PDS5B

Summary

PDS5B (PDS5 cohesin associated factor B, HGNC:20418) is a protein-coding gene on chromosome 13q13.1, encoding Sister chromatid cohesion protein PDS5 homolog B (Q9NTI5). Regulator of sister chromatid cohesion in mitosis which may stabilize cohesin complex association with chromatin.

This gene encodes a protein that interacts with the conserved protein complex termed cohesin. The cohesin complex holds together sister chromatids and facilitates accurate chromosome segregation during mitosis and meiosis. This protein is also a negative regulator of cell proliferation and may be a tumor-suppressor gene.

Source: NCBI Gene 23047 — RefSeq curated summary.

At a glance

• GWAS associations: 16
• Clinical variants (ClinVar): 158 total
• Druggable target: yes
• MANE Select transcript: NM_015032

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20418
Approved symbol	PDS5B
Name	PDS5 cohesin associated factor B
Location	13q13.1
Locus type	gene with protein product
Status	Approved
Aliases	AS3, KIAA0979, FLJ23236, CG008
Ensembl gene	ENSG00000083642
Ensembl biotype	protein_coding
OMIM	605333
Entrez	23047

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 15 protein_coding, 6 retained_intron, 1 nonsense_mediated_decay

ENST00000315596, ENST00000447833, ENST00000450460, ENST00000466078, ENST00000474274, ENST00000481616, ENST00000482955, ENST00000493653, ENST00000498550, ENST00000877451, ENST00000877452, ENST00000877453, ENST00000921964, ENST00000921965, ENST00000921966, ENST00000921967, ENST00000921968, ENST00000921969, ENST00000921970, ENST00000921971, ENST00000921972, ENST00000921973

RefSeq mRNA: 1 — MANE Select: NM_015032 NM_015032

CCDS: CCDS41878

Canonical transcript exons

ENST00000315596 — 35 exons

Exon	Start	End
ENSE00001094420	32764489	32764594
ENSE00001094424	32770121	32770560
ENSE00001094440	32760575	32760720
ENSE00001174719	32758534	32758653
ENSE00001184410	32759628	32759690
ENSE00001319639	32770654	32770761
ENSE00001361142	32773189	32773324
ENSE00001371098	32775017	32778019
ENSE00001604215	32696854	32696902
ENSE00001624195	32699730	32699869
ENSE00001657461	32709946	32710106
ENSE00001675295	32742591	32742727
ENSE00001678193	32688456	32688569
ENSE00001699950	32755842	32755956
ENSE00001717883	32745977	32746100
ENSE00001718449	32735172	32735330
ENSE00001720858	32758087	32758219
ENSE00001763186	32701323	32701438
ENSE00001774967	32741080	32741148
ENSE00001775182	32732101	32732224
ENSE00001788262	32694223	32694304
ENSE00001806176	32753332	32753536
ENSE00001842722	32586452	32586593
ENSE00003489587	32675844	32675959
ENSE00003494250	32659154	32659280
ENSE00003495574	32687134	32687285
ENSE00003513782	32706934	32707039
ENSE00003566864	32667764	32667844
ENSE00003585288	32658434	32658531
ENSE00003585910	32648754	32648880
ENSE00003600413	32683878	32684023
ENSE00003604840	32673216	32673356
ENSE00003609286	32658239	32658325
ENSE00003623627	32678835	32678929
ENSE00003648916	32651804	32652007

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 95.80.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.5488 / max 401.9012, expressed in 1762 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
134710	7.9249	1608
134709	4.1622	1427
134708	4.1390	1323
134707	0.3228	162

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	95.80	gold quality
sural nerve	UBERON:0015488	95.23	gold quality
endothelial cell	CL:0000115	94.78	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	94.63	gold quality
colonic epithelium	UBERON:0000397	94.34	gold quality
ventricular zone	UBERON:0003053	93.03	gold quality
cortical plate	UBERON:0005343	92.09	gold quality
buccal mucosa cell	CL:0002336	91.19	gold quality
tibia	UBERON:0000979	91.01	gold quality
bone marrow cell	CL:0002092	90.91	gold quality
oocyte	CL:0000023	90.24	gold quality
ganglionic eminence	UBERON:0004023	90.05	gold quality
tendon	UBERON:0000043	89.53	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.41	gold quality
adrenal tissue	UBERON:0018303	88.88	gold quality
endometrium	UBERON:0001295	88.78	gold quality
middle temporal gyrus	UBERON:0002771	88.77	gold quality
epithelium of nasopharynx	UBERON:0001951	88.69	gold quality
nasopharynx	UBERON:0001728	88.68	gold quality
monocyte	CL:0000576	88.65	gold quality
endocervix	UBERON:0000458	88.65	gold quality
stromal cell of endometrium	CL:0002255	88.51	gold quality
Brodmann (1909) area 23	UBERON:0013554	88.36	gold quality
mononuclear cell	CL:0000842	88.15	gold quality
leukocyte	CL:0000738	88.04	gold quality
primary visual cortex	UBERON:0002436	88.00	gold quality
bone marrow	UBERON:0002371	87.92	gold quality
islet of Langerhans	UBERON:0000006	87.84	gold quality
body of uterus	UBERON:0009853	87.74	gold quality
embryo	UBERON:0000922	87.61	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.69
E-CURD-88	no	3.80

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

298 targeting PDS5B, 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-513A-5P	100.00	69.77	2465
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-656-3P	100.00	72.15	2788
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954

Literature-anchored findings (GeneRIF, showing 19)

• AS3 is a mediator of the proliferative arrest in the normal rat prostate in situ and that its expression is androgen-induced (AS3 protein) (PMID:12072405)
• The results of this study indicate that the aberrant expression of AS3 may be involved in the tumorigenesis of esophagus and is responsible for the male predominance of ESCC. (PMID:18499069)
• identified a functional missense mutation (R1292Q) in the PDS5B DNA-binding domain in a family with Cornelia de Lange syndrome, in which affected individuals also develop megacolon (PMID:19412548)
• Pard-3 and AS3 genes are mutationally inactivated in prostate cancer cells. (PMID:19737411)
• Loss of a cohesin-linked suppressor APRIN (Pds5b) disrupts stem cell programs in embryonal carcinoma. (PMID:20383194)
• Here, the authors use proteomic profiling to identify APRIN (PDS5B), a cohesion-associated protein, as a BRCA2-associated protein. (PMID:22293751)
• Frameshift mutations of SGOL1 and PDS5B and the loss of their expression may be a feature of gastric and colorectal cancers with high microsatellite instability. (PMID:23850494)
• Pds5 stabilizes a transient, open state of cohesin to promote its release from chromosomes. (PMID:26971492)
• Pds5B forms an integral part of the cohesin ring by contacting all other cohesin subunits, a property that may reflect the complex role of Pds5 proteins in controlling cohesin-DNA interactions. (PMID:27549742)
• APRIN expression levels correlate with a better survival in ovarian cancer patients and that APRIN depletion sensitizes cells to the PARP inhibitor Olaparib in xenografted zebrafish. (PMID:27924011)
• The mitotic histone kinase Haspin binds to the cohesin regulatory subunit Pds5B through a conserved YGA/R motif in its non-catalytic N terminus, which is similar to the recently reported YSR-motif-dependent binding of Wapl to Pds5B. (PMID:28343965)
• The authors’ data identify the HIM of Pds5 as a binding motif for Haspin/Hrk1 in fission yeast. The authors’ analyses also show that human PDS5B binds Haspin through the same HIM-PIM interaction module, indicating that the Haspin localization mechanism is highly conserved. (PMID:28343969)
• The results show that cohesin has an essential genome-wide function in mediating long-range chromatin interactions and support the hypothesis that cohesin creates these by loop extrusion, until it is delayed by CTCF in a manner dependent on PDS5 proteins, or until it is released from DNA by WAPL. (PMID:29217591)
• MAGI2-AS3 plays an important role as a tumour suppressor by targeting Fas and FasL signalling. (PMID:29679339)
• Pds5b/Ptch2 axis regulates cell proliferation and invasion in pancreatic tumor cells. (PMID:31233836)
• our study uncovers a protein complex, which consists of SWS1, SWSAP1, SPIDR and PDS5B, involved in DNA repair and provides insight into Shu complex function and composition. (PMID:31665741)
• PDS5 proteins are required for proper cohesin dynamics and participate in replication fork protection. (PMID:31757807)
• PDS5A and PDS5B in Cohesin Function and Human Disease. (PMID:34070827)
• [PDS5B inhibits the proliferation of A549 human lung cancer cells via downregulation of Wnt5a]. (PMID:36631010)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	pds5b	ENSDARG00000098897
mus_musculus	Pds5b	ENSMUSG00000034021
rattus_norvegicus	Pds5b	ENSRNOG00000001098
drosophila_melanogaster	pds5	FBGN0260012
caenorhabditis_elegans		WBGENE00001352

Paralogs (1): PDS5A (ENSG00000121892)

Protein

Protein identifiers

Sister chromatid cohesion protein PDS5 homolog B — Q9NTI5 (reviewed: Q9NTI5)

Alternative names: Androgen-induced proliferation inhibitor, Androgen-induced prostate proliferative shutoff-associated protein AS3

All UniProt accessions (2): Q9NTI5, A9IYQ1

UniProt curated annotations — full annotation on UniProt →

Function. Regulator of sister chromatid cohesion in mitosis which may stabilize cohesin complex association with chromatin. May couple sister chromatid cohesion during mitosis to DNA replication. Cohesion ensures that chromosome partitioning is accurate in both meiotic and mitotic cells and plays an important role in DNA repair. Plays a role in androgen-induced proliferative arrest in prostate cells.

Subunit / interactions. Interacts with the cohesin complex. Interacts with RAD21; the interaction is direct. Interacts with WAPL (via FGF motifs) or CDCA5 (via the FGF motif); the interaction is direct, cohesin-dependent and competitive.

Subcellular location. Nucleus.

Tissue specificity. Widely expressed.

Induction. By the synthetic androgen R1881 in prostate carcinoma cells undergoing proliferative arrest. Maximum levels occur 18-20 hours after androgen exposure.

Similarity. Belongs to the PDS5 family.

Isoforms (5)

UniProt ID	Names	Canonical?
Q9NTI5-1	1	yes
Q9NTI5-2	2
Q9NTI5-3	3
Q9NTI5-4	4
Q9NTI5-5	5

RefSeq proteins (1): NP_055847* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011989	ARM-like	Homologous_superfamily
IPR016024	ARM-type_fold	Homologous_superfamily
IPR039776	Pds5	Family

Pfam: PF20168

UniProt features (139 total): helix 72, modified residue 21, compositionally biased region 13, sequence conflict 11, splice variant 7, turn 5, strand 4, DNA-binding region 3, chain 1, repeat 1, region of interest 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
5HDT	X-RAY DIFFRACTION	2.71

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NTI5-F1	80.85	0.69

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 (21): 1136, 1140, 1162, 1166, 1176, 1182, 1191, 1255, 1257, 1259, 1283, 1319, 1334, 1358, 1366, 1367, 1369, 1370, 1381, 1383 …

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-2467813	Separation of Sister Chromatids
R-HSA-2468052	Establishment of Sister Chromatid Cohesion
R-HSA-2470946	Cohesin Loading onto Chromatin
R-HSA-2500257	Resolution of Sister Chromatid Cohesion

MSigDB gene sets: 278 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, GOBP_CHROMOSOME_ORGANIZATION, E2F_Q4_01, MULLIGHAN_NPM1_SIGNATURE_3_UP, CCAWYNNGAAR_UNKNOWN, DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_DN, MITSIADES_RESPONSE_TO_APLIDIN_DN, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_UP, DARWICHE_PAPILLOMA_RISK_HIGH_UP, DARWICHE_SQUAMOUS_CELL_CARCINOMA_UP, ATGCAGT_MIR217, AAAYRNCTG_UNKNOWN, chr13q13, E2F_Q3

GO Biological Process (5): mitotic sister chromatid cohesion (GO:0007064), cell population proliferation (GO:0008283), negative regulation of cell population proliferation (GO:0008285), regulation of cell population proliferation (GO:0042127), cell division (GO:0051301)

GO Molecular Function (3): DNA binding (GO:0003677), cohesin unloader activity (GO:0140670), protein binding (GO:0005515)

GO Cellular Component (6): chromosome, centromeric region (GO:0000775), chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), chromosome (GO:0005694), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
Mitotic Anaphase	1
S Phase	1
Mitotic Telophase/Cytokinesis	1
Mitotic Prometaphase	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
cellular process	2
cell population proliferation	2
sister chromatid cohesion	1
regulation of cell population proliferation	1
negative regulation of cellular process	1
regulation of cellular process	1
nucleic acid binding	1
catalytic activity, acting on DNA	1
binding	1
chromosomal region	1
chromosome	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular membraneless organelle	1
cytoplasm	1

Protein interactions and networks

STRING

2315 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PDS5B	WAPL	Q7Z5K2	995
PDS5B	NIPBL	Q6KC79	951
PDS5B	CDCA5	Q96FF9	937
PDS5B	STAG2	Q8N3U4	900
PDS5B	RAD21	O60216	890
PDS5B	BRCA2	P51587	861
PDS5B	SMC1A	Q14683	852
PDS5B	SMC3	Q9UQE7	852
PDS5B	MAU2	Q9Y6X3	831
PDS5B	PTGDR	Q13258	816
PDS5B	SMC1B	Q8NDV3	741
PDS5B	REC8	O95072	728
PDS5B	STAG1	Q8WVM7	668
PDS5B	SWSAP1	Q6NVH7	654
PDS5B	CTCF	P49711	643

IntAct

149 interactions, top by confidence:

A	B	Type	Score
BRCA2	RAD51	psi-mi:“MI:0914”(association)	0.980
STAG2	RAD21	psi-mi:“MI:0914”(association)	0.970
SMC3	RAD21	psi-mi:“MI:0914”(association)	0.960
SMC3	RAD21	psi-mi:“MI:0915”(physical association)	0.960
STAG1	RAD21	psi-mi:“MI:0914”(association)	0.930
SMC1A	RAD21	psi-mi:“MI:0914”(association)	0.930
SMC1A	RAD21	psi-mi:“MI:0915”(physical association)	0.930
RAD21	SMC1A	psi-mi:“MI:0914”(association)	0.930
WAPL	RAD21	psi-mi:“MI:0914”(association)	0.910
WAPL	RAD21	psi-mi:“MI:0915”(physical association)	0.910
PDS5B	RAD21	psi-mi:“MI:0914”(association)	0.860
PDS5B	RAD21	psi-mi:“MI:0915”(physical association)	0.860
SEPTIN12	SEPTIN6	psi-mi:“MI:0914”(association)	0.830
PDS5B	SMC3	psi-mi:“MI:0915”(physical association)	0.760
SGO1	RAD21	psi-mi:“MI:0914”(association)	0.740
PDS5B	WAPL	psi-mi:“MI:0915”(physical association)	0.730
WAPL	PDS5B	psi-mi:“MI:0915”(physical association)	0.730

BioGRID (296): PDS5B (Affinity Capture-MS), PDS5B (Affinity Capture-MS), PDS5B (Affinity Capture-MS), PDS5B (Affinity Capture-MS), PDS5B (Affinity Capture-MS), PDS5B (Affinity Capture-MS), PDS5B (Affinity Capture-MS), PDS5B (Affinity Capture-MS), PDS5B (Affinity Capture-MS), PDS5B (Affinity Capture-MS), PDS5B (Affinity Capture-Western), PDS5B (Affinity Capture-Western), BRCA2 (Affinity Capture-Western), PDS5B (Two-hybrid), RAD51 (Affinity Capture-Western)

ESM2 similar proteins: A0A0R4ITC5, A1L1F4, A4L9P7, E9Q8I9, F1MKX4, F1QFR9, F1R2X6, F8VPU6, O94915, P21359, P42345, P42346, P51593, P97526, Q04690, Q14997, Q29RF7, Q2HJG5, Q498H0, Q4KLU7, Q4QXM3, Q4VA53, Q5F3U9, Q5F3V3, Q5R6J0, Q5SSW2, Q5TBA9, Q5U241, Q5VYK3, Q6A026, Q6DDM4, Q6GP04, Q6NRP2, Q6P4S8, Q6PDI5, Q6TRW4, Q7PX35, Q7TMY8, Q7Z3U7, Q7Z6Z7

Diamond homologs: A1L1F4, A4L9P7, A8MRD9, Q29RF7, Q498H0, Q4KLU7, Q4QXM3, Q4VA53, Q5F3U9, Q5F3V3, Q5U241, Q6A026, Q6TRW4, Q9NTI5, B6EUB3, O04716, Q6K431, Q8GUP3, Q9S9P0

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
PDS5B	“form complex”	“SHU complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 126 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:

Pathway	Partners	Fold	FDR
Meiosis	5	17.8×	5e-04
S Phase	6	13.6×	4e-04
Reproduction	5	11.9×	3e-03
Resolution of Sister Chromatid Cohesion	9	9.7×	3e-05
SUMOylation of DNA damage response and repair proteins	5	9.2×	5e-03
Meiotic synapsis	5	8.8×	6e-03
ESR-mediated signaling	5	8.0×	9e-03
Mitotic Metaphase and Anaphase	6	7.3×	5e-03

GO biological processes:

GO term	Partners	Fold	FDR
sister chromatid cohesion	5	37.5×	7e-05
cell division	10	4.5×	8e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	116
Likely benign	3
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

6762 predictions. Top by Δscore:

Variant	Effect	Δscore
13:32629437:T:G	donor_gain	1.0000
13:32629437:T:TG	donor_gain	1.0000
13:32629441:G:GG	donor_gain	1.0000
13:32648748:TTTCA:T	acceptor_loss	1.0000
13:32648750:TCA:T	acceptor_loss	1.0000
13:32648751:CAGG:C	acceptor_loss	1.0000
13:32648752:A:AG	acceptor_gain	1.0000
13:32648752:AGG:A	acceptor_gain	1.0000
13:32648753:G:GT	acceptor_gain	1.0000
13:32648753:GGG:G	acceptor_gain	1.0000
13:32648878:AAG:A	donor_gain	1.0000
13:32648879:AG:A	donor_gain	1.0000
13:32648880:GG:G	donor_gain	1.0000
13:32648881:G:GG	donor_gain	1.0000
13:32651802:A:AG	acceptor_gain	1.0000
13:32651802:AGAT:A	acceptor_gain	1.0000
13:32651803:G:GG	acceptor_gain	1.0000
13:32651803:GATG:G	acceptor_gain	1.0000
13:32654077:T:G	donor_gain	1.0000
13:32658532:G:GG	donor_gain	1.0000
13:32659148:TTGCA:T	acceptor_loss	1.0000
13:32659149:TGCAG:T	acceptor_loss	1.0000
13:32659150:GCAGC:G	acceptor_loss	1.0000
13:32659151:CAGCA:C	acceptor_loss	1.0000
13:32659152:A:AG	acceptor_gain	1.0000
13:32659152:AGCA:A	acceptor_loss	1.0000
13:32659153:G:GA	acceptor_gain	1.0000
13:32659153:GC:G	acceptor_gain	1.0000
13:32659153:GCA:G	acceptor_gain	1.0000
13:32659153:GCAA:G	acceptor_gain	1.0000

AlphaMissense

9594 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:32648815:T:G	Y15D	1.000
13:32648819:C:A	P16Q	1.000
13:32648828:T:A	V19D	1.000
13:32648837:T:A	I22K	1.000
13:32648837:T:G	I22R	1.000
13:32648873:G:C	R34P	1.000
13:32648876:T:C	L35S	1.000
13:32651836:G:C	Q47H	1.000
13:32651836:G:T	Q47H	1.000
13:32651874:C:A	A60D	1.000
13:32651883:T:A	L63H	1.000
13:32651883:T:C	L63P	1.000
13:32651922:T:A	V76D	1.000
13:32651928:T:C	L78S	1.000
13:32651931:T:C	L79P	1.000
13:32651937:C:A	A81D	1.000
13:32651939:T:C	C82R	1.000
13:32651940:G:A	C82Y	1.000
13:32651941:C:G	C82W	1.000
13:32651942:T:C	C83R	1.000
13:32651943:G:A	C83Y	1.000
13:32651944:C:G	C83W	1.000
13:32651946:T:C	L84P	1.000
13:32651948:G:C	A85P	1.000
13:32651949:C:A	A85D	1.000
13:32651951:G:C	D86H	1.000
13:32651951:G:T	D86Y	1.000
13:32651952:A:C	D86A	1.000
13:32651952:A:G	D86G	1.000
13:32651952:A:T	D86V	1.000

dbSNP variants (sampled 300 via entrez): RS1000056137 (13:32647692 C>G), RS1000059050 (13:32740889 T>C), RS1000059464 (13:32616754 C>T), RS1000062325 (13:32712470 T>G), RS1000066330 (13:32757807 C>T), RS1000086967 (13:32647414 G>C), RS1000100665 (13:32659564 A>G), RS1000107622 (13:32702076 A>G), RS1000128575 (13:32607249 T>A), RS1000132556 (13:32639251 T>C), RS1000145704 (13:32672975 A>G), RS1000161363 (13:32592583 T>TC), RS1000168794 (13:32691888 T>C), RS1000169588 (13:32716266 G>C), RS1000245991 (13:32639546 C>T)

Disease associations

OMIM: gene MIM:605333 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

16 associations (top):

Study	Trait	p-value
GCST000892_8	Total ventricular volume (Alzheimer’s disease interaction)	5.000000e-06
GCST001956_78	Height	2.000000e-10
GCST002783_246	Body mass index	6.000000e-06
GCST002783_425	Body mass index	6.000000e-06
GCST003831_34	Asthma	4.000000e-06
GCST004253_4	Accelerated cognitive decline after conversion of mild cognitive impairment to Alzheimer’s disease (Alzhiemer’s diagnosis trajectory interaction)	2.000000e-06
GCST004599_200	Mean platelet volume	6.000000e-15
GCST004748_28	Lung cancer	2.000000e-10
GCST004750_1	Squamous cell lung carcinoma	9.000000e-12
GCST004750_2	Squamous cell lung carcinoma	3.000000e-06
GCST005194_120	Coronary artery disease	1.000000e-09
GCST006491_15	Circulating fibroblast growth factor 23 levels	7.000000e-07
GCST007010_2	Logical memory (delayed recall)	1.000000e-06
GCST010866_102	Coronary artery disease	3.000000e-09
GCST010984_29	Allergic disease (asthma, hay fever and/or eczema) (multivariate analysis)	2.000000e-10
GCST90013405_1	Liver enzyme levels (alanine transaminase)	5.000000e-14

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0007710	cognitive decline measurement
EFO:0004874	memory performance

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067140 (SINGLE PROTEIN)

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).

pChembl	Type	Value	Unit	Molecule
7.43	Kd	36.89	nM	CHEMBL5653589
7.43	ED50	36.89	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 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.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2148971: Binding affinity to human PDS5B incubated for 45 mins by Kinobead based pull down assay	kd	0.0369	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, increases expression	3
trichostatin A	affects expression, increases expression	2
sodium arsenite	decreases expression, increases expression	2
Estradiol	affects cotreatment, increases expression, decreases expression	2
Quercetin	increases phosphorylation, decreases expression	2
Valproic Acid	decreases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
TAK-243	decreases sumoylation	1
dicrotophos	decreases expression	1
2,4,6-tribromophenol	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
butyraldehyde	decreases expression	1
perfluorooctanoic acid	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
coumarin	affects phosphorylation	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
chromium hexavalent ion	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
2-palmitoylglycerol	increases expression	1
abrine	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
jinfukang	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Acetaminophen	decreases expression	1
Androgens	increases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652013	Binding	Binding affinity to human PDS5B incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

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