CENPN

Summary

CENPN (centromere protein N, HGNC:30873) is a protein-coding gene on chromosome 16q23.2, encoding Centromere protein N (Q96H22). Component of the CENPA-NAC (nucleosome-associated) complex, a complex that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation. It is a common-essential gene (DepMap: required in 98.8% of cancer cell lines).

The protein encoded by this gene forms part of the nucleosome-associated complex and is important for kinetochore assembly. It is bound to kinetochores during S phase and G2 and recruits other proteins to the centromere. Pseudogenes of this gene are located on chromosome 2. Alternative splicing results in multiple transcript variants that encode different protein isoforms.

Source: NCBI Gene 55839 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 87 total
• Cancer dependency (DepMap): dependent in 98.8% of screened cell lines (common-essential)
• MANE Select transcript: NM_001100624

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30873
Approved symbol	CENPN
Name	centromere protein N
Location	16q23.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ13607, FLJ22660, BM039
Ensembl gene	ENSG00000166451
Ensembl biotype	protein_coding
OMIM	611509
Entrez	55839

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 9 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000299572, ENST00000305850, ENST00000393335, ENST00000428963, ENST00000439957, ENST00000562943, ENST00000564669, ENST00000568445, ENST00000569461, ENST00000936235, ENST00000958173

RefSeq mRNA: 5 — MANE Select: NM_001100624 NM_001100624, NM_001100625, NM_001270473, NM_001270474, NM_018455

CCDS: CCDS10931, CCDS42199, CCDS42200, CCDS58482, CCDS58483

Canonical transcript exons

ENST00000305850 — 11 exons

Exon	Start	End
ENSE00001103078	81017758	81017834
ENSE00001122444	81026526	81026638
ENSE00001122449	81024715	81024778
ENSE00001122455	81022597	81022698
ENSE00001293527	81028171	81028297
ENSE00001827688	81028569	81031485
ENSE00001854551	81007214	81007277
ENSE00003502337	81011930	81012110
ENSE00003505514	81014136	81014181
ENSE00003630631	81017326	81017385
ENSE00003790303	81020100	81020276

Expression profiles

Bgee: expression breadth ubiquitous, 205 present calls, max score 95.15.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.8398 / max 930.7114, expressed in 1815 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
155134	19.9005	1692
155133	7.9393	1688

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	95.15	gold quality
ganglionic eminence	UBERON:0004023	92.97	gold quality
buccal mucosa cell	CL:0002336	92.32	gold quality
embryo	UBERON:0000922	91.45	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	90.88	gold quality
secondary oocyte	CL:0000655	90.11	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.33	gold quality
bone marrow	UBERON:0002371	87.85	gold quality
stromal cell of endometrium	CL:0002255	87.79	gold quality
oocyte	CL:0000023	84.90	gold quality
sperm	CL:0000019	84.44	gold quality
trabecular bone tissue	UBERON:0002483	84.08	gold quality
male germ cell	CL:0000015	82.26	gold quality
bone marrow cell	CL:0002092	81.99	gold quality
cartilage tissue	UBERON:0002418	81.86	gold quality
mucosa of transverse colon	UBERON:0004991	81.74	gold quality
prostate gland	UBERON:0002367	80.79	gold quality
adrenal tissue	UBERON:0018303	80.78	gold quality
testis	UBERON:0000473	80.54	gold quality
right testis	UBERON:0004534	80.53	gold quality
left testis	UBERON:0004533	80.16	gold quality
amniotic fluid	UBERON:0000173	80.12	gold quality
rectum	UBERON:0001052	80.11	gold quality
islet of Langerhans	UBERON:0000006	79.28	gold quality
esophagus mucosa	UBERON:0002469	78.87	gold quality
colonic epithelium	UBERON:0000397	78.44	gold quality
esophagus squamous epithelium	UBERON:0006920	78.24	gold quality
squamous epithelium	UBERON:0006914	78.16	gold quality
gingival epithelium	UBERON:0001949	78.13	gold quality
vermiform appendix	UBERON:0001154	77.61	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-HCAD-10	yes	35.52
E-HCAD-13	yes	20.55
E-HCAD-5	yes	17.33
E-GEOD-125970	yes	16.51
E-ANND-3	yes	6.27

Regulation

Is transcription factor: no

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 98.8% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 12)

• Data suggest that CENP-N interprets the information encoded within CENP-A nucleosomes and recruits other proteins to centromeric chromatin that are required for centromere function and propagation. (PMID:19543270)
• CENP-N is bound to kinetochores during S phase and G2, but is absent from kinetochores during mitosis and G1. (PMID:22100916)
• Study demonstrate that the CENP-L-N complex plays a crucial role at the core of the 16-subunit Constitutive Centromere-Associated Network through interactions with CENP-C and CENP-H-I-KM. (PMID:26698661)
• this study reports cryo-electron microscopy (cryo-EM), biophysical, biochemical, and cell biological studies of the interaction between the CENP-A nucleosome and CENP-N. (PMID:29269420)
• Collectively, these studies clarify how CENP-N and CENP-C decode and stabilize the non-canonical CENP-A nucleosome to enforce epigenetic centromere specification and kinetochore assembly. (PMID:29280735)
• CENP-N stabilizes CENP-A nucleosomes alone and additively with CENP-C in vitro. However, removal of CENP-C and CENP-N from cells, or mutating CENP-A so that it no longer interacts with CENP-C or CENP-N, had no effect on centromeric CENP-A stability in vivo. Thus, the stability of CENP-A nucleosomes in chromatin does not arise solely from its interactions with CENP-C or CENP-N. (PMID:29343552)
• The Elusive Structure of Centro-Chromatin: Molecular Order or Dynamic Heterogenetity? (PMID:33065112)
• Centromere protein N promotes lung adenocarcinoma progression by activating PI3K/AKT signaling pathway. (PMID:35150399)
• CENP-N promotes the compaction of centromeric chromatin. (PMID:35422519)
• Knockdown of CENPN Inhibits Glucose Metabolism and Induces G1 Arrest in Esophageal Cancer Cells by Regulating PI3K/AKT Signaling Pathway. (PMID:37127048)
• Dynamic phosphorylation of CENP-N by CDK1 guides accurate chromosome segregation in mitosis. (PMID:37365681)
• Clinical implications and immune features of CENPN in breast cancer. (PMID:37697245)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cenpn	ENSDARG00000043640
mus_musculus	Cenpn	ENSMUSG00000031756
rattus_norvegicus	Cenpn	ENSRNOG00000011296

Protein

Protein identifiers

Centromere protein N — Q96H22 (reviewed: Q96H22)

Alternative names: Interphase centromere complex protein 32

All UniProt accessions (4): Q96H22, H3BMC7, H3BMD5, H3BRU7

UniProt curated annotations — full annotation on UniProt →

Function. Component of the CENPA-NAC (nucleosome-associated) complex, a complex that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. CENPN is the first protein to bind specifically to CENPA nucleosomes and the direct binding of CENPA nucleosomes by CENPN is required for centromere assembly. Required for chromosome congression and efficiently align the chromosomes on a metaphase plate.

Subunit / interactions. Component of the CENPA-NAC complex, at least composed of CENPA, CENPC, CENPH, CENPM, CENPN, CENPT and CENPU. The CENPA-NAC complex interacts with the CENPA-CAD complex, composed of CENPI, CENPK, CENPL, CENPO, CENPP, CENPQ, CENPR and CENPS. Interacts directly with CENPA. Identified in a centromere complex containing histones H2A, H2B and H4, and at least CENPA, CENPB, CENPC, CENPT, CENPN, HJURP, SUPT16H, SSRP1 and RSF1.

Subcellular location. Nucleus. Chromosome. Centromere. Kinetochore.

Similarity. Belongs to the CENP-N/CHL4 family.

Isoforms (5)

UniProt ID	Names	Canonical?
Q96H22-1	1	yes
Q96H22-2	2
Q96H22-3	3
Q96H22-4	4
Q96H22-5	5

RefSeq proteins (5): NP_001094094, NP_001094095, NP_001257402, NP_001257403, NP_060925 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007902	Chl4/mis15/CENP-N	Family
IPR052011	CENP-NAC/CAD_complex	Family

Pfam: PF05238

UniProt features (46 total): strand 15, helix 13, splice variant 5, modified residue 3, sequence variant 3, turn 3, mutagenesis site 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

20 structures.

PDB	Method	Resolution (Å)
7U46	ELECTRON MICROSCOPY	2.68
28OP	ELECTRON MICROSCOPY	2.7
6EQT	X-RAY DIFFRACTION	2.73
7R5S	ELECTRON MICROSCOPY	2.83
7PKN	ELECTRON MICROSCOPY	3.2
7XHO	ELECTRON MICROSCOPY	3.29
6MUP	ELECTRON MICROSCOPY	3.5
9TAW	ELECTRON MICROSCOPY	3.54
6MUO	ELECTRON MICROSCOPY	3.6
7XHN	ELECTRON MICROSCOPY	3.71
6BUZ	ELECTRON MICROSCOPY	3.92
6C0W	ELECTRON MICROSCOPY	4
9TAX	ELECTRON MICROSCOPY	4.5
7R5V	ELECTRON MICROSCOPY	4.55
7QOO	ELECTRON MICROSCOPY	4.6
7U47	ELECTRON MICROSCOPY	7.5
7U4D	ELECTRON MICROSCOPY	8.1
7YYH	ELECTRON MICROSCOPY	8.9
7YWX	ELECTRON MICROSCOPY	12
9TAY	ELECTRON MICROSCOPY	15.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96H22-F1	85.88	0.63

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): 226, 235, 282

Mutagenesis-validated functional residues (2):

Position	Phenotype
11	decreases the binding to centromeres.
196	decreases the binding to centromeres.

Function

Pathways and Gene Ontology

Reactome pathways

21 pathways

ID	Pathway
R-HSA-141444	Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal
R-HSA-2467813	Separation of Sister Chromatids
R-HSA-2500257	Resolution of Sister Chromatid Cohesion
R-HSA-5663220	RHO GTPases Activate Formins
R-HSA-606279	Deposition of new CENPA-containing nucleosomes at the centromere
R-HSA-68877	Mitotic Prometaphase
R-HSA-9648025	EML4 and NUDC in mitotic spindle formation
R-HSA-141424	Amplification of signal from the kinetochores
R-HSA-162582	Signal Transduction
R-HSA-1640170	Cell Cycle
R-HSA-194315	Signaling by Rho GTPases
R-HSA-195258	RHO GTPase Effectors
R-HSA-2555396	Mitotic Metaphase and Anaphase
R-HSA-68882	Mitotic Anaphase
R-HSA-68886	M Phase
R-HSA-69278	Cell Cycle, Mitotic
R-HSA-69618	Mitotic Spindle Checkpoint
R-HSA-69620	Cell Cycle Checkpoints
R-HSA-73886	Chromosome Maintenance
R-HSA-774815	Nucleosome assembly
R-HSA-9716542	Signaling by Rho GTPases, Miro GTPases and RHOBTB3

MSigDB gene sets: 254 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, GOBP_CHROMOSOME_ORGANIZATION, ELVIDGE_HYPOXIA_DN, HORIUCHI_WTAP_TARGETS_DN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN, SMID_BREAST_CANCER_LUMINAL_A_DN, GOBP_ORGANELLE_ASSEMBLY, FUJII_YBX1_TARGETS_DN, SMID_BREAST_CANCER_RELAPSE_IN_BRAIN_UP, DODD_NASOPHARYNGEAL_CARCINOMA_UP, TIEN_INTESTINE_PROBIOTICS_24HR_UP, FISCHER_DREAM_TARGETS, WANG_RESPONSE_TO_FORSKOLIN_UP

GO Biological Process (2): chromosome segregation (GO:0007059), CENP-A containing chromatin assembly (GO:0034080)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (7): inner kinetochore (GO:0000939), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829), chromosome, centromeric region (GO:0000775), kinetochore (GO:0000776), chromosome (GO:0005694)

Reactome top-level categories

Rollup of top-14 pathways:

Category	Pathways
Cell Cycle	3
Mitotic Prometaphase	2
M Phase	2
Amplification of signal from the kinetochores	1
Mitotic Anaphase	1
RHO GTPase Effectors	1
Nucleosome assembly	1
Mitotic Spindle Checkpoint	1
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	1
Signaling by Rho GTPases	1
Mitotic Metaphase and Anaphase	1
Cell Cycle, Mitotic	1
Cell Cycle Checkpoints	1
Chromosome Maintenance	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
intracellular membraneless organelle	2
cell cycle process	1
chromatin organization	1
kinetochore assembly	1
protein localization to CENP-A containing chromatin	1
binding	1
kinetochore	1
protein-containing complex	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoplasm	1
chromosomal region	1
condensed chromosome, centromeric region	1
supramolecular complex	1

Protein interactions and networks

STRING

1372 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CENPN	CENPT	Q96BT3	995
CENPN	CENPU	Q71F23	994
CENPN	CENPH	Q9H3R5	988
CENPN	CENPK	Q9BS16	988
CENPN	CENPC	Q03188	986
CENPN	CENPI	Q92674	984
CENPN	CENPA	P49450	982
CENPN	CENPO	Q9BU64	977
CENPN	CENPM	Q9NSP4	976
CENPN	CENPL	Q8N0S6	960
CENPN	CENPP	Q6IPU0	958
CENPN	CENPQ	Q7L2Z9	952
CENPN	CENPS	Q8N2Z9	943
CENPN	CENPW	Q5EE01	937
CENPN	ITGB3BP	Q13352	857

IntAct

65 interactions, top by confidence:

A	B	Type	Score
ITGB3BP	CENPU	psi-mi:“MI:0914”(association)	0.710
RPL37A	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
ZNF71	NVL	psi-mi:“MI:0914”(association)	0.530
SCN3B	ABCC5	psi-mi:“MI:0914”(association)	0.530
KNOP1	DHX15	psi-mi:“MI:0914”(association)	0.530
RPL30	RRP8	psi-mi:“MI:0914”(association)	0.530
CENPH	ITGB3BP	psi-mi:“MI:0914”(association)	0.530
PCDHGB1	FAM171A2	psi-mi:“MI:0914”(association)	0.530
RBM34	NVL	psi-mi:“MI:0914”(association)	0.530
RBM4	NVL	psi-mi:“MI:0914”(association)	0.530
NIFK	RSL1D1	psi-mi:“MI:0914”(association)	0.530
RPL7A	NVL	psi-mi:“MI:0914”(association)	0.530
CENPH	PSMD11	psi-mi:“MI:0914”(association)	0.530
GORASP1	PPP6R2	psi-mi:“MI:0914”(association)	0.530
RPL13	RRP8	psi-mi:“MI:0914”(association)	0.530
CENPN	NCL	psi-mi:“MI:0915”(physical association)	0.400
AKTIP	CENPN	psi-mi:“MI:0915”(physical association)	0.370
Cenph	CENPX	psi-mi:“MI:0914”(association)	0.350
CENPO	CENPX	psi-mi:“MI:0914”(association)	0.350
CENPQ	CENPX	psi-mi:“MI:0914”(association)	0.350
ITGB3BP	ATP5MF-PTCD1	psi-mi:“MI:0914”(association)	0.350
CENPU	CENPX	psi-mi:“MI:0914”(association)	0.350
PCDHA12	KLRG2	psi-mi:“MI:0914”(association)	0.350
PCDHGB4	FAM171A2	psi-mi:“MI:0914”(association)	0.350
PCDHGB1	FAM171A2	psi-mi:“MI:0914”(association)	0.350

BioGRID (91): CENPN (Affinity Capture-MS), CENPN (Affinity Capture-MS), CENPN (Affinity Capture-MS), CENPN (Affinity Capture-MS), CENPN (Affinity Capture-MS), CENPN (Affinity Capture-MS), CENPN (Affinity Capture-MS), CENPN (Affinity Capture-MS), CENPN (Affinity Capture-MS), CENPN (Affinity Capture-MS), CENPN (Affinity Capture-MS), CENPN (Affinity Capture-MS), CENPN (Affinity Capture-MS), CENPN (Affinity Capture-MS), CENPN (Affinity Capture-MS)

ESM2 similar proteins: A6NHR9, A9CB86, B9UYK5, C5IY43, C5IY48, D0EZM8, F1PLN3, O76024, P03070, P03071, P03072, P03271, P03272, P03273, P09507, P11623, P12539, P12540, P14999, P17520, P48752, P56695, P87552, Q0KK59, Q0WL81, Q12789, Q1T765, Q32LL9, Q3L6L5, Q5R7X0, Q5RD58, Q64749, Q65945, Q66HC3, Q6DFW0, Q6DIK0, Q6GLY5, Q6P5D8, Q8CDG3, Q8CF97

Diamond homologs: Q1T765, Q32LL9, Q5U2W4, Q5U4T8, Q5XGF1, Q5XH29, Q96H22, Q9CZW2

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
CENPN	“up-regulates activity”	“CENP-A nucleosome”	binding
CENPN	“form complex”	“CCAN complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 73 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
Nucleosome assembly	6	75.1×	9e-09
Chromosome Maintenance	6	33.4×	3e-07
Peptide chain elongation	8	26.7×	2e-08
Viral mRNA Translation	8	26.7×	2e-08
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	8	26.4×	2e-08
Amplification of signal from the kinetochores	5	25.9×	1e-05
Selenocysteine synthesis	8	25.3×	2e-08
Eukaryotic Translation Termination	8	25.3×	2e-08

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	8	25.5×	3e-07
RNA processing	5	18.9×	5e-04
chromosome segregation	6	18.0×	1e-04
translation	8	14.2×	1e-05
rRNA processing	5	12.2×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	56
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1815 predictions. Top by Δscore:

Variant	Effect	Δscore
16:81011917:T:A	acceptor_gain	1.0000
16:81011922:T:A	acceptor_gain	1.0000
16:81011925:A:AG	acceptor_gain	1.0000
16:81011926:A:AG	acceptor_gain	1.0000
16:81011926:AAAGT:A	acceptor_gain	1.0000
16:81011927:A:AG	acceptor_gain	1.0000
16:81011927:AAGT:A	acceptor_gain	1.0000
16:81011928:A:AG	acceptor_gain	1.0000
16:81011929:G:GG	acceptor_gain	1.0000
16:81011929:GT:G	acceptor_gain	1.0000
16:81011929:GTGC:G	acceptor_gain	1.0000
16:81012050:GACT:G	donor_gain	1.0000
16:81012075:G:GT	donor_gain	1.0000
16:81012082:T:TA	donor_gain	1.0000
16:81012083:A:AA	donor_gain	1.0000
16:81012109:AGGTA:A	donor_loss	1.0000
16:81012110:GGTA:G	donor_loss	1.0000
16:81012111:G:GA	donor_loss	1.0000
16:81012112:T:G	donor_loss	1.0000
16:81014179:TTT:T	donor_gain	1.0000
16:81014182:G:GG	donor_gain	1.0000
16:81014186:GT:G	donor_gain	1.0000
16:81017370:A:G	donor_gain	1.0000
16:81017748:A:AG	acceptor_gain	1.0000
16:81017748:ACTTT:A	acceptor_gain	1.0000
16:81017749:C:G	acceptor_gain	1.0000
16:81017752:T:A	acceptor_gain	1.0000
16:81017753:G:A	acceptor_gain	1.0000
16:81017754:GCAG:G	acceptor_loss	1.0000
16:81017756:A:AG	acceptor_gain	1.0000

AlphaMissense

2255 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:81028255:A:C	S299R	0.992
16:81028257:C:A	S299R	0.992
16:81028257:C:G	S299R	0.992
16:81028250:T:C	F297S	0.990
16:81020146:G:C	R134P	0.989
16:81022648:A:C	S195R	0.987
16:81022650:T:A	S195R	0.987
16:81022650:T:G	S195R	0.987
16:81012021:T:A	W28R	0.985
16:81012021:T:C	W28R	0.985
16:81017355:T:A	W83R	0.985
16:81017355:T:C	W83R	0.985
16:81028627:T:A	N332K	0.985
16:81028627:T:G	N332K	0.985
16:81020154:T:A	W137R	0.984
16:81020154:T:C	W137R	0.984
16:81028249:T:C	F297L	0.981
16:81028251:C:A	F297L	0.981
16:81028251:C:G	F297L	0.981
16:81026633:T:G	Y269D	0.978
16:81020229:T:C	F162L	0.976
16:81020231:C:A	F162L	0.976
16:81020231:C:G	F162L	0.976
16:81020139:T:A	W132R	0.975
16:81020139:T:C	W132R	0.975
16:81028273:G:C	A305P	0.974
16:81020230:T:C	F162S	0.972
16:81026594:T:C	F256L	0.972
16:81026596:T:A	F256L	0.972
16:81026596:T:G	F256L	0.972

dbSNP variants (sampled 300 via entrez): RS1000100660 (16:81022280 G>A,C), RS1000176981 (16:81007757 A>G), RS1000359233 (16:81012341 C>A,T), RS1000407108 (16:81021960 T>C), RS1000455764 (16:81008244 T>A,C), RS1000459321 (16:81022473 A>G,T), RS1000489059 (16:81022696 C>A), RS1000600677 (16:81027505 C>T), RS1000832667 (16:81008033 G>A), RS1000898531 (16:81027262 G>A,C), RS1000948978 (16:81027490 CAAAG>C), RS1001144589 (16:81032123 A>T), RS1001219182 (16:81007747 T>C), RS1001245430 (16:81007984 G>A,C,T), RS1001280689 (16:81028799 G>A,T)

Disease associations

OMIM: gene MIM:611509 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): breast ductal adenocarcinoma (MONDO:0005590)

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST005958_20	Waist-to-hip ratio adjusted for BMI (age >50)	4.000000e-06
GCST005962_30	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	1.000000e-06
GCST009066_43	Mosaic loss of chromosome Y (Y chromosome dosage)	5.000000e-09
GCST009067_34	Mosaic loss of chromosome Y (Y chromosome dosage)	5.000000e-25
GCST009375_14	Mosaic loss of chromosome Y (Y chromosome dosage)	7.000000e-11

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0007783	mosaic loss of chromosome Y measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D018270	Carcinoma, Ductal, Breast	C04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, decreases expression	4
bisphenol A	decreases expression, increases expression	2
Resveratrol	affects cotreatment, increases expression	2
Estradiol	increases expression	2
Cyclosporine	decreases expression, increases expression	2
aristolochic acid I	increases expression	1
FR900359	decreases phosphorylation	1
propionaldehyde	decreases expression	1
sodium arsenite	increases expression	1
perfluorooctanoic acid	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, increases expression	1
16-hydroxycleroda-3,13(14)-dien-15,16-olide	decreases expression	1
jinfukang	increases expression	1
incobotulinumtoxinA	decreases expression	1
Dasatinib	decreases expression	1
Sunitinib	decreases expression	1
Vorinostat	increases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	affects methylation	1
Coumestrol	affects cotreatment, increases expression	1
Hydralazine	affects cotreatment, increases expression	1
Methyl Methanesulfonate	increases expression	1
Nickel	increases expression	1
Phthalic Acids	increases methylation	1
Plant Extracts	increases expression, affects cotreatment	1
Polychlorinated Biphenyls	increases expression	1
Progesterone	increases expression	1
Smoke	decreases expression	1
Dihydrotestosterone	increases expression	1
Tetrachlorodibenzodioxin	affects expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03414970	PHASE3	ACTIVE_NOT_RECRUITING	Hypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00461344	PHASE2	TERMINATED	Docetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999	PHASE2	NOT_YET_RECRUITING	Randomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT00637364	PHASE1/PHASE2	SUSPENDED	High Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855	PHASE1/PHASE2	COMPLETED	Talimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908	EARLY_PHASE1	COMPLETED	Broccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041	EARLY_PHASE1	COMPLETED	Intraoperative Imaging of Breast Cancer With Indocyanine Green
NCT01208974	Not specified	ACTIVE_NOT_RECRUITING	Nipple-Areola Complex (NAC) Irradiation After Nipple-Sparing Mastectomy and Reconstruction
NCT01875198	Not specified	TERMINATED	Oncologic Impact of Splenectomy-omitting Radical Pancreatectomy in Well-selected Left-sided Pancreatic Cancer
NCT03543397	Not specified	UNKNOWN	MRI in Ductal Carcinoma in Situ (DCIS)
NCT03834532	Not specified	COMPLETED	Living Well After Breast Surgery