SPC25

Summary

SPC25 (SPC25 component of NDC80 kinetochore complex, HGNC:24031) is a protein-coding gene on chromosome 2q31.1, encoding Kinetochore protein Spc25 (Q9HBM1). Acts as a component of the essential kinetochore-associated NDC80 complex, which is required for chromosome segregation and spindle checkpoint activity. It is a common-essential gene (DepMap: required in 99.8% of cancer cell lines).

This gene encodes a protein that may be involved in kinetochore-microtubule interaction and spindle checkpoint activity.

Source: NCBI Gene 57405 — RefSeq curated summary.

At a glance

• GWAS associations: 24
• Clinical variants (ClinVar): 44 total
• Cancer dependency (DepMap): dependent in 99.8% of screened cell lines (common-essential)
• MANE Select transcript: NM_020675

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24031
Approved symbol	SPC25
Name	SPC25 component of NDC80 kinetochore complex
Location	2q31.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC22228, AD024
Ensembl gene	ENSG00000152253
Ensembl biotype	protein_coding
OMIM	609395
Entrez	57405

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 11 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000282074, ENST00000451987, ENST00000472216, ENST00000479309, ENST00000861849, ENST00000861850, ENST00000861851, ENST00000929949, ENST00000929950, ENST00000929951, ENST00000929952, ENST00000929953, ENST00000929954

RefSeq mRNA: 1 — MANE Select: NM_020675 NM_020675

CCDS: CCDS2229

Canonical transcript exons

ENST00000282074 — 7 exons

Exon	Start	End
ENSE00001254029	168870891	168871555
ENSE00001370676	168890318	168890430
ENSE00003509826	168873585	168873683
ENSE00003547347	168876072	168876176
ENSE00003618563	168889226	168889291
ENSE00003678024	168889387	168889533
ENSE00003786018	168877238	168877384

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 95.13.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.3070 / max 221.5980, expressed in 1323 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
31718	11.1077	1271
31719	0.1993	95

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	95.13	gold quality
ganglionic eminence	UBERON:0004023	93.91	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.88	gold quality
islet of Langerhans	UBERON:0000006	91.58	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.14	gold quality
mucosa of transverse colon	UBERON:0004991	81.44	gold quality
adrenal tissue	UBERON:0018303	79.96	gold quality
endometrium	UBERON:0001295	79.29	gold quality
placenta	UBERON:0001987	78.15	gold quality
bone marrow	UBERON:0002371	77.75	gold quality
rectum	UBERON:0001052	77.31	gold quality
vermiform appendix	UBERON:0001154	76.84	gold quality
lymph node	UBERON:0000029	76.81	gold quality
stromal cell of endometrium	CL:0002255	76.38	gold quality
pancreas	UBERON:0001264	75.68	gold quality
tonsil	UBERON:0002372	75.48	gold quality
duodenum	UBERON:0002114	74.71	gold quality
esophagus mucosa	UBERON:0002469	74.00	gold quality
bone marrow cell	CL:0002092	72.07	gold quality
lower esophagus mucosa	UBERON:0035834	70.03	gold quality
testis	UBERON:0000473	69.38	gold quality
body of pancreas	UBERON:0001150	68.20	gold quality
right testis	UBERON:0004534	68.16	gold quality
transverse colon	UBERON:0001157	67.91	gold quality
left testis	UBERON:0004533	67.78	gold quality
smooth muscle tissue	UBERON:0001135	67.59	gold quality
metanephros cortex	UBERON:0010533	66.75	gold quality
small intestine	UBERON:0002108	66.30	gold quality
small intestine Peyer’s patch	UBERON:0003454	66.00	gold quality
cortical plate	UBERON:0005343	65.93	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-10	yes	37.48
E-MTAB-7037	yes	36.08
E-ANND-3	yes	5.43
E-GEOD-99795	no	14.61

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

51 targeting SPC25, 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-6870-5P	99.99	68.55	2115
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-8080	99.82	67.52	1342
HSA-MIR-548A-3P	99.76	70.58	3524
HSA-MIR-5580-3P	99.70	69.41	2052
HSA-MIR-379-3P	99.69	69.60	1524
HSA-MIR-411-3P	99.69	69.63	1524
HSA-MIR-4499	99.62	67.29	1470
HSA-MIR-190A-5P	99.54	71.45	933

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.8% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 14)

• hSPC25 is an essential kinetochore component that plays a significant role in proper execution of mitotic events (PMID:14699129)
• the Spc24, Spc25, Nuf2, and Ndc80/Hec1 complex is a faithful copy of the endogenous Ndc80 complex (PMID:15961401)
• SPC25 overexpression is associated with Breast Cancer. (PMID:27197203)
• SPC25 overexpression significantly increased the cancer stem cell properties and invasion of A549 cells. (PMID:29432994)
• SPC25 expressed by extracellular matrix stiffening is required for lung cancer cell proliferation. (PMID:29709477)
• These data suggest that SPC25 may be highly expressed in the CSC-like cells in PrC and could be a promising target for effective treatment of PrC. (PMID:30408771)
• These findings suggest that SPC25 levels are higher in more malignant breast cancer subtypes and are associated with poor prognosis in breast cancer patients (PMID:31400751)
• SPC25 overexpression promotes tumor proliferation and is prognostic of poor survival in hepatocellular carcinoma. (PMID:33408271)
• SPC25 promotes hepatocellular carcinoma metastasis via activating the FAK/PI3K/AKT signaling pathway through ITGB4. (PMID:35293598)
• Spindle pole body component 25 and platelet-derived growth factor mediate crosstalk between tumor-associated macrophages and prostate cancer cells. (PMID:35967419)
• SPC25 promotes proliferation and stemness of hepatocellular carcinoma cells via the DNA-PK/AKT/Notch1 signaling pathway. (PMID:36147467)
• SPC25 as a novel therapeutic and prognostic biomarker and its association with glycolysis, ferroptosis and ceRNA in lung adenocarcinoma. (PMID:38217547)
• SPC25 Functions as a Prognostic-Related Biomarker, and Its High Expression Correlates with Tumor Immune Infiltration and UCEC Progression. (PMID:38420826)
• PLEK2 activates the PI3K/AKT signaling pathway to drive lung adenocarcinoma progression by upregulating SPC25. (PMID:38894536)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	spc25	ENSDARG00000078433
mus_musculus	Spc25	ENSMUSG00000005233
rattus_norvegicus	Spc25	ENSRNOG00000006731

Protein

Protein identifiers

Kinetochore protein Spc25 — Q9HBM1 (reviewed: Q9HBM1)

All UniProt accessions (2): C9JW94, Q9HBM1

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a component of the essential kinetochore-associated NDC80 complex, which is required for chromosome segregation and spindle checkpoint activity. Required for kinetochore integrity and the organization of stable microtubule binding sites in the outer plate of the kinetochore. The NDC80 complex synergistically enhances the affinity of the SKA1 complex for microtubules and may allow the NDC80 complex to track depolymerizing microtubules.

Subunit / interactions. Component of the NDC80 complex, which consists of NDC80/HEC1, CDCA1, SPBC24 and SPBC25. The NDC80 complex is formed by two subcomplexes composed of NDC80/HEC1-CDCA1 and SPBC24-SPBC25. Each subcomplex is formed by parallel interactions through the coiled-coil domains of individual subunits. Formation of a tetrameric complex is mediated by interactions between the C-terminal regions of both subunits of the NDC80/HEC1-CDCA1 subcomplex and the N-terminal regions of both subunits of the SPBC24-SPBC25 complex. The tetrameric NDC80 complex has an elongated rod-like structure with globular domains at either end.

Subcellular location. Nucleus. Chromosome. Centromere. Kinetochore.

Similarity. Belongs to the SPC25 family.

RefSeq proteins (1): NP_065726* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013255	Spc25_C	Domain
IPR045143	Spc25	Family

Pfam: PF08234

UniProt features (19 total): strand 6, helix 5, region of interest 3, turn 2, chain 1, coiled-coil region 1, modified residue 1

Structure

Experimental structures (PDB)

4 structures.

PDB	Method	Resolution (Å)
2VE7	X-RAY DIFFRACTION	2.88
8PPR	ELECTRON MICROSCOPY	3
8Q5H	ELECTRON MICROSCOPY	4.5
3IZ0	ELECTRON MICROSCOPY	8.6

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9HBM1-F1	91.13	0.68

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): 12

Function

Pathways and Gene Ontology

Reactome pathways

18 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-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-9716542	Signaling by Rho GTPases, Miro GTPases and RHOBTB3

MSigDB gene sets: 306 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, GOBP_CHROMOSOME_ORGANIZATION, GOBP_ATTACHMENT_OF_SPINDLE_MICROTUBULES_TO_KINETOCHORE, HORIUCHI_WTAP_TARGETS_DN, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, CCAWYNNGAAR_UNKNOWN, GOBP_REGULATION_OF_NUCLEAR_DIVISION, CROONQUIST_NRAS_SIGNALING_DN, GOBP_CHROMOSOME_LOCALIZATION, GOBP_CELL_CYCLE_PHASE_TRANSITION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_CHROMOSOME_SEPARATION, KONG_E2F3_TARGETS

GO Biological Process (5): mitotic spindle organization (GO:0007052), chromosome segregation (GO:0007059), mitotic spindle assembly checkpoint signaling (GO:0007094), attachment of spindle microtubules to kinetochore (GO:0008608), cell division (GO:0051301)

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

GO Cellular Component (7): kinetochore (GO:0000776), outer kinetochore (GO:0000940), nucleus (GO:0005634), cytosol (GO:0005829), Ndc80 complex (GO:0031262), chromosome, centromeric region (GO:0000775), chromosome (GO:0005694)

Reactome top-level categories

Rollup of top-13 pathways:

Category	Pathways
Mitotic Prometaphase	2
M Phase	2
Cell Cycle	2
Amplification of signal from the kinetochores	1
Mitotic Anaphase	1
RHO GTPase Effectors	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
Signal Transduction	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
mitotic cell cycle	2
cell cycle process	2
intracellular membraneless organelle	2
protein-containing complex	2
spindle organization	1
microtubule cytoskeleton organization involved in mitosis	1
negative regulation of mitotic metaphase/anaphase transition	1
spindle assembly checkpoint signaling	1
mitotic spindle checkpoint signaling	1
microtubule binding	1
metaphase chromosome alignment	1
cellular process	1
binding	1
condensed chromosome, centromeric region	1
supramolecular complex	1
kinetochore	1
intracellular membrane-bounded organelle	1
cytoplasm	1
cellular anatomical structure	1
outer kinetochore	1
chromosomal region	1

Protein interactions and networks

STRING

1364 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPC25	SPC24	Q8NBT2	956
SPC25	NUF2	Q9BZD4	947
SPC25	NDC80	O14777	943
SPC25	SKA3	Q8IX90	515
SPC25	MAD2L1	Q13257	395
SPC25	TTK	P33981	394
SPC25	DSN1	Q9H410	394
SPC25	JAGN1	Q8N5M9	379
SPC25	RNFT2	Q96EX2	360
SPC25	SKA1	Q96BD8	358
SPC25	KIF2C	Q99661	346
SPC25	SLC35A3	Q9Y2D2	337
SPC25	INCENP	Q9NQS7	329
SPC25	SGO2	Q562F6	327
SPC25	CENPT	Q96BT3	326

IntAct

100 interactions, top by confidence:

A	B	Type	Score
NDC80	SPC25	psi-mi:“MI:0915”(physical association)	0.940
SPC25	NDC80	psi-mi:“MI:0915”(physical association)	0.940
ZWINT	NDC80	psi-mi:“MI:0914”(association)	0.940
SPC25	NDC80	psi-mi:“MI:0914”(association)	0.940
ATG13	ULK1	psi-mi:“MI:2364”(proximity)	0.940
PSMD9	PSMC3	psi-mi:“MI:0914”(association)	0.940
SPC25	SPC24	psi-mi:“MI:0915”(physical association)	0.930
SPC25	SPC24	psi-mi:“MI:0403”(colocalization)	0.930
SPC24	SPC25	psi-mi:“MI:0915”(physical association)	0.930
NDC80	SPC24	psi-mi:“MI:0915”(physical association)	0.920
NDC80	SPC24	psi-mi:“MI:0914”(association)	0.920
SPC24	NDC80	psi-mi:“MI:0914”(association)	0.920
MIS12	ZWINT	psi-mi:“MI:0914”(association)	0.900
MIS12	NDC80	psi-mi:“MI:0914”(association)	0.850

BioGRID (149): SPC25 (Affinity Capture-MS), SPC25 (Affinity Capture-MS), SPC25 (Affinity Capture-MS), SPC25 (Affinity Capture-MS), SPC25 (Affinity Capture-MS), SPC25 (Affinity Capture-MS), SPECC1L (Affinity Capture-MS), CASC5 (Affinity Capture-MS), EPS15 (Affinity Capture-MS), NDC80 (Affinity Capture-MS), KTN1 (Affinity Capture-MS), EPS15L1 (Affinity Capture-MS), MYO18A (Affinity Capture-MS), AP2A1 (Affinity Capture-MS), HDGFRP2 (Affinity Capture-MS)

ESM2 similar proteins: A1A4P9, A4QNG1, B1WB06, B8JLV7, F4HVW5, F4IRM4, F4J264, F4JTI1, K7TQE3, O48781, O65573, O80462, O81893, O82387, Q0IY07, Q0WPN7, Q3EBL9, Q3KPR1, Q3ZBK3, Q5BK13, Q5M7V7, Q5M856, Q5MK23, Q5MK24, Q5RHZ2, Q6BDI9, Q6E7H0, Q7X6P3, Q7ZYB4, Q84JN1, Q84M47, Q84WF5, Q8IYF3, Q8L7N4, Q8LBH4, Q8RXH2, Q8S9J3, Q8W032, Q8W4F0, Q94BM7

Diamond homologs: P0CR66, P0CR67, Q10430, Q2UPH5, Q3UA16, Q3ZBK3, Q4IMM0, Q59PT6, Q5M856, Q751Z6, Q9HBM1, Q6DF39, Q6SKR5

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
SPC25	“up-regulates activity”	RIOK1	binding
SPC25	“up-regulates activity”	MYH9	binding
SPC25	“form complex”	“Ndc80 complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 68 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
Amplification of signal from the kinetochores	8	31.5×	6e-09
Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal	13	30.3×	6e-14
Mitotic Spindle Checkpoint	8	25.4×	3e-08
EML4 and NUDC in mitotic spindle formation	13	24.1×	4e-13
Resolution of Sister Chromatid Cohesion	13	22.5×	8e-13
RHO GTPases Activate Formins	13	20.2×	3e-12
Separation of Sister Chromatids	15	18.2×	2e-13
Mitotic Prometaphase	13	18.0×	1e-11

GO biological processes:

GO term	Partners	Fold	FDR
attachment of spindle microtubules to kinetochore	8	129.1×	3e-13
mitotic spindle assembly checkpoint signaling	6	58.1×	1e-07
mitotic sister chromatid segregation	5	41.5×	1e-05
chromosome segregation	9	27.0×	1e-08
cell division	13	10.3×	4e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	29
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3186 predictions. Top by Δscore:

Variant	Effect	Δscore
2:168834225:A:AG	acceptor_gain	1.0000
2:168834226:G:GG	acceptor_gain	1.0000
2:168834326:GT:G	donor_loss	1.0000
2:168834327:T:G	donor_loss	1.0000
2:168851277:A:AG	acceptor_gain	1.0000
2:168851278:G:GG	acceptor_gain	1.0000
2:168851405:G:GG	donor_gain	1.0000
2:168862048:GG:G	donor_gain	1.0000
2:168862049:GG:G	donor_gain	1.0000
2:168871556:C:CC	acceptor_gain	1.0000
2:168873681:CAC:C	acceptor_gain	1.0000
2:168873684:CTGAA:C	acceptor_loss	1.0000
2:168876070:A:AC	donor_gain	1.0000
2:168876070:AC:A	donor_gain	1.0000
2:168876071:C:CT	donor_gain	1.0000
2:168876071:CC:C	donor_gain	1.0000
2:168876071:CCAT:C	donor_gain	1.0000
2:168876071:CCATA:C	donor_gain	1.0000
2:168876172:AATAG:A	acceptor_gain	1.0000
2:168876173:ATAG:A	acceptor_gain	1.0000
2:168876174:TAG:T	acceptor_gain	1.0000
2:168876174:TAGC:T	acceptor_loss	1.0000
2:168876175:AG:A	acceptor_gain	1.0000
2:168876175:AGC:A	acceptor_loss	1.0000
2:168876176:GCTGA:G	acceptor_loss	1.0000
2:168876177:C:CC	acceptor_gain	1.0000
2:168876177:C:CG	acceptor_loss	1.0000
2:168876180:A:AC	acceptor_gain	1.0000
2:168876181:T:C	acceptor_gain	1.0000
2:168876181:T:TC	acceptor_gain	1.0000

AlphaMissense

1503 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:168873668:A:G	F156S	0.994
2:168871462:C:G	R215P	0.992
2:168876092:A:G	L144P	0.990
2:168871465:A:T	V214D	0.989
2:168876083:C:G	R147P	0.988
2:168871452:A:C	F218L	0.985
2:168871452:A:T	F218L	0.985
2:168871454:A:G	F218L	0.985
2:168873674:A:G	L154S	0.985
2:168873662:A:G	F158S	0.984
2:168871453:A:G	F218S	0.983
2:168876086:A:G	I146T	0.982
2:168871476:A:C	F210L	0.981
2:168871476:A:T	F210L	0.981
2:168871477:A:G	F210S	0.981
2:168871478:A:G	F210L	0.981
2:168873620:A:G	F172S	0.978
2:168873661:G:C	F158L	0.978
2:168873661:G:T	F158L	0.978
2:168873663:A:G	F158L	0.978
2:168873667:A:C	F156L	0.976
2:168873667:A:T	F156L	0.976
2:168873669:A:G	F156L	0.976
2:168876086:A:C	I146S	0.974
2:168871474:A:T	L211H	0.973
2:168873614:A:G	L174S	0.972
2:168873625:A:C	F170L	0.972
2:168873625:A:T	F170L	0.972
2:168873627:A:G	F170L	0.972
2:168873671:T:G	Q155P	0.971

dbSNP variants (sampled 300 via entrez): RS1000128698 (2:168880277 G>A), RS1000132080 (2:168888743 GTGTA>G), RS1000431673 (2:168890546 GA>G,GAA), RS1000480806 (2:168885841 G>A,T), RS1000607418 (2:168885852 G>A), RS1000638675 (2:168885615 C>A), RS1000771286 (2:168863864 T>A,C), RS1000816655 (2:168876261 A>T), RS1000822600 (2:168890610 G>A,T), RS1000856703 (2:168872247 C>A,T), RS1001108482 (2:168878974 A>T), RS1001155809 (2:168865644 A>G), RS1001199201 (2:168877715 C>T), RS1001280774 (2:168888266 G>A), RS1001297835 (2:168862261 C>A,G,T)

Disease associations

OMIM: gene MIM:609395 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

24 associations (top):

Study	Trait	p-value
GCST004610_48	White blood cell count	5.000000e-16
GCST004613_82	Sum neutrophil eosinophil counts	1.000000e-14
GCST004614_132	Granulocyte count	6.000000e-15
GCST004620_47	Sum basophil neutrophil counts	1.000000e-14
GCST004626_20	Myeloid white cell count	1.000000e-16
GCST004629_25	Neutrophil count	5.000000e-14
GCST005913_2	Fasting blood glucose	4.000000e-08
GCST006993_3	Hippocampal volume in Alzheimer’s disease dementia	1.000000e-06
GCST008163_593	Height	3.000000e-06
GCST008674_2	Glycemic traits (pleiotropy)	5.000000e-11
GCST009391_1136	Metabolite levels	3.000000e-07
GCST009391_1629	Metabolite levels	7.000000e-06
GCST010270_1	Circulating leptin levels or HOMA-B	1.000000e-15
GCST010698_85	Subcortical volume (min-P)	4.000000e-19
GCST010699_3	Brain morphology (min-P)	4.000000e-11
GCST010700_55	Cortical thickness (MOSTest)	7.000000e-120
GCST010701_34	Cortical surface area (MOSTest)	1.000000e-26
GCST010702_11	Subcortical volume (MOSTest)	4.000000e-08
GCST010703_69	Brain morphology (MOSTest)	2.000000e-08
GCST90002381_52	Eosinophil count	4.000000e-09
GCST90002393_386	Monocyte count	7.000000e-21
GCST90002398_107	Neutrophil count	2.000000e-23
GCST90002407_75	White blood cell count	3.000000e-26
GCST90020028_100	Hip circumference adjusted for BMI	3.000000e-09

EFO canonical traits (13, from GWAS)

EFO ID	Trait name
EFO:0004833	neutrophil count
EFO:0004842	eosinophil count
EFO:0007987	granulocyte count
EFO:0005090	basophil count
EFO:0005035	hippocampal volume
EFO:0004469	HOMA-B
EFO:0010458	alpha-hydroxybutyric acid measurement
EFO:0010465	beta-hydroxybutyric acid measurement
EFO:0005000	leptin measurement
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness
EFO:0005091	monocyte count
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression, affects cotreatment	5
Cyclosporine	decreases expression, increases methylation	5
bisphenol A	affects expression, decreases expression, decreases methylation	4
Benzo(a)pyrene	decreases expression, increases expression	4
Tretinoin	affects cotreatment, decreases expression	3
Valproic Acid	decreases expression, decreases methylation, increases expression	3
cobaltous chloride	decreases expression	2
Coumestrol	affects cotreatment, increases expression, affects reaction	2
Estradiol	increases expression	2
Silicon Dioxide	decreases expression	2
Particulate Matter	decreases expression, increases abundance	2
aristolochic acid I	decreases expression	1
afuresertib	decreases expression	1
dicrotophos	decreases expression	1
alpha phellandrene	increases expression	1
propionaldehyde	decreases expression	1
6-hydroxy-5-((p- sulfophenyl)azo)-2-naphthalenesulfonic acid disodium salt	affects cotreatment, decreases expression	1
arsenite	affects binding, increases reaction	1
o,p’-DDT	decreases expression	1
mono-(2-ethylhexyl)phthalate	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
16 alpha-ethyl-21-hydroxy-19-nor-4-pregnene-3,20-dione	decreases expression	1
perfluorooctanoic acid	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, increases expression	1
beta-methylcholine	affects expression	1
corosolic acid	decreases expression	1
2-palmitoylglycerol	increases expression	1
K 7174	decreases expression	1
fenpyroximate	increases expression	1
4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamide	increases expression	1

Clinical trials (associated diseases)

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