YAF2

gene
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Summary

YAF2 (YY1 associated factor 2, HGNC:17363) is a protein-coding gene on chromosome 12q12, encoding YY1-associated factor 2 (Q8IY57). Binds to MYC and inhibits MYC-mediated transactivation.

This gene encodes a zinc finger containing protein that functions in the regulation of transcription. This protein was identified as an interacting partner of transcriptional repressor protein Yy1, and also interacts with other transcriptional regulators, including Myc and Polycomb. This protein can promote proteolysis of Yy1. Multiple alternatively spliced transcript variants have been found.

Source: NCBI Gene 10138 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 31 total — 1 likely-pathogenic
  • Druggable target: yes
  • MANE Select transcript: NM_005748

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17363
Approved symbolYAF2
NameYY1 associated factor 2
Location12q12
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000015153
Ensembl biotypeprotein_coding
OMIM607534
Entrez10138

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 7 nonsense_mediated_decay, 6 protein_coding, 4 retained_intron, 3 protein_coding_CDS_not_defined

ENST00000327791, ENST00000380790, ENST00000534854, ENST00000541702, ENST00000546726, ENST00000546782, ENST00000546972, ENST00000547254, ENST00000547351, ENST00000547622, ENST00000547724, ENST00000548661, ENST00000548917, ENST00000550315, ENST00000551268, ENST00000551528, ENST00000552109, ENST00000552928, ENST00000555248, ENST00000880607

RefSeq mRNA: 5 — MANE Select: NM_005748 NM_001190977, NM_001190979, NM_001190980, NM_001320080, NM_005748

CCDS: CCDS31775, CCDS53778, CCDS53779, CCDS53780

Canonical transcript exons

ENST00000534854 — 4 exons

ExonStartEnd
ENSE000013283124215710442160826
ENSE000034836724223815542238248
ENSE000035245114223759942237724
ENSE000035724034216161342161765

Expression profiles

Bgee: expression breadth ubiquitous, 203 present calls, max score 92.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.2914 / max 265.9175, expressed in 1793 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1304819.44371745
1304835.18061621
1304820.8561589
1304800.4595201
1304790.3515171

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right atrium auricular regionUBERON:000663192.61gold quality
calcaneal tendonUBERON:000370192.49gold quality
gastrocnemiusUBERON:000138891.63gold quality
colonic epitheliumUBERON:000039791.26gold quality
muscle of legUBERON:000138391.21gold quality
heart left ventricleUBERON:000208490.80gold quality
cardiac ventricleUBERON:000208290.29gold quality
hindlimb stylopod muscleUBERON:000425290.22gold quality
ventricular zoneUBERON:000305390.19gold quality
sural nerveUBERON:001548889.47gold quality
cortical plateUBERON:000534389.35gold quality
cardiac atriumUBERON:000208189.29gold quality
ganglionic eminenceUBERON:000402389.23gold quality
heartUBERON:000094889.12gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099188.62gold quality
stromal cell of endometriumCL:000225588.24gold quality
left lobe of thyroid glandUBERON:000112088.04gold quality
monocyteCL:000057687.76gold quality
prefrontal cortexUBERON:000045187.75gold quality
tibial arteryUBERON:000761087.48gold quality
popliteal arteryUBERON:000225087.47gold quality
mononuclear cellCL:000084287.36gold quality
leukocyteCL:000073887.31gold quality
right lobe of thyroid glandUBERON:000111987.31gold quality
endocervixUBERON:000045886.79gold quality
aortaUBERON:000094786.57gold quality
adrenal tissueUBERON:001830386.24gold quality
thyroid glandUBERON:000204686.04gold quality
ectocervixUBERON:001224985.94gold quality
thoracic aortaUBERON:000151585.81gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.64

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

138 targeting YAF2, 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-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-340-5P100.0072.504437
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-3613-3P100.0076.367965
HSA-MIR-6740-5P100.0065.64932
HSA-MIR-5692A100.0074.406850
HSA-MIR-3924100.0072.092394
HSA-MIR-3163100.0077.238605
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-428299.9975.366408
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-548N99.9871.944170
HSA-MIR-56899.9869.862084
HSA-MIR-569699.9872.364487
HSA-MIR-477599.9875.006394
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-9-3P99.9670.882068
HSA-MIR-590-3P99.9674.346478
HSA-MIR-365899.9673.874379
HSA-MIR-570-3P99.9672.414910
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-335-3P99.9373.364958

Literature-anchored findings (GeneRIF, showing 5)

  • YEAF1/RYBP and YAF-2 are functionally distinct members of a cofactor family for the YY1 and E4TF1/hGABP transcription factors. (PMID:11953439)
  • These findings uncovered an apoptotic signaling cascade linking YAF2, PDCD5, and TP53 during genotoxic stress responses. (PMID:25603536)
  • LINC00341 interacts with miR-141 to suppress its functional binding to the 3’-untranslated region of YAF2 messenger RNA whereby supporting chondrocyte survival and preventing osteoarthritis progression. (PMID:30672021)
  • miR-34b inhibits the migration/invasion and promotes apoptosis of non-small-cell lung cancer cells by YAF2. (PMID:30915747)
  • YAF2 exerts anti-apoptotic effect in human tumor cells in a FANK1- and phosphorylation-dependent manner. (PMID:33784512)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioyaf2ENSDARG00000015966
mus_musculusYaf2ENSMUSG00000022634
rattus_norvegicusYaf2ENSRNOG00000004773
drosophila_melanogasterRYBPFBGN0034763
caenorhabditis_elegansWBGENE00016937

Paralogs (1): RYBP (ENSG00000163602)

Protein

Protein identifiers

YY1-associated factor 2Q8IY57 (reviewed: Q8IY57)

All UniProt accessions (8): Q8IY57, A0A0B4J255, F8VRE5, F8VZR2, F8W0B9, G3V1X5, G3V212, G3V219

UniProt curated annotations — full annotation on UniProt →

Function. Binds to MYC and inhibits MYC-mediated transactivation. Also binds to MYCN and enhances MYCN-dependent transcriptional activation. Increases calpain 2-mediated proteolysis of YY1 in vitro. Component of the E2F6.com-1 complex, a repressive complex that methylates ‘Lys-9’ of histone H3, suggesting that it is involved in chromatin-remodeling.

Subunit / interactions. Interacts with MYC, MYCN, RNF2/RING1B and YY1. Part of the E2F6.com-1 complex in G0 phase composed of E2F6, MGA, MAX, TFDP1, CBX3, BAT8, EUHMTASE1, RING1, RNF2, MBLR, L3MBTL2 and YAF2.

Subcellular location. Nucleus.

Isoforms (4)

UniProt IDNamesCanonical?
Q8IY57-11yes
Q8IY57-52
Q8IY57-33
Q8IY57-44

RefSeq proteins (5): NP_001177906, NP_001177908, NP_001177909, NP_001307009, NP_005739* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001876Znf_RanBP2Domain
IPR033774YAF2_RYBPConserved_site
IPR036443Znf_RanBP2_sfHomologous_superfamily
IPR039958RYBP/YAF2Family

Pfam: PF00641, PF17219

UniProt features (18 total): compositionally biased region 5, splice variant 4, region of interest 3, strand 2, chain 1, zinc finger region 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2D9GSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8IY57-F168.380.22

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 (1): 167

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-8939243RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
R-HSA-8953750Transcriptional Regulation by E2F6

MSigDB gene sets: 205 (showing top): BENPORATH_ES_WITH_H3K27ME3, MORF_MSH3, XU_GH1_AUTOCRINE_TARGETS_UP, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, MORF_BRCA1, MORF_ATRX, chr12q12, BROWNE_HCMV_INFECTION_16HR_UP, ATGCAGT_MIR217, PUJANA_CHEK2_PCC_NETWORK, GOBP_NEGATIVE_REGULATION_OF_GENE_EXPRESSION_EPIGENETIC, CAGCAGG_MIR370, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_DN, GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN

GO Biological Process (3): regulation of DNA-templated transcription (GO:0006355), negative regulation of DNA-templated transcription (GO:0045892), positive regulation of DNA-templated transcription (GO:0045893)

GO Molecular Function (7): DNA binding (GO:0003677), transcription coregulator activity (GO:0003712), transcription coactivator activity (GO:0003713), transcription corepressor activity (GO:0003714), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Transcriptional regulation by RUNX11
Generic Transcription Pathway1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
DNA-templated transcription3
regulation of DNA-templated transcription2
transcription coregulator activity2
cellular anatomical structure2
regulation of gene expression1
regulation of RNA biosynthetic process1
negative regulation of RNA biosynthetic process1
positive regulation of RNA biosynthetic process1
nucleic acid binding1
transcription regulator activity1
positive regulation of DNA-templated transcription1
negative regulation of DNA-templated transcription1
transition metal ion binding1
binding1
cation binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cytoplasm1

Protein interactions and networks

STRING

584 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
YAF2RING1Q06587998
YAF2PCGF1Q9BSM1995
YAF2RNF2Q99496992
YAF2PCGF6Q9BYE7977
YAF2YY1P25490971
YAF2KDM2BQ8NHM5965
YAF2RYBPQ8N488948
YAF2PCGF3Q3KNV8903
YAF2PCGF2P35227897
YAF2CBX2Q14781883
YAF2GABPB1Q06547864
YAF2PCGF5Q86SE9862
YAF2SKP1P34991823
YAF2BMI1P35226799
YAF2R4GMX3R4GMX3799

IntAct

88 interactions, top by confidence:

ABTypeScore
BMI1CBX4psi-mi:“MI:0914”(association)0.900
YAF2RING1psi-mi:“MI:0915”(physical association)0.880
RING1YAF2psi-mi:“MI:0915”(physical association)0.880
PCGF5CSNK2A2psi-mi:“MI:0914”(association)0.880
PCGF2CBX4psi-mi:“MI:0914”(association)0.840
CSNK2A2EIF3Jpsi-mi:“MI:0914”(association)0.790
RING1CBX4psi-mi:“MI:0914”(association)0.730
RNF2E2F6psi-mi:“MI:0914”(association)0.730
DCAF7DIAPH1psi-mi:“MI:0914”(association)0.730
L3MBTL2E2F6psi-mi:“MI:0914”(association)0.730
MAXE2F6psi-mi:“MI:0914”(association)0.710
WDR5MEN1psi-mi:“MI:0914”(association)0.710
XAGE1AYAF2psi-mi:“MI:0915”(physical association)0.670
RNF2CBX4psi-mi:“MI:0914”(association)0.660
YAF2E2F6psi-mi:“MI:0914”(association)0.640
P4HA3FAM171A2psi-mi:“MI:0914”(association)0.640
YAF2YY1psi-mi:“MI:0915”(physical association)0.590
YY1YAF2psi-mi:“MI:0407”(direct interaction)0.590

BioGRID (384): YAF2 (Two-hybrid), YAF2 (Two-hybrid), SETBP1 (Two-hybrid), YAF2 (Affinity Capture-MS), YAF2 (Affinity Capture-MS), YAF2 (Affinity Capture-MS), YAF2 (Affinity Capture-MS), YAF2 (Affinity Capture-MS), YAF2 (Affinity Capture-MS), RING1 (Two-hybrid), YAF2 (Affinity Capture-MS), YAF2 (Affinity Capture-MS), YAF2 (Affinity Capture-MS), YAF2 (Affinity Capture-MS), YAF2 (Affinity Capture-MS)

ESM2 similar proteins: A0A8I6G705, A1L3K1, B5DFF2, B5DFI8, G3MWR8, O19048, O19137, O88508, P06730, P29338, P57721, P57722, P60335, Q12800, Q13888, Q15365, Q15366, Q16763, Q1LZ53, Q1RML1, Q28D01, Q2TBV5, Q4W5Z4, Q5E9A3, Q5FVR7, Q5NVP9, Q5TDH0, Q61990, Q6AYU1, Q6DH13, Q6P1K8, Q6ZRY4, Q7RTP6, Q8C6G8, Q8CCI5, Q8CJ19, Q8IY57, Q8N488, Q8VC52, Q921J4

Diamond homologs: Q5EG55, Q7SYB3, Q8CCI5, Q8IY57, Q8N488, Q99LW6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 87 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
SUMOylation of DNA methylation proteins558.9×1e-06
Transcriptional Regulation by E2F6946.2×5e-11
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known842.2×1e-09
SUMOylation of transcription cofactors521.3×1e-04
SUMOylation of RNA binding proteins520.9×1e-04
Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)820.6×4e-07
SUMOylation of chromatin organization proteins616.7×8e-05
Regulation of PTEN gene transcription515.7×5e-04

GO biological processes:

GO termPartnersFoldFDR
anatomical structure morphogenesis712.8×2e-04
chromatin remodeling1312.5×1e-08
transcription by RNA polymerase II76.5×5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance22
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
1048618GRCh37/hg19 12q11-13.12(chr12:37873948-49578619)x3Likely pathogenic

SpliceAI

1895 predictions. Top by Δscore:

VariantEffectΔscore
12:42160827:C:CCacceptor_gain1.0000
12:42161608:TTTAC:Tdonor_loss1.0000
12:42161609:TTA:Tdonor_loss1.0000
12:42161610:TA:Tdonor_loss1.0000
12:42161612:C:CAdonor_loss1.0000
12:42161761:GTTTC:Gacceptor_gain1.0000
12:42161763:TTC:Tacceptor_gain1.0000
12:42161764:TC:Tacceptor_gain1.0000
12:42161764:TCC:Tacceptor_loss1.0000
12:42161765:CCTG:Cacceptor_gain1.0000
12:42161766:C:CCacceptor_gain1.0000
12:42161768:G:Cacceptor_gain1.0000
12:42161768:G:GCacceptor_gain1.0000
12:42161770:G:Cacceptor_gain1.0000
12:42161770:G:GCacceptor_gain1.0000
12:42161773:C:CTacceptor_gain1.0000
12:42161774:A:ACacceptor_gain1.0000
12:42161774:A:Cacceptor_gain1.0000
12:42161776:G:Cacceptor_gain1.0000
12:42161776:G:GCacceptor_gain1.0000
12:42161777:T:Cacceptor_gain1.0000
12:42161777:T:TCacceptor_gain1.0000
12:42210543:CTTA:Cdonor_loss1.0000
12:42210544:TTACC:Tdonor_loss1.0000
12:42210545:TA:Tdonor_loss1.0000
12:42210546:ACCTT:Adonor_gain1.0000
12:42210547:CCTTC:Cdonor_gain1.0000
12:42210550:T:Adonor_gain1.0000
12:42210685:C:CTacceptor_gain1.0000
12:42238150:GTTAC:Gdonor_loss1.0000

AlphaMissense

1182 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:42160742:A:CF130L1.000
12:42160742:A:TF130L1.000
12:42160743:A:GF130S1.000
12:42160744:A:GF130L1.000
12:42160752:A:CI127S1.000
12:42160752:A:GI127T1.000
12:42160752:A:TI127N1.000
12:42160758:A:TV125D1.000
12:42160764:A:GL123P1.000
12:42160779:A:TV118D1.000
12:42160818:A:GL105S1.000
12:42161762:T:AK52N1.000
12:42161762:T:GK52N1.000
12:42161764:T:CK52E1.000
12:42237602:G:AT50I1.000
12:42237605:G:AS49F1.000
12:42237605:G:TS49Y1.000
12:42237608:G:AT48I1.000
12:42237611:C:AG47V1.000
12:42237611:C:TG47D1.000
12:42237612:C:AG47C1.000
12:42237612:C:GG47R1.000
12:42237612:C:TG47S1.000
12:42237613:C:AK46N1.000
12:42237613:C:GK46N1.000
12:42237614:T:AK46M1.000
12:42237614:T:GK46T1.000
12:42237615:T:CK46E1.000
12:42237615:T:GK46Q1.000
12:42237625:G:CC42W1.000

dbSNP variants (sampled 300 via entrez): RS1000032843 (12:42210093 C>G,T), RS1000126663 (12:42167864 C>T), RS1000183378 (12:42215894 C>A,G,T), RS1000186416 (12:42225198 C>T), RS1000187627 (12:42173856 T>C), RS1000192547 (12:42218471 ATTG>A), RS1000228968 (12:42198898 A>T), RS1000263244 (12:42161558 A>C), RS1000347459 (12:42224557 G>A,T), RS1000357006 (12:42180985 C>A,T), RS1000371485 (12:42180686 C>G,T), RS1000425295 (12:42180424 T>C), RS1000457366 (12:42232199 GT>G), RS1000496459 (12:42238974 G>A,T), RS1000552563 (12:42210363 T>G)

Disease associations

OMIM: gene MIM:607534 | 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):

StudyTraitp-value
GCST010002_215Refractive error3.000000e-11

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6193827 (PROTEIN-PROTEIN INTERACTION)

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Air Pollutantsaffects cotreatment, decreases expression, increases abundance2
Benzo(a)pyreneincreases methylation, increases expression2
FR900359affects phosphorylation1
alpha-pineneaffects cotreatment, decreases expression, increases abundance1
bisphenol Aaffects cotreatment, increases methylation, decreases methylation1
sodium arseniteincreases abundance, increases expression, affects cotreatment1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
methacrylaldehydeincreases abundance, affects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
abrineincreases expression1
bisphenol Sincreases methylation1
jinfukangaffects cotreatment, decreases expression1
Irinotecandecreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibdecreases expression1
Fulvestrantincreases methylation, affects cotreatment1
Acetaldehydeincreases expression1
Acroleinaffects cotreatment, decreases expression, increases abundance1
Arsenicincreases expression, affects cotreatment, increases abundance1
Caffeineincreases phosphorylation1
Carbamazepineaffects expression1
Cisplatinaffects cotreatment, decreases expression1
Coaldecreases expression, increases abundance1
Dietary Carbohydratesdecreases expression1
Doxorubicindecreases expression1
Manganeseincreases abundance, increases expression, affects cotreatment1
Ozonedecreases expression, increases abundance, affects cotreatment1
Phenobarbitalaffects expression1
Plant Extractsaffects cotreatment, increases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5548053BindingPROTAC activity at CRBN/YAF in human K562 cells assessed as degradation of YAF protein expression at 1 to 10 uM incubated for 24 hrs by Western blotting analysisDiscovery and Characterization of a Novel Cereblon-Recruiting PRC1 Bridged PROTAC Degrader. — J Med Chem

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.