCAM1	P13591	390
YPEL1	PPM1F	P49593	389
YPEL1	FNDC5	Q8NAU1	380
YPEL1	KIF12	Q96FN5	379
YPEL1	LYSET	Q8N6I4	368
YPEL1	R3HCC1	Q9Y3T6	365
YPEL1	GSC2	O15499	348
YPEL1	CEP78	Q5JTW2	348
YPEL1	GLB1L2	Q8IW92	340
YPEL1	ENOX2	Q16206	333

IntAct

4 interactions, top by confidence:

A	B	Type	Score
YPEL1	STRN3	psi-mi:“MI:0914”(association)	0.530
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (13): YPEL1 (Affinity Capture-MS), CTTNBP2NL (Affinity Capture-MS), FBXL20 (Affinity Capture-MS), FBXL2 (Affinity Capture-MS), STRN4 (Affinity Capture-MS), STRIP1 (Affinity Capture-MS), STRN3 (Affinity Capture-MS), STRN4 (Affinity Capture-MS), STRN3 (Affinity Capture-MS), FBXL2 (Affinity Capture-MS), CTTNBP2NL (Affinity Capture-MS), FBXL20 (Affinity Capture-MS), YPEL1 (Affinity Capture-RNA)

ESM2 similar proteins: A2VE01, A6QPH8, D3ZRP6, O60688, P00860, P11926, P27117, P27118, P27119, P27120, P48455, P61236, P61237, Q16HW7, Q1RMS5, Q24208, Q2YDI3, Q3SYW1, Q5EBF1, Q5PQL4, Q5RDN9, Q5VST6, Q5XID5, Q5ZIZ4, Q5ZJ01, Q65Z54, Q65Z56, Q65Z57, Q65Z58, Q65Z59, Q65Z93, Q65Z95, Q6AY17, Q6DCC5, Q6DEY3, Q6DKB0, Q6NWI4, Q7M759, Q8L5V0, Q96NS1

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.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	4
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1111 predictions. Top by Δscore:

Variant	Effect	Δscore
22:21701134:C:CA	donor_gain	1.0000
22:21703368:A:AC	donor_gain	1.0000
22:21703369:C:CC	donor_gain	1.0000
22:21703369:CGT:C	donor_gain	1.0000
22:21735613:A:AC	donor_gain	1.0000
22:21735613:ACGG:A	donor_gain	1.0000
22:21735614:C:CC	donor_gain	1.0000
22:21735614:CGG:C	donor_gain	1.0000
22:21735614:CGGC:C	donor_gain	1.0000
22:21701131:A:AC	donor_gain	0.9900
22:21701132:C:CC	donor_gain	0.9900
22:21703361:GGCAC:G	donor_loss	0.9900
22:21703362:GCAC:G	donor_loss	0.9900
22:21703363:CACTC:C	donor_loss	0.9900
22:21703364:AC:A	donor_loss	0.9900
22:21703365:CTC:C	donor_loss	0.9900
22:21703366:T:TA	donor_loss	0.9900
22:21703367:CACGT:C	donor_loss	0.9900
22:21703368:A:AG	donor_loss	0.9900
22:21703369:CGTA:C	donor_gain	0.9900
22:21703369:CGTAT:C	donor_gain	0.9900
22:21703372:A:AC	donor_gain	0.9900
22:21703372:ATTT:A	donor_gain	0.9900
22:21703474:TCACC:T	acceptor_gain	0.9900
22:21703475:CACC:C	acceptor_gain	0.9900
22:21703475:CACCC:C	acceptor_gain	0.9900
22:21703476:ACC:A	acceptor_gain	0.9900
22:21703477:CC:C	acceptor_gain	0.9900
22:21703477:CCC:C	acceptor_gain	0.9900
22:21703478:CC:C	acceptor_gain	0.9900

AlphaMissense

795 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:21701166:T:A	E108V	1.000
22:21701167:C:T	E108K	1.000
22:21701172:A:T	I106N	1.000
22:21701186:C:A	K101N	1.000
22:21701186:C:G	K101N	1.000
22:21701187:T:A	K101M	1.000
22:21701188:T:C	K101E	1.000
22:21701188:T:G	K101Q	1.000
22:21701190:T:C	Y100C	1.000
22:21701191:A:G	Y100H	1.000
22:21701195:C:A	Q98H	1.000
22:21701195:C:G	Q98H	1.000
22:21701211:G:T	A93D	1.000
22:21703371:T:C	Y90C	1.000
22:21703372:A:G	Y90H	1.000
22:21703376:C:A	W88C	1.000
22:21703376:C:G	W88C	1.000
22:21703377:C:A	W88L	1.000
22:21703377:C:G	W88S	1.000
22:21703378:A:G	W88R	1.000
22:21703378:A:T	W88R	1.000
22:21703380:C:A	G87V	1.000
22:21703380:C:T	G87E	1.000
22:21703381:C:A	G87W	1.000
22:21703381:C:G	G87R	1.000
22:21703381:C:T	G87R	1.000
22:21703394:G:C	C82W	1.000
22:21703395:C:A	C82F	1.000
22:21703395:C:T	C82Y	1.000
22:21703396:A:G	C82R	1.000

dbSNP variants (sampled 300 via entrez): RS1000044355 (22:21737634 A>C,T), RS1000133861 (22:21715658 T>C), RS1000274827 (22:21719222 C>A,T), RS1000276816 (22:21701871 G>A,C), RS1000424062 (22:21732478 A>G,T), RS1000436750 (22:21732004 C>A,T), RS1000462287 (22:21712386 C>A,T), RS1000546421 (22:21708659 A>C,G), RS1000614017 (22:21702939 G>C), RS1000640603 (22:21708079 C>T), RS1000740703 (22:21714473 A>C,G), RS1000756932 (22:21733764 C>A,T), RS1000784248 (22:21725365 A>C,G), RS1000806198 (22:21697310 A>T), RS10009 (22:21697420 A>G)

Disease associations

OMIM: gene MIM:608082 | 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
GCST008103_64	Bipolar disorder	6.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases methylation	9
trichostatin A	affects cotreatment, decreases expression	3
(+)-JQ1 compound	increases expression	3
entinostat	decreases expression, affects cotreatment	2
Phenylmercuric Acetate	decreases expression, affects cotreatment	2
GSK-J4	increases expression	1
OTX015	increases expression	1
mivebresib	increases expression	1
triphenyl phosphate	affects expression	1
propionaldehyde	decreases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
benzo(e)pyrene	increases methylation	1
beta-methylcholine	affects expression	1
pentanal	decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
abrine	decreases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	decreases expression	1
Vorinostat	decreases expression	1
Panobinostat	affects cotreatment, decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, decreases expression	1
Aldehydes	decreases expression	1
Arsenic	affects expression	1
Benzo(a)pyrene	increases methylation	1
Catechin	affects cotreatment, decreases expression	1
Estradiol	decreases expression	1

Clinical trials (associated diseases)

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