PWWP2B

gene
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Also known as bA432J24.1FLJ46823

Summary

PWWP2B (PWWP domain containing 2B, HGNC:25150) is a protein-coding gene on chromosome 10q26.3, encoding PWWP domain-containing protein 2B (Q6NUJ5). Chromatin-binding protein that acts as an adapter between distinct nucleosome components (H3K36me3 or H2A.Z) and chromatin-modifying complexes, contributing to the regulation of the levels of histone acetylation at actively transcribed genes.

Enables NuRD complex binding activity. Predicted to be involved in chromatin remodeling; positive regulation of transcription elongation by RNA polymerase II; and regulation of cold-induced thermogenesis. Located in nucleoplasm.

Source: NCBI Gene 170394 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 136 total
  • Druggable target: yes — 1 molecules with ChEMBL bioactivity
  • MANE Select transcript: NM_138499

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25150
Approved symbolPWWP2B
NamePWWP domain containing 2B
Location10q26.3
Locus typegene with protein product
StatusApproved
AliasesbA432J24.1, FLJ46823
Ensembl geneENSG00000171813
Ensembl biotypeprotein_coding
Entrez170394

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000305233, ENST00000631148, ENST00000856284, ENST00000962282

RefSeq mRNA: 2 — MANE Select: NM_138499 NM_001098637, NM_138499

CCDS: CCDS44497, CCDS7667

Canonical transcript exons

ENST00000305233 — 3 exons

ExonStartEnd
ENSE00001611851132417061132417859
ENSE00001676363132404626132406289
ENSE00003845279132397200132397351

Expression profiles

Bgee: expression breadth ubiquitous, 240 present calls, max score 98.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.6454 / max 488.4674, expressed in 1156 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
1077111.8346833
1077161.4179568
1077150.3602132
1077120.03268

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
pancreatic ductal cellCL:000207998.99silver quality
mucosa of transverse colonUBERON:000499192.95gold quality
amniotic fluidUBERON:000017392.36gold quality
lower esophagus mucosaUBERON:003583492.32gold quality
kidney epitheliumUBERON:000481992.11gold quality
nasal cavity epitheliumUBERON:000538490.45silver quality
right adrenal glandUBERON:000123389.14gold quality
right adrenal gland cortexUBERON:003582788.74gold quality
adrenal cortexUBERON:000123588.54gold quality
left adrenal glandUBERON:000123488.53gold quality
body of pancreasUBERON:000115088.50gold quality
cerebellar vermisUBERON:000472088.45gold quality
left adrenal gland cortexUBERON:003582588.27gold quality
vena cavaUBERON:000408787.51gold quality
parotid glandUBERON:000183187.32gold quality
hindlimb stylopod muscleUBERON:000425286.71gold quality
ileal mucosaUBERON:000033186.68gold quality
putamenUBERON:000187486.50gold quality
spleenUBERON:000210686.44gold quality
apex of heartUBERON:000209886.41gold quality
adrenal glandUBERON:000236986.38gold quality
gastrocnemiusUBERON:000138886.15gold quality
nucleus accumbensUBERON:000188286.15gold quality
left ventricle myocardiumUBERON:000656686.00gold quality
heart right ventricleUBERON:000208085.47silver quality
transverse colonUBERON:000115785.31gold quality
olfactory segment of nasal mucosaUBERON:000538685.17gold quality
caudate nucleusUBERON:000187384.88gold quality
muscle of legUBERON:000138384.77gold quality
body of tongueUBERON:001187684.77gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.29

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting PWWP2B, 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-4481100.0066.421669
HSA-MIR-497-5P99.9271.832674
HSA-MIR-627-3P99.9071.423316
HSA-MIR-15A-5P99.9072.802787
HSA-MIR-15B-5P99.9072.782798
HSA-MIR-16-5P99.9072.802780
HSA-MIR-195-5P99.9072.812805
HSA-MIR-424-5P99.8971.902641
HSA-MIR-6838-5P99.8971.942690
HSA-MIR-360999.5269.892587
HSA-MIR-548AH-5P99.5269.732626
HSA-MIR-6839-3P99.3968.861301
HSA-MIR-312599.1468.492269
HSA-MIR-450499.1069.141328
HSA-MIR-391698.9968.042155
HSA-MIR-6859-5P98.9968.072049
HSA-MIR-58398.7167.441791
HSA-MIR-5187-5P98.5467.94952
HSA-MIR-366197.8367.30705
HSA-MIR-366597.7365.08975
HSA-MIR-63197.0566.93602
HSA-MIR-6767-3P93.9966.01204
HSA-MIR-6812-3P90.5863.8060

Literature-anchored findings (GeneRIF, showing 2)

  • Study in HeLa, HEK293F, and mouse embryonic stem cells reveal that loss of PWWP2A/B leads to increases in histone acetylation predominantly at highly expressed genes, accompanied by decreases in Pol II elongation. Collectively, these findings suggest a role for PWWP2A/B in regulating transcription through the fine-tuning of histone acetylation dynamics at actively transcribed genes. (PMID:30228260)
  • PWWP2B promotes DNA end resection and homologous recombination. (PMID:35582821)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriopwwp2bENSDARG00000101080
mus_musculusPwwp2bENSMUSG00000060260
rattus_norvegicusPwwp2bENSRNOG00000036649

Paralogs (4): DNMT3B (ENSG00000088305), DNMT3A (ENSG00000119772), DNMT3L (ENSG00000142182), PWWP2A (ENSG00000170234)

Protein

Protein identifiers

PWWP domain-containing protein 2BQ6NUJ5 (reviewed: Q6NUJ5)

All UniProt accessions (1): Q6NUJ5

UniProt curated annotations — full annotation on UniProt →

Function. Chromatin-binding protein that acts as an adapter between distinct nucleosome components (H3K36me3 or H2A.Z) and chromatin-modifying complexes, contributing to the regulation of the levels of histone acetylation at actively transcribed genes. Competes with CHD4 and MBD3 for interaction with MTA1 to form a NuRD subcomplex, preventing the formation of full NuRD complex (containing CHD4 and MBD3), leading to recruitment of HDACs to gene promoters resulting in turn in the deacetylation of nearby H3K27 and H2A.Z. Plays a role in facilitating transcriptional elongation through regulation of histone acetylation. Negatively regulates brown adipocyte thermogenesis by interacting with and stabilizing HDAC1 at the UCP1 gene promoter, thereby promoting histone deacetylation at the promoter leading to the repression of UCP1 expression.

Subunit / interactions. Component of a MTA1-specific subcomplex of the NuRD complex composed of PWWP2B, MTA1 and HDAC1 but does not contain CHD4 and MBD3. Interacts with MTA1 and HDAC1. Interacts with MTA2, MTA3, HDAC2, RBBP4, RBBP7, BRCC3 and ZNF516. Does not interact with CHD4 and MBD3.

Post-translational modifications. Deubiquitinated by BRCC3; leading to its stabilization.

Isoforms (2)

UniProt IDNamesCanonical?
Q6NUJ5-11yes
Q6NUJ5-22

RefSeq proteins (2): NP_001092107, NP_612508* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000313PWWP_domDomain
IPR050390C5-MethyltransferaseFamily

Pfam: PF00855

UniProt features (33 total): strand 8, modified residue 5, region of interest 4, helix 4, compositionally biased region 4, splice variant 2, sequence variant 2, turn 2, chain 1, domain 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
4LD6X-RAY DIFFRACTION1.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6NUJ5-F160.710.15

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 (5): 84, 186, 206, 250, 447

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-9937850NuRD complex assembly

MSigDB gene sets: 93 (showing top): ZHAN_MULTIPLE_MYELOMA_PR_DN, CHANDRAN_METASTASIS_DN, GATA6_01, LIAO_METASTASIS, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, AACTTT_UNKNOWN, GOBP_MULTICELLULAR_ORGANISMAL_LEVEL_HOMEOSTASIS, HAND1E47_01, DOUGLAS_BMI1_TARGETS_UP, YY1_01, GOBP_CHROMATIN_REMODELING, GOBP_TEMPERATURE_HOMEOSTASIS, GOBP_POSITIVE_REGULATION_OF_DNA_TEMPLATED_TRANSCRIPTION_ELONGATION, GOBP_REGULATION_OF_DNA_TEMPLATED_TRANSCRIPTION_ELONGATION, CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP

GO Biological Process (3): chromatin remodeling (GO:0006338), positive regulation of transcription elongation by RNA polymerase II (GO:0032968), regulation of cold-induced thermogenesis (GO:0120161)

GO Molecular Function (2): NuRD complex binding (GO:0120325), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
CHD3, CHD4, CHD5 subfamily1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
chromatin organization1
transcription elongation by RNA polymerase II1
positive regulation of DNA-templated transcription, elongation1
regulation of transcription elongation by RNA polymerase II1
positive regulation of transcription by RNA polymerase II1
regulation of multicellular organismal process1
cold-induced thermogenesis1
protein-containing complex binding1
binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1

Protein interactions and networks

STRING

304 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PWWP2BLYSETQ8N6I4607
PWWP2BRBBP4P31149603
PWWP2BASB12Q8WXK4549
PWWP2BRBM12Q9NTZ6512
PWWP2BTAF5LO75529488
PWWP2BC2orf68Q2NKX9474
PWWP2BATP8B2P98198469
PWWP2BZMYM2Q9UBW7449
PWWP2BKRTAP4-8Q9BYQ9444
PWWP2BPPEF1O14829440
PWWP2BRLIMQ9NVW2436
PWWP2BBRD4O60885421
PWWP2BHDGFL1Q5TGJ6420
PWWP2BGPR101Q96P66403
PWWP2BNSD3Q9BZ95399

IntAct

20 interactions, top by confidence:

ABTypeScore
HDAC1CDK2AP1psi-mi:“MI:0914”(association)0.840
HDAC1TNRC18psi-mi:“MI:0914”(association)0.790
RBBP4CDK2AP1psi-mi:“MI:0914”(association)0.790
P4HA3FAM171A2psi-mi:“MI:0914”(association)0.640
PSMA3PWWP2Bpsi-mi:“MI:0915”(physical association)0.560
PWWP2BPSMA3psi-mi:“MI:0915”(physical association)0.560
GOLGA6L9PWWP2Bpsi-mi:“MI:0915”(physical association)0.560
PWWP2BABI2psi-mi:“MI:0915”(physical association)0.560
RBBP4TNRC18psi-mi:“MI:0914”(association)0.530
RBBP7EPOPpsi-mi:“MI:0914”(association)0.530
PWWP2BPRKDCpsi-mi:“MI:0915”(physical association)0.400
BRD2POLR2Bpsi-mi:“MI:0914”(association)0.350
PNMA8AAP3B1psi-mi:“MI:0914”(association)0.350
PWWP2BGOLGA6L9psi-mi:“MI:0915”(physical association)0.000
PWWP2BABI2psi-mi:“MI:0915”(physical association)0.000

BioGRID (23): PWWP2B (Two-hybrid), PWWP2B (Affinity Capture-MS), PWWP2B (Affinity Capture-MS), PWWP2B (Affinity Capture-MS), PWWP2B (Affinity Capture-MS), PWWP2B (Affinity Capture-RNA), PWWP2B (Two-hybrid), GOLGA6L9 (Two-hybrid), PWWP2B (Proximity Label-MS), PWWP2B (Affinity Capture-MS), PWWP2B (Affinity Capture-MS), PWWP2B (Affinity Capture-MS), PWWP2B (Affinity Capture-MS), PWWP2B (Affinity Capture-MS), PWWP2B (Affinity Capture-MS)

ESM2 similar proteins: A0JNJ4, A4IHR5, A6H7J1, A7UKY7, D4AE48, E9Q9M8, O15209, O35615, O75081, O95785, P03966, P04198, P39881, P49796, P52746, Q01101, Q1LY51, Q29RS4, Q32KV8, Q4KLY2, Q505G8, Q5T6C5, Q5TJE2, Q61976, Q62511, Q63379, Q63ZV0, Q6AY75, Q6NUJ5, Q6NV74, Q6P0F9, Q7T3H2, Q8BG80, Q8CDC7, Q8CE64, Q8IX07, Q8N554, Q8R4U1, Q96C00, Q96JP5

Diamond homologs: A0A1L8GR68, E9Q9M8, F7AQ22, O88508, Q1LZ53, Q4W5Z4, Q69Z61, Q6NUJ5, Q96N64, Q9FNE4, Q9UBC3, Q9Y6K1, O88509, Q923W4, Q9JMG7, Q9Y3E1, P00476, P09915, P0DOY1, P34906, Q10SU5, Q1LZ50, Q2RBJ4, Q9CWR8, Q9LXE5, Q9M548, Q9UJW3, Q9MA56, A4FUF0, F4IN78, F4IZM8, O75475, P51858, P51859, Q175F8, Q29NG1, Q32N87, Q3UMU9, Q49A26, Q562D5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance118
Likely benign10
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1002 predictions. Top by Δscore:

VariantEffectΔscore
10:132397352:G:GGdonor_gain1.0000
10:132404618:ATT:Aacceptor_gain1.0000
10:132404623:CAG:Cacceptor_loss1.0000
10:132404625:G:Aacceptor_loss1.0000
10:132397348:AAAAG:Adonor_loss0.9900
10:132397350:AA:Adonor_gain0.9900
10:132397350:AAG:Adonor_loss0.9900
10:132397351:AGT:Adonor_loss0.9900
10:132397352:GTGA:Gdonor_loss0.9900
10:132397353:T:Gdonor_loss0.9900
10:132397354:GA:Gdonor_loss0.9900
10:132404618:A:AGacceptor_gain0.9900
10:132404620:T:TAacceptor_gain0.9900
10:132404624:A:AGacceptor_gain0.9900
10:132404625:G:GCacceptor_gain0.9900
10:132404625:GGT:Gacceptor_gain0.9900
10:132404625:GGTCC:Gacceptor_gain0.9900
10:132417055:CCCAA:Cacceptor_loss0.9900
10:132417056:CCAA:Cacceptor_loss0.9900
10:132417057:CAAGG:Cacceptor_loss0.9900
10:132417058:AAGG:Aacceptor_loss0.9900
10:132417059:A:AGacceptor_loss0.9900
10:132417059:A:Gacceptor_gain0.9900
10:132417060:G:GCacceptor_loss0.9900
10:132397349:AAA:Adonor_gain0.9800
10:132404619:T:Gacceptor_gain0.9800
10:132417058:A:AGacceptor_gain0.9800
10:132397292:G:GAdonor_gain0.9700
10:132417047:T:Aacceptor_loss0.9700
10:132417060:G:GGacceptor_gain0.9700

AlphaMissense

3781 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:132405981:T:AV494D1.000
10:132405983:T:AW495R1.000
10:132405983:T:CW495R1.000
10:132405264:T:CI255T0.999
10:132405985:G:CW495C0.999
10:132405985:G:TW495C0.999
10:132406010:T:AW504R0.999
10:132406010:T:CW504R0.999
10:132406014:C:AP505Q0.999
10:132406023:T:AV508D0.999
10:132406088:T:AW530R0.999
10:132406088:T:CW530R0.999
10:132405264:T:GI255S0.998
10:132406012:G:CW504C0.998
10:132406012:G:TW504C0.998
10:132406013:C:TP505S0.998
10:132406083:T:AV528D0.998
10:132406090:G:CW530C0.998
10:132406090:G:TW530C0.998
10:132406091:T:CF531L0.998
10:132406093:T:AF531L0.998
10:132406093:T:GF531L0.998
10:132397326:G:TG34W0.997
10:132405306:T:CI269T0.997
10:132405972:G:TG491V0.997
10:132405984:G:CW495S0.997
10:132406001:T:CF501L0.997
10:132406003:T:AF501L0.997
10:132406003:T:GF501L0.997
10:132406007:T:AW503R0.997

dbSNP variants (sampled 300 via entrez): RS1000007315 (10:132405579 A>C), RS1000097449 (10:132405591 G>C), RS1000148235 (10:132410257 G>C), RS1000314373 (10:132396401 G>T), RS1000343746 (10:132397741 G>A), RS1000519981 (10:132410047 G>A,T), RS1000554207 (10:132405776 G>A), RS1000750152 (10:132413138 TCAA>T), RS1000795797 (10:132414288 A>G), RS1000870701 (10:132399043 A>C,G), RS1000918060 (10:132416874 C>G), RS1000942274 (10:132396866 G>C), RS1001041057 (10:132397601 G>A,T), RS1001123173 (10:132408953 T>C), RS1001163504 (10:132417234 C>A,G,T)

Disease associations

OMIM: gene `` | 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
GCST012048_13Triglyceride levels8.000000e-07

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004530triglyceride measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066163 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,538 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL1232461MOLIBRESIB21,538

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).

pChemblTypeValueUnitMolecule
7.60Kd25nMMOLIBRESIB
7.40IC5040nMMOLIBRESIB

PubChem BioAssay actives

2 with measured affinity, of 7 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.

CompoundAssayTypeValueUnit
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide2179188: Binding affinity against PWWP2B (unknown origin) assessed as apparent dissociation constant incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysiskd0.0250uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, increases methylation6
trichostatin Aaffects cotreatment, increases expression3
mercuric bromideincreases expression, affects cotreatment2
Phenylmercuric Acetateaffects cotreatment, increases expression2
p-Chloromercuribenzoic Acidincreases expression, affects cotreatment2
aristolochic acid Iincreases expression1
GSK-J4increases expression1
FR900359affects phosphorylation1
methylmercuric chlorideincreases expression1
methyleugenolincreases expression1
ethyl-p-hydroxybenzoateincreases expression1
11-nor-delta(9)-tetrahydrocannabinol-9-carboxylic acidincreases abundance, affects methylation1
cobaltous chlorideincreases expression1
aflatoxin B2decreases methylation1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
(+)-JQ1 compounddecreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Panobinostatincreases expression, affects cotreatment1
Benzo(a)pyreneaffects methylation1
Caffeinedecreases phosphorylation1
Cannabinoidsaffects methylation, increases abundance1
Cisplatindecreases expression1
Diethylhexyl Phthalateincreases expression1
Doxorubicindecreases expression1
Estradiolaffects cotreatment, decreases expression1
Smokedecreases expression1
Tretinoindecreases expression1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5697380BindingInhibition of PWWP2B (unknown origin) assessed as fold change at 10 uM incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysisInhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. — Nature

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_TH78HAP1 PWWP2B (-) 1Cancer cell lineMale
CVCL_TH79HAP1 PWWP2B (-) 2Cancer cell lineMale

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.