PWWP3A

Summary

PWWP3A (PWWP domain containing 3A, DNA repair factor, HGNC:29641) is a protein-coding gene on chromosome 19p13.3, encoding PWWP domain-containing DNA repair factor 3A (Q2TAK8). Involved in the DNA damage response pathway by contributing to the maintenance of chromatin architecture.

Enables nucleosome binding activity. Involved in DNA repair and chromatin organization. Located in cytosol and nucleoplasm.

Source: NCBI Gene 84939 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 170 total
• MANE Select transcript: NM_001369789

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29641
Approved symbol	PWWP3A
Name	PWWP domain containing 3A, DNA repair factor
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Aliases	MUM-1, EXPAND1
Ensembl gene	ENSG00000160953
Ensembl biotype	protein_coding
Entrez	84939

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 13 protein_coding, 4 retained_intron, 4 protein_coding_CDS_not_defined, 3 nonsense_mediated_decay

ENST00000415183, ENST00000585399, ENST00000586067, ENST00000586996, ENST00000587460, ENST00000588810, ENST00000588888, ENST00000590695, ENST00000590866, ENST00000591337, ENST00000591433, ENST00000591453, ENST00000591627, ENST00000591806, ENST00000592374, ENST00000627377, ENST00000652273, ENST00000853246, ENST00000853247, ENST00000853248, ENST00000853249, ENST00000913149, ENST00000913150, ENST00000945202

RefSeq mRNA: 12 — MANE Select: NM_001369789 NM_001369789, NM_001369790, NM_001369792, NM_001369793, NM_001369794, NM_001369795, NM_001369796, NM_001369797, NM_001382408, NM_001382409, NM_001382410, NM_032853

CCDS: CCDS12062, CCDS92480

Canonical transcript exons

ENST00000591337 — 14 exons

Exon	Start	End
ENSE00002769087	1354959	1355135
ENSE00003497820	1356324	1356449
ENSE00003500271	1369596	1369646
ENSE00003516442	1358394	1358464
ENSE00003539460	1373072	1373160
ENSE00003547846	1370642	1371078
ENSE00003585906	1367160	1367220
ENSE00003637679	1364509	1364579
ENSE00003639949	1369265	1369340
ENSE00003642041	1362250	1362351
ENSE00003643603	1360136	1361032
ENSE00003687979	1366305	1366381
ENSE00003787766	1357009	1357094
ENSE00003911859	1376519	1378429

Expression profiles

Bgee: expression breadth ubiquitous, 272 present calls, max score 97.08.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.1884 / max 217.0966, expressed in 1661 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
172947	4.9615	1618
172950	1.0978	522
172948	0.0856	23
172949	0.0435	16

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	97.08	gold quality
cerebellar hemisphere	UBERON:0002245	96.95	gold quality
left testis	UBERON:0004533	96.93	gold quality
right testis	UBERON:0004534	96.89	gold quality
cerebellar cortex	UBERON:0002129	96.85	gold quality
cerebellum	UBERON:0002037	96.04	gold quality
right frontal lobe	UBERON:0002810	95.69	gold quality
testis	UBERON:0000473	95.65	gold quality
right uterine tube	UBERON:0001302	95.60	gold quality
adenohypophysis	UBERON:0002196	95.56	gold quality
sural nerve	UBERON:0015488	95.48	gold quality
pituitary gland	UBERON:0000007	95.39	gold quality
left ovary	UBERON:0002119	95.00	gold quality
anterior cingulate cortex	UBERON:0009835	94.77	gold quality
nucleus accumbens	UBERON:0001882	94.75	gold quality
mucosa of stomach	UBERON:0001199	94.70	gold quality
cingulate cortex	UBERON:0003027	94.70	gold quality
right ovary	UBERON:0002118	94.66	gold quality
amygdala	UBERON:0001876	94.26	gold quality
right lobe of liver	UBERON:0001114	94.25	gold quality
caudate nucleus	UBERON:0001873	94.25	gold quality
medial globus pallidus	UBERON:0002477	94.23	gold quality
Brodmann (1909) area 9	UBERON:0013540	94.20	gold quality
ovary	UBERON:0000992	94.01	gold quality
putamen	UBERON:0001874	93.86	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	93.60	gold quality
body of uterus	UBERON:0009853	93.59	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	93.57	gold quality
brain	UBERON:0000955	93.39	gold quality
neocortex	UBERON:0001950	93.36	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.63
E-GEOD-137537	yes	6.46

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

36 targeting PWWP3A, 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-188-3P	100.00	68.76	1240
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4745-5P	99.98	65.95	1028
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-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-5003-5P	99.61	69.13	1624
HSA-MIR-4276	99.56	67.66	2514
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-889-3P	99.40	69.76	2103
HSA-MIR-4251	99.40	69.19	3363
HSA-MIR-4685-5P	99.25	65.99	1563
HSA-MIR-6837-5P	99.25	65.47	1632
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-6799-5P	99.14	65.72	2093
HSA-MIR-6809-5P	99.13	68.45	1223
HSA-MIR-922	99.02	67.23	1838
HSA-MIR-625-5P	99.02	68.64	2031
HSA-MIR-181A-2-3P	98.91	67.60	1168
HSA-MIR-5006-5P	98.79	66.92	1246
HSA-MIR-5000-3P	98.79	65.63	1251
HSA-MIR-4755-3P	98.77	65.59	1915
HSA-MIR-5008-5P	98.42	65.87	1019
HSA-MIR-4436A	98.05	64.83	1140

Literature-anchored findings (GeneRIF, showing 1)

• report the identification of the PWWP domain-containing protein EXPAND1/MUM1 as an architectural component of the chromatin, which in response to DNA damage serves as an accessory factor to promote cell survival. (PMID:20347427)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:dkey-57k2.7	ENSDARG00000060395
mus_musculus	Pwwp3a	ENSMUSG00000020156
rattus_norvegicus	Pwwp3a	ENSRNOG00000024549

Paralogs (2): PWWP3B (ENSG00000157502), PWWP4 (ENSG00000278803)

Protein

Protein identifiers

PWWP domain-containing DNA repair factor 3A — Q2TAK8 (reviewed: Q2TAK8)

Alternative names: Mutated melanoma-associated antigen 1, PWWP domain-containing protein MUM1, Protein expandere

All UniProt accessions (6): Q2TAK8, A0A0D9SGJ8, J3KNX4, K7END0, K7EP97, K7ES53

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the DNA damage response pathway by contributing to the maintenance of chromatin architecture. Recruited to the vicinity of DNA breaks by TP53BP1 and plays an accessory role to facilitate damage-induced chromatin changes and promoting chromatin relaxation. Required for efficient DNA repair and cell survival following DNA damage.

Subunit / interactions. Interacts with TP53BP1 (via BRCT domain); the interaction is not dependent on its phosphorylation status. Binds nucleosomes. Interacts with trimethylated ‘Lys-36’ of histone H3 (H3K36me3) (in vitro).

Subcellular location. Nucleus.

Domain organisation. The PWWP domain mediates the interaction with nucleosomes.

Miscellaneous. Acts as an antigenic peptide recognized by cytolytic T-lymphocytes in a melanoma.

Similarity. Belongs to the PWWP3A family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q2TAK8-1	1	yes
Q2TAK8-2	2
Q2TAK8-3	3

RefSeq proteins (11): NP_001356718, NP_001356719, NP_001356721, NP_001356722, NP_001356723, NP_001356725, NP_001356726, NP_001369337, NP_001369338, NP_001369339, NP_116242 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR035504	MUM1-like_PWWP	Domain
IPR040263	PWP3A_3B_4	Family
IPR048765	PWP3A_3B_4_N	Domain
IPR048795	PWP3A_3B_4_C	Domain

Pfam: PF20884, PF20886, PF20887

UniProt features (29 total): helix 6, strand 4, compositionally biased region 4, modified residue 3, splice variant 3, region of interest 3, sequence variant 2, chain 1, domain 1, sequence conflict 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
3PMI	X-RAY DIFFRACTION	2.82

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q2TAK8-F1	64.44	0.23

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 (3): 374, 375, 161

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 48 (showing top): MITSIADES_RESPONSE_TO_APLIDIN_DN, GROSS_HYPOXIA_VIA_ELK3_UP, GOBP_DNA_DAMAGE_RESPONSE, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, GOMF_CHROMATIN_BINDING, chr19p13, GOBP_DNA_METABOLIC_PROCESS, GOMF_NUCLEOSOME_BINDING, GOBP_DNA_REPAIR, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN, BRUINS_UVC_RESPONSE_LATE, WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D, ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN, KUMAR_PATHOGEN_LOAD_BY_MACROPHAGES, GOMF_PROTEIN_CONTAINING_COMPLEX_BINDING

GO Biological Process (3): DNA repair (GO:0006281), chromatin organization (GO:0006325), DNA damage response (GO:0006974)

GO Molecular Function (2): nucleosome binding (GO:0031491), protein binding (GO:0005515)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
DNA metabolic process	1
DNA damage response	1
cellular component organization	1
cellular response to stress	1
chromatin binding	1
protein-containing complex binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoplasm	1

Protein interactions and networks

STRING

1667 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PWWP3A	TP53BP1	Q12888	445
PWWP3A	BCL6	P41182	400
PWWP3A	MME	P08473	372
PWWP3A	MDC1	Q14676	368
PWWP3A	RNF8	O76064	357
PWWP3A	RNF168	Q8IYW5	337
PWWP3A	SHROOM1	Q2M3G4	327
PWWP3A	PAXIP1	Q6ZW49	323
PWWP3A	HDGFL2	Q7Z4V5	304
PWWP3A	CD79A	P11912	297
PWWP3A	KLHL34	Q8N239	292
PWWP3A	UIMC1	Q96RL1	288
PWWP3A	ATP5F1D	P30049	281
PWWP3A	MT-ATP6	P00846	281
PWWP3A	ATP5F1A	P25705	281

IntAct

19 interactions, top by confidence:

A	B	Type	Score
PWWP3A	SMC6	psi-mi:“MI:0914”(association)	0.530
SMC6	IFT88	psi-mi:“MI:0914”(association)	0.350
MKI67	ARHGAP10	psi-mi:“MI:0914”(association)	0.350
PTGES3	SBNO1	psi-mi:“MI:0914”(association)	0.350
CDH23	GTPBP10	psi-mi:“MI:0914”(association)	0.350
PCDHB6	KLRG2	psi-mi:“MI:0914”(association)	0.350
HNRNPCL2	SMCHD1	psi-mi:“MI:0914”(association)	0.350
ZNG1B	NME4	psi-mi:“MI:0914”(association)	0.350
CCT8L2	DVL2	psi-mi:“MI:0914”(association)	0.350
ZNG1A	TCERG1	psi-mi:“MI:0914”(association)	0.350
PPP1R15A	POLR3A	psi-mi:“MI:0914”(association)	0.350
FEM1A	RNF113A	psi-mi:“MI:0914”(association)	0.350
KLK1	SLC25A20	psi-mi:“MI:0914”(association)	0.350
NMNAT2	MYCBP2	psi-mi:“MI:0914”(association)	0.350
PWWP3A	PPFIBP1	psi-mi:“MI:0914”(association)	0.350
FEM1A	DHRS3	psi-mi:“MI:0914”(association)	0.350
	ILVBL	psi-mi:“MI:0914”(association)	0.350
MDC1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (38): MUM1 (Two-hybrid), MUM1 (Two-hybrid), MUM1 (Two-hybrid), MUM1 (Two-hybrid), GSTO2 (Two-hybrid), MUM1 (Affinity Capture-MS), MUM1 (Affinity Capture-MS), BAIAP2L1 (Affinity Capture-MS), SMC6 (Affinity Capture-MS), MUM1 (Affinity Capture-MS), MUM1 (Proximity Label-MS), MUM1 (Affinity Capture-MS), MUM1 (Affinity Capture-MS), MUM1 (Affinity Capture-MS), MUM1 (Affinity Capture-MS)

ESM2 similar proteins: A4Q9E5, A4Q9F1, A6PVC2, B1H224, D2GZW6, E1BP92, E1CHH8, E9PT87, O15037, O43918, O94966, O95238, P27987, P29473, P42335, P48778, P59729, Q1ECV4, Q2TAK8, Q3SYK4, Q3UIZ8, Q3UJD6, Q4R739, Q5JYT7, Q6B0I6, Q6DID5, Q6J1Y9, Q6NZK8, Q75NR7, Q7TSI1, Q80U38, Q810F8, Q8BV79, Q8BWG4, Q8CHB8, Q8N841, Q8NC06, Q8NE63, Q8TB24, Q8VDG6

Diamond homologs: A0A494C071, B1H224, Q08DK9, Q2TAK8, Q4VA55, Q5H9M0, Q6DID5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	128
Likely benign	17
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2544 predictions. Top by Δscore:

Variant	Effect	Δscore
19:1357096:T:G	donor_gain	1.0000
19:1357096:T:TG	donor_gain	1.0000
19:1358391:CA:C	acceptor_loss	1.0000
19:1358392:A:AC	acceptor_loss	1.0000
19:1358392:A:AG	acceptor_gain	1.0000
19:1358393:G:GT	acceptor_gain	1.0000
19:1358393:GA:G	acceptor_gain	1.0000
19:1358393:GAA:G	acceptor_gain	1.0000
19:1358393:GAAT:G	acceptor_gain	1.0000
19:1358393:GAATT:G	acceptor_gain	1.0000
19:1358461:TTAGG:T	donor_loss	1.0000
19:1358462:TAG:T	donor_loss	1.0000
19:1358463:AGGT:A	donor_loss	1.0000
19:1358464:GGTAA:G	donor_loss	1.0000
19:1358465:G:GC	donor_loss	1.0000
19:1358466:T:G	donor_loss	1.0000
19:1358583:ACAAG:A	acceptor_gain	1.0000
19:1358585:AAG:A	acceptor_gain	1.0000
19:1358585:AAGG:A	acceptor_gain	1.0000
19:1358586:A:G	acceptor_gain	1.0000
19:1358753:G:GT	donor_gain	1.0000
19:1360134:A:AG	acceptor_gain	1.0000
19:1360135:G:GG	acceptor_gain	1.0000
19:1369336:GTTAG:G	donor_gain	1.0000
19:1371077:AGG:A	donor_loss	1.0000
19:1371078:GGTGA:G	donor_loss	1.0000
19:1371079:GT:G	donor_loss	1.0000
19:1371080:T:A	donor_loss	1.0000
19:1373070:A:AG	acceptor_gain	1.0000
19:1373071:G:GG	acceptor_gain	1.0000

AlphaMissense

1677 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:1356438:T:A	W16R	0.988
19:1356438:T:C	W16R	0.988
19:1356442:C:A	P17H	0.986
19:1356440:G:C	W16C	0.985
19:1356440:G:T	W16C	0.985
19:1357076:T:C	I42T	0.984
19:1360202:C:A	A94D	0.984
19:1356412:T:A	V7D	0.982
19:1356444:G:C	A18P	0.982
19:1360193:T:A	L91H	0.981
19:1360180:T:G	Y87D	0.979
19:1360193:T:C	L91P	0.979
19:1356441:C:T	P17S	0.977
19:1356445:C:A	A18E	0.975
19:1360201:G:C	A94P	0.969
19:1356442:C:G	P17R	0.967
19:1357076:T:G	I42S	0.967
19:1360185:A:C	R88S	0.966
19:1360185:A:T	R88S	0.966
19:1360196:G:C	R92P	0.965
19:1356425:G:C	W11C	0.964
19:1356425:G:T	W11C	0.964
19:1356441:C:A	P17T	0.962
19:1357070:T:A	V40E	0.960
19:1360190:C:G	S90W	0.960
19:1360189:T:C	S90P	0.956
19:1356417:T:C	C9R	0.954
19:1356439:G:C	W16S	0.953
19:1356419:C:G	C9W	0.952
19:1360184:G:C	R88T	0.952

dbSNP variants (sampled 300 via entrez): RS1000005371 (19:1357903 C>G), RS1000158184 (19:1359132 C>G), RS1000266374 (19:1367587 C>T), RS1000291983 (19:1375627 TTTATA>T), RS1000298729 (19:1370105 G>A,C), RS1000345258 (19:1371167 G>A,T), RS1000386287 (19:1374457 C>T), RS1000517032 (19:1361587 C>G,T), RS1000539181 (19:1356159 C>A,G), RS1000567498 (19:1369967 C>A,T), RS1000577575 (19:1374426 G>A), RS1000644200 (19:1375296 G>C), RS1000787222 (19:1365873 G>C,T), RS1000925742 (19:1378121 G>A), RS1000937878 (19:1354846 G>A)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases methylation, affects cotreatment, decreases expression	6
trichostatin A	affects cotreatment, decreases expression	2
Acetaminophen	decreases expression	2
Benzo(a)pyrene	decreases expression, increases methylation	2
aristolochic acid I	decreases expression	1
GSK-J4	decreases expression	1
testosterone enanthate	affects expression	1
methylmercuric chloride	decreases expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
pirinixic acid	affects binding, decreases expression, increases activity	1
bisphenol A	decreases expression	1
arsenite	increases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
cobaltous chloride	increases expression	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
CGP 52608	increases reaction, affects binding	1
CPG-oligonucleotide	decreases expression	1
K 7174	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
ICG 001	increases expression	1
abrine	decreases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, increases expression	1
PCI 5002	affects cotreatment, increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Temozolomide	decreases expression	1
Arsenic Trioxide	decreases expression	1
Leflunomide	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_XQ78	HAP1 MUM1 (-)	Cancer cell line	Male

Clinical trials (associated diseases)

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