SPC24

Summary

SPC24 (SPC24 component of NDC80 kinetochore complex, HGNC:26913) is a protein-coding gene on chromosome 19p13.2, encoding Kinetochore protein Spc24 (Q8NBT2). 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 100.0% of cancer cell lines).

Predicted to contribute to microtubule binding activity. Involved in attachment of spindle microtubules to kinetochore. Located in kinetochore; nucleolus; and nucleoplasm. Part of Ndc80 complex.

Source: NCBI Gene 147841 — RefSeq curated summary.

At a glance

• GWAS associations: 15
• Clinical variants (ClinVar): 26 total
• Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
• MANE Select transcript: NM_182513

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26913
Approved symbol	SPC24
Name	SPC24 component of NDC80 kinetochore complex
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ90806
Ensembl gene	ENSG00000161888
Ensembl biotype	protein_coding
OMIM	609394
Entrez	147841

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 nonsense_mediated_decay

ENST00000423327, ENST00000585486, ENST00000585567, ENST00000586708, ENST00000591396, ENST00000592540, ENST00000592967

RefSeq mRNA: 8 — MANE Select: NM_182513 NM_001317031, NM_001317032, NM_001394314, NM_001394315, NM_001394316, NM_001394317, NM_001394318, NM_182513

CCDS: CCDS45974

Canonical transcript exons

ENST00000592540 — 5 exons

Exon	Start	End
ENSE00001725027	11149094	11149238
ENSE00002754065	11145493	11147289
ENSE00002914681	11155617	11155782
ENSE00003506373	11147818	11147894
ENSE00003655725	11148013	11148117

Expression profiles

Bgee: expression breadth ubiquitous, 165 present calls, max score 89.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.3835 / max 564.8939, expressed in 1507 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179191	31.7401	1493
179192	2.6434	879

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	89.67	gold quality
ganglionic eminence	UBERON:0004023	88.43	gold quality
stromal cell of endometrium	CL:0002255	85.03	gold quality
trabecular bone tissue	UBERON:0002483	82.74	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.71	gold quality
bone marrow	UBERON:0002371	80.37	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.26	gold quality
mucosa of transverse colon	UBERON:0004991	80.17	gold quality
esophagus squamous epithelium	UBERON:0006920	78.52	gold quality
bone marrow cell	CL:0002092	76.50	gold quality
adrenal tissue	UBERON:0018303	76.07	gold quality
esophagus mucosa	UBERON:0002469	72.93	gold quality
ileal mucosa	UBERON:0000331	72.49	silver quality
vermiform appendix	UBERON:0001154	72.34	gold quality
gingival epithelium	UBERON:0001949	72.23	gold quality
lower esophagus mucosa	UBERON:0035834	71.90	gold quality
pancreatic ductal cell	CL:0002079	69.89	silver quality
mucosa of stomach	UBERON:0001199	69.42	gold quality
esophagus	UBERON:0001043	69.20	gold quality
apex of heart	UBERON:0002098	69.08	gold quality
amniotic fluid	UBERON:0000173	68.73	silver quality
rectum	UBERON:0001052	68.65	gold quality
transverse colon	UBERON:0001157	67.92	gold quality
gingiva	UBERON:0001828	67.83	gold quality
placenta	UBERON:0001987	67.83	gold quality
lymph node	UBERON:0000029	67.07	gold quality
heart left ventricle	UBERON:0002084	66.89	gold quality
duodenum	UBERON:0002114	66.74	gold quality
caecum	UBERON:0001153	66.33	gold quality
cardiac ventricle	UBERON:0002082	66.27	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-MTAB-7051	yes	1794.43
E-GEOD-75140	yes	449.93
E-ENAD-17	yes	286.90
E-GEOD-81383	yes	284.70
E-MTAB-6678	yes	9.86
E-ANND-3	yes	5.76

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

68 targeting SPC24, 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-7110-3P	100.00	73.18	2486
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-6772-5P	99.94	67.01	577
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-6794-5P	99.76	66.38	1048
HSA-MIR-2116-3P	99.74	64.32	889
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-8064	99.45	66.92	875

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 100.0% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 7)

• hSPC24 is a component of the human NDC80 kinetochore complex (PMID:14699129)
• the Spc24, Spc25, Nuf2, and Ndc80/Hec1 complex is a faithful copy of the endogenous Ndc80 complex (PMID:15961401)
• Data indicate that kinetochore protein Spc24 (SPC24) may be a promising molecular target for hepatocellular carcinoma (HCC) therapy. (PMID:26515591)
• our data demonstrates that SPC24 can serve as a promising prognostic biomarker of anaplastic thyroid cancer cells (PMID:28423533)
• SPC24 is up-regulated in human breast cancer.SPC24 regulates PI3K/AKT kinase pathway in breast cancer. (PMID:30180968)
• hsa-miR-7-5p suppresses proliferation, migration and promotes apoptosis in hepatocellular carcinoma cell lines by inhibiting SPC24 expression. (PMID:34020142)
• LINC02154 promotes the proliferation and metastasis of hepatocellular carcinoma by enhancing SPC24 promoter activity and activating the PI3K-AKT signaling pathway. (PMID:35543858)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	spc24	ENSDARG00000093622
mus_musculus	Spc24	ENSMUSG00000074476
rattus_norvegicus	Spc24	ENSRNOG00000029862

Protein

Protein identifiers

Kinetochore protein Spc24 — Q8NBT2 (reviewed: Q8NBT2)

All UniProt accessions (7): A0A0A0MSN0, Q8NBT2, K7EJH0, K7EJV2, K7EMX1, K7ERQ7, K7ESQ2

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 SPC24 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8NBT2-1	1	yes
Q8NBT2-2	2

RefSeq proteins (8): NP_001303960, NP_001303961, NP_001381243, NP_001381244, NP_001381245, NP_001381246, NP_001381247, NP_872319* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013252	Ndc80_Spc24	Family

Pfam: PF08286

UniProt features (17 total): strand 4, region of interest 3, turn 3, helix 3, chain 1, coiled-coil region 1, modified residue 1, splice variant 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-Q8NBT2-F1	91.51	0.75

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): 11

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: 240 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, GOBP_CHROMOSOME_ORGANIZATION, GOBP_ATTACHMENT_OF_SPINDLE_MICROTUBULES_TO_KINETOCHORE, HORIUCHI_WTAP_TARGETS_DN, GOBP_REGULATION_OF_NUCLEAR_DIVISION, GOBP_CHROMOSOME_LOCALIZATION, GOBP_CELL_CYCLE_PHASE_TRANSITION, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_UP, GOBP_CHROMOSOME_SEPARATION, DARWICHE_PAPILLOMA_RISK_HIGH_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_ORGANELLE_FISSION

GO Biological Process (4): 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 (2): protein binding (GO:0005515), microtubule binding (GO:0008017)

GO Cellular Component (9): kinetochore (GO:0000776), outer kinetochore (GO:0000940), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytosol (GO:0005829), Ndc80 complex (GO:0031262), chromosome, centromeric region (GO:0000775), nucleus (GO:0005634), 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
intracellular membraneless organelle	3
cell cycle process	2
protein-containing complex	2
nuclear lumen	2
cellular anatomical structure	2
mitotic cell cycle	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
tubulin binding	1
condensed chromosome, centromeric region	1
supramolecular complex	1
kinetochore	1
cytoplasm	1
outer kinetochore	1
chromosomal region	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1146 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPC24	NUF2	Q9BZD4	999
SPC24	NDC80	O14777	998
SPC24	SPC25	Q9HBM1	956
SPC24	CENPT	Q96BT3	930
SPC24	DSN1	Q9H410	899
SPC24	KNL1	Q8NG31	837
SPC24	MIS12	Q9H081	817
SPC24	CENPA	P49450	739
SPC24	SKA1	Q96BD8	730
SPC24	CENPI	Q92674	695
SPC24	CENPH	Q9H3R5	694
SPC24	ZWINT	O95229	670
SPC24	CENPM	Q9NSP4	652
SPC24	CENPE	Q02224	633
SPC24	CENPC	Q03188	621

IntAct

105 interactions, top by confidence:

A	B	Type	Score
NUF2	NDC80	psi-mi:“MI:0914”(association)	0.950
ZWINT	NDC80	psi-mi:“MI:0914”(association)	0.940
SPC25	NDC80	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
MED4	MED19	psi-mi:“MI:2364”(proximity)	0.900
DSN1	ZWINT	psi-mi:“MI:0914”(association)	0.900
MIS12	ZWINT	psi-mi:“MI:0914”(association)	0.900
MIS12	NDC80	psi-mi:“MI:0914”(association)	0.850
DSN1	NDC80	psi-mi:“MI:0914”(association)	0.790
MED23	MED19	psi-mi:“MI:2364”(proximity)	0.770
KNL1	SPC24	psi-mi:“MI:0914”(association)	0.760

BioGRID (170): SPC24 (Affinity Capture-MS), SPC24 (Affinity Capture-MS), SPC24 (Affinity Capture-MS), SPC24 (Affinity Capture-MS), SPC24 (Affinity Capture-MS), SPC24 (Affinity Capture-MS), SPC24 (Affinity Capture-MS), ASPM (Affinity Capture-MS), CASC5 (Affinity Capture-MS), NDC80 (Affinity Capture-MS), SPC25 (Affinity Capture-MS), CCDC101 (Affinity Capture-MS), PMF1 (Affinity Capture-MS), PLD2 (Affinity Capture-MS), MIS12 (Affinity Capture-MS)

ESM2 similar proteins: A0PJT0, D3ZND0, D4A4K3, G9G127, I1VZH0, O60826, O75800, P86182, Q1RMI8, Q1T769, Q1T7C1, Q24JY3, Q28G12, Q2TBK4, Q2YD98, Q4V909, Q503N2, Q5REX6, Q5XGL1, Q61043, Q67XT3, Q6AXZ5, Q6NRW3, Q6NVC9, Q6NY52, Q6P8A1, Q6PA15, Q6PA69, Q6ZNE5, Q7SYB5, Q7TMK6, Q80YF0, Q86UA6, Q8BHX1, Q8BIJ7, Q8C2K1, Q8C3S2, Q8CDJ3, Q8N4C6, Q8NBT2

Diamond homologs: Q24JY3, Q503N2, Q6NRW3, Q6P8A1, Q8NBT2, Q9D083

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
SPC24	“form complex”	“Ndc80 complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 74 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 unattached kinetochores via a MAD2 inhibitory signal	12	31.8×	4e-13
Amplification of signal from the kinetochores	7	31.3×	9e-08
EML4 and NUDC in mitotic spindle formation	12	25.3×	4e-12
Mitotic Spindle Checkpoint	7	25.2×	4e-07
Resolution of Sister Chromatid Cohesion	12	23.6×	6e-12
RHO GTPases Activate Formins	12	21.2×	1e-11
Mitotic Prometaphase	12	18.9×	4e-11
Separation of Sister Chromatids	13	17.9×	1e-11

GO biological processes:

GO term	Partners	Fold	FDR
attachment of spindle microtubules to kinetochore	8	118.9×	5e-13
mitotic spindle assembly checkpoint signaling	6	53.5×	2e-07
mitotic sister chromatid segregation	5	38.2×	2e-05
chromosome segregation	8	22.1×	4e-07
mitotic spindle organization	5	21.6×	3e-04
cell division	16	11.7×	7e-11
transcription by RNA polymerase II	6	6.7×	9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	20
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

780 predictions. Top by Δscore:

Variant	Effect	Δscore
19:11148012:CA:C	donor_gain	1.0000
19:11148012:CACGG:C	donor_gain	1.0000
19:11149148:T:TA	donor_gain	1.0000
19:11155612:CTCAC:C	donor_loss	1.0000
19:11155613:TCACC:T	donor_loss	1.0000
19:11155615:A:AC	donor_gain	1.0000
19:11155615:A:AT	donor_loss	1.0000
19:11155616:C:CC	donor_gain	1.0000
19:11155616:CCT:C	donor_gain	1.0000
19:11155616:CCTCG:C	donor_gain	1.0000
19:11148011:A:AC	donor_gain	0.9900
19:11148012:C:CC	donor_gain	0.9900
19:11148114:C:CC	acceptor_gain	0.9900
19:11149133:T:TA	donor_gain	0.9900
19:11155623:G:C	donor_gain	0.9900
19:11147952:TCA:T	donor_gain	0.9800
19:11149103:G:A	donor_gain	0.9800
19:11149121:T:TA	donor_gain	0.9800
19:11149236:TCT:T	acceptor_gain	0.9600
19:11149237:CT:C	acceptor_gain	0.9600
19:11149237:CTC:C	acceptor_gain	0.9600
19:11149238:TCT:T	acceptor_gain	0.9600
19:11149239:C:CC	acceptor_gain	0.9600
19:11155612:C:T	donor_gain	0.9600
19:11148052:T:TA	donor_gain	0.9500
19:11148113:GC:G	acceptor_loss	0.9500
19:11148115:T:C	acceptor_loss	0.9500
19:11149235:ATCTC:A	acceptor_loss	0.9500
19:11149237:CTCTG:C	acceptor_loss	0.9500
19:11149238:TCTGC:T	acceptor_loss	0.9500

AlphaMissense

1284 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:11147854:A:G	W151R	0.994
19:11147854:A:T	W151R	0.994
19:11147209:A:G	W190R	0.987
19:11147209:A:T	W190R	0.987
19:11147864:A:C	S147R	0.985
19:11147864:A:T	S147R	0.985
19:11147866:T:G	S147R	0.985
19:11147852:C:A	W151C	0.983
19:11147852:C:G	W151C	0.983
19:11147188:A:G	W197R	0.978
19:11147188:A:T	W197R	0.978
19:11147821:C:G	G162R	0.978
19:11147853:C:G	W151S	0.970
19:11147878:A:C	Y143D	0.966
19:11147207:C:A	W190C	0.964
19:11147207:C:G	W190C	0.964
19:11147211:A:G	L189P	0.962
19:11147820:C:T	G162D	0.961
19:11148025:A:G	I133T	0.957
19:11147225:G:C	F184L	0.956
19:11147225:G:T	F184L	0.956
19:11147227:A:G	F184L	0.956
19:11155765:G:C	F4L	0.956
19:11155765:G:T	F4L	0.956
19:11155767:A:G	F4L	0.956
19:11147186:C:A	W197C	0.955
19:11147186:C:G	W197C	0.955
19:11147219:G:C	S186R	0.955
19:11147219:G:T	S186R	0.955
19:11147221:T:G	S186R	0.955

dbSNP variants (sampled 300 via entrez): RS1000223596 (19:11150355 G>A), RS1000420984 (19:11156274 T>C), RS1000595410 (19:11150589 G>A), RS1000754176 (19:11155051 T>C), RS1000962783 (19:11148827 A>G), RS1001092654 (19:11153281 CA>C,CAA), RS1001125479 (19:11153024 G>A), RS1001208338 (19:11151481 G>A,T), RS1001271403 (19:11147671 T>G), RS1001408132 (19:11156956 C>T), RS1001459210 (19:11157162 T>C), RS1001639750 (19:11151306 G>A), RS1001709255 (19:11148646 TATTGATTG>T,TATTG,TATTGATTGATTG), RS1002132169 (19:11148378 T>C), RS1002192377 (19:11152321 T>C)

Disease associations

OMIM: gene MIM:609394 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

15 associations (top):

Study	Trait	p-value
GCST001904_5	HDL cholesterol	3.000000e-09
GCST002321_8	Lipid traits	7.000000e-06
GCST004780_8	Cortisol levels (saliva)	6.000000e-06
GCST005580_155	Intraocular pressure	7.000000e-09
GCST007442_7	Low density lipoprotein cholesterol levels	3.000000e-09
GCST009438_14	Voxel-wise structural brain imaging measurements in Alzheimer’s disease	8.000000e-07
GCST010241_192	Apolipoprotein A1 levels	2.000000e-26
GCST010242_155	HDL cholesterol levels	7.000000e-12
GCST010867_20	Coronary artery disease	1.000000e-13
GCST90000025_556	Appendicular lean mass	4.000000e-18
GCST90002385_494	High light scatter reticulocyte count	4.000000e-16
GCST90002386_64	High light scatter reticulocyte percentage of red cells	7.000000e-15
GCST90002405_533	Reticulocyte count	1.000000e-13
GCST90002406_485	Reticulocyte fraction of red cells	3.000000e-12
GCST90014033_72	Haemorrhoidal disease	2.000000e-14

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0005843	cortisol measurement
EFO:0004695	intraocular pressure measurement
EFO:0004346	neuroimaging measurement
EFO:0004614	apolipoprotein A 1 measurement
EFO:0004980	appendicular lean mass
EFO:0007986	reticulocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects expression, decreases expression, affects cotreatment, increases abundance, increases expression	5
bisphenol A	affects expression, decreases expression	2
Acetaminophen	decreases expression, increases expression	2
Benzo(a)pyrene	affects methylation, decreases expression	2
Estradiol	increases expression, decreases expression	2
Cadmium Chloride	decreases expression	2
Particulate Matter	increases abundance, affects cotreatment, decreases expression	2
TAK-243	increases sumoylation	1
methylmercuric chloride	decreases expression	1
propionaldehyde	decreases expression	1
2-methyl-4-isothiazolin-3-one	decreases expression	1
3,4-dichloroaniline	decreases expression	1
beta-lapachone	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	decreases expression	1
perfluorooctanoic acid	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, increases expression	1
coumarin	decreases phosphorylation	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
polyhexamethyleneguanidine	affects expression	1
pentabromodiphenyl ether	decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	decreases expression	1
ICG 001	decreases expression	1
abrine	decreases expression	1
palbociclib	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
(+)-JQ1 compound	decreases expression	1

Clinical trials (associated diseases)

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