NUSAP1

Summary

NUSAP1 (nucleolar and spindle associated protein 1, HGNC:18538) is a protein-coding gene on chromosome 15q14, encoding Nucleolar and spindle-associated protein 1 (Q9BXS6). Microtubule-associated protein with the capacity to bundle and stabilize microtubules.

NUSAP1 is a nucleolar-spindle-associated protein that plays a role in spindle microtubule organization (Raemaekers et al., 2003 [PubMed 12963707]).

Source: NCBI Gene 51203 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 86 total — 1 likely-pathogenic
• MANE Select transcript: NM_016359

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18538
Approved symbol	NUSAP1
Name	nucleolar and spindle associated protein 1
Location	15q14
Locus type	gene with protein product
Status	Approved
Aliases	FLJ13421, LNP, ANKT, SAPL, BM037, PRO0310p1, Q0310
Ensembl gene	ENSG00000137804
Ensembl biotype	protein_coding
OMIM	612818
Entrez	51203

Gene structure

Transcript identifiers

Ensembl transcripts: 30 — 23 protein_coding, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000260359, ENST00000414849, ENST00000450592, ENST00000557840, ENST00000558123, ENST00000558582, ENST00000559046, ENST00000559596, ENST00000559659, ENST00000560177, ENST00000560318, ENST00000560747, ENST00000560898, ENST00000668273, ENST00000891639, ENST00000891640, ENST00000891641, ENST00000891642, ENST00000891643, ENST00000891644, ENST00000891645, ENST00000891646, ENST00000891647, ENST00000891648, ENST00000924131, ENST00000924132, ENST00000924133, ENST00000963298, ENST00000963299, ENST00000963300

RefSeq mRNA: 6 — MANE Select: NM_016359 NM_001243142, NM_001243143, NM_001243144, NM_001301136, NM_016359, NM_018454

CCDS: CCDS45234, CCDS45236, CCDS58356, CCDS58357, CCDS58358, CCDS73708

Canonical transcript exons

ENST00000559596 — 11 exons

Exon	Start	End
ENSE00002563931	41380093	41381046
ENSE00003510322	41371527	41371684
ENSE00003542708	41349098	41349241
ENSE00003569925	41377196	41377304
ENSE00003585392	41342386	41342454
ENSE00003593991	41365402	41365589
ENSE00003610224	41350988	41351129
ENSE00003611800	41356039	41356140
ENSE00003651372	41358149	41358258
ENSE00003694425	41375712	41375828
ENSE00003843090	41332881	41333050

Expression profiles

Bgee: expression breadth ubiquitous, 138 present calls, max score 99.28.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 46.3414 / max 1177.6738, expressed in 1636 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
146175	46.3414	1636

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	99.28	gold quality
ganglionic eminence	UBERON:0004023	98.31	gold quality
embryo	UBERON:0000922	98.30	gold quality
bone marrow	UBERON:0002371	96.24	gold quality
bone marrow cell	CL:0002092	95.19	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	93.81	gold quality
vermiform appendix	UBERON:0001154	90.27	gold quality
adrenal tissue	UBERON:0018303	89.93	gold quality
lymph node	UBERON:0000029	89.56	gold quality
stromal cell of endometrium	CL:0002255	89.14	gold quality
rectum	UBERON:0001052	89.12	gold quality
right adrenal gland cortex	UBERON:0035827	88.53	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.43	gold quality
lower esophagus mucosa	UBERON:0035834	87.29	gold quality
right adrenal gland	UBERON:0001233	87.15	gold quality
placenta	UBERON:0001987	87.06	gold quality
esophagus mucosa	UBERON:0002469	86.88	gold quality
left adrenal gland cortex	UBERON:0035825	86.32	gold quality
left adrenal gland	UBERON:0001234	86.22	gold quality
mucosa of transverse colon	UBERON:0004991	86.18	gold quality
duodenum	UBERON:0002114	86.10	gold quality
adrenal gland	UBERON:0002369	85.92	gold quality
endometrium	UBERON:0001295	85.81	gold quality
testis	UBERON:0000473	81.48	gold quality
right testis	UBERON:0004534	80.69	gold quality
left testis	UBERON:0004533	80.63	gold quality
blood	UBERON:0000178	80.12	gold quality
smooth muscle tissue	UBERON:0001135	79.47	gold quality
tonsil	UBERON:0002372	78.99	gold quality
skin of abdomen	UBERON:0001416	78.72	gold quality

Single-cell (SCXA)

Detected in 30 experiment(s), a significant marker in 30.

Experiment	Marker?	Max mean expression
E-GEOD-75140	yes	2013.35
E-MTAB-8894	yes	1452.99
E-GEOD-93593	yes	1429.72
E-MTAB-10485	yes	1393.15
E-MTAB-6379	yes	973.91
E-GEOD-81383	yes	950.55
E-GEOD-124472	yes	924.68
E-HCAD-5	yes	898.18
E-GEOD-114530	yes	667.93
E-ENAD-20	yes	610.02
E-GEOD-124858	yes	552.95
E-ANND-5	yes	552.67
E-MTAB-6308	yes	542.60
E-HCAD-6	yes	541.73
E-MTAB-10432	yes	462.47

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F1, E2F4

miRNA regulators (miRDB)

46 targeting NUSAP1, 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-1252-5P	100.00	69.80	2774
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-580-3P	99.67	69.23	1841
HSA-MIR-587	99.64	70.86	2611
HSA-MIR-651-5P	99.64	68.49	1104
HSA-MIR-2113	99.58	71.22	1521
HSA-MIR-2053	99.57	69.15	1635
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-186-3P	99.51	66.24	1685
HSA-MIR-208A-5P	99.42	70.83	1913
HSA-MIR-208B-5P	99.42	70.83	1952
HSA-MIR-3140-5P	99.39	69.04	1136
HSA-MIR-520F-5P	99.34	70.40	1632
HSA-MIR-7854-3P	99.08	66.26	1117
HSA-MIR-4796-3P	99.08	68.38	1681
HSA-MIR-12135	98.99	70.26	1814

Literature-anchored findings (GeneRIF, showing 38)

• NuSAP1 is recognized as an immunogenic antigen in 65% of patients with AML following allogeneic HCT and suggests a tumor antigen role. (PMID:20053754)
• Interphase NuSAP-chromatin interaction suggests additional functions for NuSAP, as recently identified for other nuclear spindle assembly factors with a role in gene expression or DNA damage response. (PMID:21782797)
• Phosphorylation of NuSAP by Cdk1 is an important mechanism to regulate microtubule dynamics during cell cycle progression. (PMID:22101338)
• NuSAP is a novel biomarker for prostate cancer recurrence after surgery and its overexpression appears to be driven in part by E2F1 activation (PMID:22349817)
• High NUSAP1 expression is associated with cervical cancer. (PMID:23405241)
• A novel association between BRCA1 and NUSAP1 is revealed and a mechanism whereby NUSAP1 is involved in carcinogenesis was elusidated. (PMID:24521615)
• High levels of NuSAP1 expression were related to poor disease-free survival, particularly in triple-negative breast cancer. (PMID:26485712)
• NUSAP1 may be a crucial biomarker for oral squamous cell carcinoma. down-regulated NUSAP1 expression suppresses tumor proliferation and also enhances anti-tumor effect of paclitaxel by activating apoptotic pathways. (PMID:26554377)
• Our results reveal an underlying mechanism by which NuSAP controls kinetochore microtubule dynamics spatially and temporally by modulating the depolymerisation function of MCAK in an Aurora B kinase-dependent manner. (PMID:26733216)
• NuSAP governs chromosome oscillation via regulation of Kid, facilitating the Kid-generated polar ejection force. Depletion of NuSAP significantly suppresses the amplitude and velocity of chromosome oscillation. (PMID:26839278)
• our work provides a better understanding of the function of NUSAP1 in aggressive prostate cancers, provides rationale for using NUSAP1 as a prognostic biomarker, and sets the stage for developing improved therapeutic strategies for prostate and other cancers. (PMID:28404898)
• Findings indicated that NUSAP1 played an important role in promoting aggressiveness in astrocytoma via activating the HH pathway. (PMID:28899410)
• NUSAP1 contributes to accurate chromosome segregation by acting as a co-factor for RanBP2-RanGAP1-UBC9 during cell division. (PMID:28900032)
• Study suggests that NUSAP1 might be involved in glioma progression and can serve as a prognosis biomarker for glioma patients. NUSAP1 silencing suppresses malignant phenotypes of glioma cells, which offer a theoretical foundation for further investigation of NUSAP1 as a possible target with advantages for glioma treatment. (PMID:29336114)
• NUSAP1 silencing by siRNA inhibited colorectal cancer cell proliferation, and induces cell apoptosis. Moreover, NUSAP1 knockdown suppressed cell migration, cell invasion, and epithelial-to-mesenchymal transition. (PMID:29608915)
• NUSAP1 is overexpressed in colon cancer and high expression of NUSAP1 acts as an independent predictive factor for poor prognosis in colon cancer (PMID:29853313)
• Study provides new insights and evidence that Nucleolar and spindle-associated protein (NUSAP1) over-expression was significantly correlated with progression and prognosis of glioblastoma multiforme. Furthermore, knockdown of NUSAP1 revealed its regulation on G2/M progression and cell proliferation (both in vitro and in vivo). (PMID:29995176)
• Study provides evidence that downregulation of NUSAP1 can inhibit the proliferation, migration, and invasion of IBC cells by regulating CDK1 and DLGAP5 expression and enhances the drug susceptibility to E-ADM. (PMID:30476929)
• The inhibition of NUSAP1 by siRNAs induced resistance to Galiellalactone (GL)in DU145 cells, suggesting that NUSAP1 may be a target for GL and could be useful as a biomarker for the responsiveness of the antitumor activity of GL. (PMID:30626528)
• Our results demonstrate thatNUSAP1 upregulation contributes to metastasis of cervical cancer by promoting CSC properties and EMT via Wnt/beta-catenin signaling and XAV-939 might serve as a potential tailored therapeutic option for patients with NUSAP1-ovexpressed cervical cancer. (PMID:30678687)
• NUSAP1 knockdown inhibits cell growth and metastasis of non-small-cell lung cancer through regulating BTG2/PI3K/Akt signaling. (PMID:31603257)
• The role of nucleolar spindle-associated protein 1 in human ovarian cancer. (PMID:32031285)
• NuSAP1 is a carcinogen that facilitates progression of triple-negative breast cancer through the Wnt/beta-catenin and epithelial-mesenchymal transition pathways. (PMID:32298762)
• NUSAP1 potentiates chemoresistance in glioblastoma through its SAP domain to stabilize ATR. (PMID:32317623)
• MCM2 and NUSAP1 Are Potential Biomarkers for the Diagnosis and Prognosis of Pancreatic Cancer. (PMID:32420375)
• [NUSAP1 promotes lung cancer progression by activating AKT/mTOR signaling pathway]. (PMID:32842441)
• Nucleolar and spindleassociated protein 1 promotes nonsmall cell lung cancer progression and serves as an effector of myocyte enhancer factor 2D. (PMID:33650655)
• Increased NUSAP1 expression is associated with lymph node metastasis and survival prognosis in bladder urothelial carcinoma. (PMID:35487972)
• Knockdown of NUSAP1 inhibits cell proliferation and invasion through downregulation of TOP2A in human glioblastoma. (PMID:35532155)
• Prognostic Value of NUSAP1 and Its Correlation with Immune Infiltrates in Human Breast Cancer. (PMID:35695609)
• Evaluate the diagnostic and prognostic value of NUSAP1 in papillary thyroid carcinoma and identify the relationship with genes, proteins, and immune factors. (PMID:35710427)
• Identification and clinical validation of NUSAP1 as a novel prognostic biomarker in ovarian cancer. (PMID:35739489)
• NUSAP1, a novel stemness-related protein, promotes early recurrence of hepatocellular carcinoma. (PMID:36106345)
• A recurrent de novo variant in NUSAP1 escapes nonsense-mediated decay and leads to microcephaly, epilepsy, and developmental delay. (PMID:37005340)
• NUSAP1 Binds ILF2 to Modulate R-Loop Accumulation and DNA Damage in Prostate Cancer. (PMID:37047232)
• NUSAP1 regulates basal cell carcinoma migration, invasion and DNA damage through activation of the Hedgehog signaling pathway. (PMID:37200136)
• NuSAP regulates microtubule flux and Kif2A localization to ensure accurate chromosome congression. (PMID:38117947)
• NUSAP1 promotes pancreatic ductal adenocarcinoma progression by drives the epithelial-mesenchymal transition and reduces AMPK phosphorylation. (PMID:38229038)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	nusap1	ENSDARG00000002403
mus_musculus	Nusap1	ENSMUSG00000027306
rattus_norvegicus	Nusap1	ENSRNOG00000004921

Protein

Protein identifiers

Nucleolar and spindle-associated protein 1 — Q9BXS6 (reviewed: Q9BXS6)

All UniProt accessions (4): Q9BXS6, H0YKA7, H0YM18, H0YMD2

UniProt curated annotations — full annotation on UniProt →

Function. Microtubule-associated protein with the capacity to bundle and stabilize microtubules. May associate with chromosomes and promote the organization of mitotic spindle microtubules around them.

Subunit / interactions. Interacts with DNA and microtubules. Microtubule bundling is inhibited by IPO7, KPNA2 and KPNB1 while association with DNA is also inhibited by IPO7 and KPNA2.

Subcellular location. Cytoplasm. Nucleus. Nucleolus. Cytoskeleton. Spindle. Chromosome.

Post-translational modifications. Ubiquitinated. Ubiquitination by FZR1 may lead to proteasome-dependent degradation of this protein. Phosphorylation by ATM in G2/M-phase induces mitotic arrest.

Domain organisation. The KEN box is required for the FZR1-dependent degradation of this protein subsequent to ubiquitination.

Similarity. Belongs to the NUSAP family.

Isoforms (7)

UniProt ID	Names	Canonical?
Q9BXS6-1	1	yes
Q9BXS6-2	2
Q9BXS6-3	3
Q9BXS6-4	4
Q9BXS6-5	5
Q9BXS6-6	6
Q9BXS6-7	7

RefSeq proteins (6): NP_001230071, NP_001230072, NP_001230073, NP_001288065, NP_057443, NP_060924 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026756	NuSAP	Family

Pfam: PF16006

UniProt features (42 total): modified residue 16, compositionally biased region 6, region of interest 5, splice variant 5, sequence conflict 5, sequence variant 2, chain 1, coiled-coil region 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BXS6-F1	62.63	0.21

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 (16): 124, 135, 182, 240, 244, 247, 255, 269, 276, 311, 314, 338, 349, 352, 363, 411

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 393 (showing top): GOBP_MITOTIC_CYTOKINESIS, GOBP_CHROMOSOME_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_MITOTIC_NUCLEAR_DIVISION, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, HORIUCHI_WTAP_TARGETS_DN, KANG_DOXORUBICIN_RESISTANCE_UP, GNF2_CENPF, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_REGULATION_OF_NUCLEAR_DIVISION, GOBP_SPINDLE_LOCALIZATION, MATTIOLI_MGUS_VS_PCL, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GNF2_H2AFX, MITSIADES_RESPONSE_TO_APLIDIN_DN, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION

GO Biological Process (7): mitotic sister chromatid segregation (GO:0000070), mitotic cytokinesis (GO:0000281), mitotic chromosome condensation (GO:0007076), establishment of mitotic spindle localization (GO:0040001), positive regulation of mitotic nuclear division (GO:0045840), microtubule cytoskeleton organization (GO:0000226), cell division (GO:0051301)

GO Molecular Function (4): DNA binding (GO:0003677), RNA binding (GO:0003723), microtubule binding (GO:0008017), protein binding (GO:0005515)

GO Cellular Component (8): chromosome (GO:0005694), nucleolus (GO:0005730), cytoplasm (GO:0005737), microtubule (GO:0005874), mitotic spindle (GO:0072686), nucleus (GO:0005634), spindle (GO:0005819), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membraneless organelle	4
mitotic cell cycle process	3
mitotic cell cycle	3
mitotic nuclear division	2
nucleic acid binding	2
microtubule cytoskeleton	2
sister chromatid segregation	1
cytoskeleton-dependent cytokinesis	1
mitotic sister chromatid segregation	1
chromosome condensation	1
establishment of spindle localization	1
microtubule cytoskeleton organization involved in mitosis	1
regulation of mitotic nuclear division	1
positive regulation of nuclear division	1
positive regulation of cell cycle process	1
cytoskeleton organization	1
microtubule-based process	1
cellular process	1
tubulin binding	1
binding	1
nuclear lumen	1
intracellular anatomical structure	1
cellular anatomical structure	1
polymeric cytoskeletal fiber	1
spindle	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1524 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NUSAP1	TOP2A	P11388	795
NUSAP1	TPX2	Q9ULW0	768
NUSAP1	CCNB2	O95067	761
NUSAP1	UBE2C	O00762	755
NUSAP1	DLGAP5	Q15398	753
NUSAP1	RRM2	P31350	747
NUSAP1	KIF11	P52732	739
NUSAP1	BIRC5	O15392	724
NUSAP1	CDCA8	Q53HL2	724
NUSAP1	BUB1B	O60566	696
NUSAP1	KIF2C	Q99661	669
NUSAP1	MKI67	P46013	665
NUSAP1	KIF20A	O95235	645
NUSAP1	HJURP	Q8NCD3	642
NUSAP1	CDK1	P06493	641

IntAct

68 interactions, top by confidence:

A	B	Type	Score
CEP70	NUSAP1	psi-mi:“MI:0915”(physical association)	0.560
N	RBM47	psi-mi:“MI:0914”(association)	0.530
KPNB1	POM121C	psi-mi:“MI:0914”(association)	0.530
MAGEB2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
RPL13	RRP8	psi-mi:“MI:0914”(association)	0.530
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
Ranbp2		psi-mi:“MI:0915”(physical association)	0.400
ANXA2	NUSAP1	psi-mi:“MI:0915”(physical association)	0.400
NUSAP1	ANXA2	psi-mi:“MI:0915”(physical association)	0.400
JUN		psi-mi:“MI:0914”(association)	0.350
Mecom	ESYT2	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
HEXIM1	SART1	psi-mi:“MI:0914”(association)	0.350
N	RBM47	psi-mi:“MI:0914”(association)	0.350
LIN28A	MEX3A	psi-mi:“MI:0914”(association)	0.350
CSNK2B	OSBPL8	psi-mi:“MI:0914”(association)	0.350
IPO7	NSA2	psi-mi:“MI:0914”(association)	0.350

BioGRID (154): CEP70 (Two-hybrid), KPNB1 (Affinity Capture-MS), IPO7 (Affinity Capture-MS), GAPDHS (Affinity Capture-MS), RANBP2 (Affinity Capture-MS), CST6 (Affinity Capture-MS), NUP153 (Affinity Capture-MS), S100P (Affinity Capture-MS), C5orf30 (Affinity Capture-MS), GSTA2 (Affinity Capture-MS), NUSAP1 (Affinity Capture-MS), CHAF1A (Co-fractionation), NUSAP1 (Reconstituted Complex), NUSAP1 (Proximity Label-MS), NUSAP1 (Proximity Label-MS)

ESM2 similar proteins: A0JMK9, A0JMT0, A0JMZ1, A1L3I5, A2BIL7, A6QLA6, A8DZJ1, A8PUI7, B0BLU1, B7ZD04, O13024, Q0IHP2, Q12495, Q12830, Q13111, Q1MTN9, Q1W1G1, Q24595, Q2YDJ0, Q32N93, Q3T8J9, Q4FZB7, Q535K8, Q5BKG8, Q5R1T0, Q5R789, Q65Z40, Q68F53, Q6DD45, Q6INS5, Q6NZY4, Q76FK4, Q7Z5K2, Q801E2, Q86BP6, Q8IYH5, Q8K298, Q8RWK8, Q8WML3, Q98TA5

Diamond homologs: A0JMZ1, A1L2F3, A1L3I5, Q1W1G1, Q2YDJ0, Q5BKG8, Q5ZJU5, Q9BXS6, Q9ERH4

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
CDK1	down-regulates	NUSAP1	phosphorylation
miR-129-5p	“down-regulates quantity by destabilization”	NUSAP1	“post transcriptional regulation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 75 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
Nuclear import of Rev protein	6	38.8×	4e-07
Rev-mediated nuclear export of HIV RNA	5	30.5×	1e-05
Formation of the ternary complex, and subsequently, the 43S complex	5	20.7×	7e-05
Influenza Infection	6	20.3×	1e-05
SARS-CoV-1-host interactions	6	20.3×	1e-05
Peptide chain elongation	8	19.5×	4e-07
Viral mRNA Translation	8	19.5×	4e-07
Formation of a pool of free 40S subunits	9	19.4×	1e-07

GO biological processes:

GO term	Partners	Fold	FDR
ribosomal large subunit biogenesis	5	33.6×	4e-05
cytoplasmic translation	9	25.2×	3e-08
ribosomal small subunit biogenesis	6	20.7×	4e-05
protein import into nucleus	7	15.3×	4e-05
nucleosome assembly	6	12.8×	5e-04
translation	7	10.9×	3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	62
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1691707	NM_016359.5(NUSAP1):c.1209C>A (p.Tyr403Ter)	Likely pathogenic

SpliceAI

2027 predictions. Top by Δscore:

Variant	Effect	Δscore
15:41331910:CGTA:C	donor_loss	1.0000
15:41331911:GTAC:G	donor_loss	1.0000
15:41331912:TACC:T	donor_loss	1.0000
15:41331914:CCTG:C	donor_gain	1.0000
15:41331979:CTC:C	acceptor_gain	1.0000
15:41332238:A:AC	donor_gain	1.0000
15:41332239:C:CC	donor_gain	1.0000
15:41332996:G:GG	donor_gain	1.0000
15:41333049:GG:G	donor_gain	1.0000
15:41333050:GG:G	donor_gain	1.0000
15:41342452:CAGGT:C	donor_loss	1.0000
15:41342453:AGGTG:A	donor_loss	1.0000
15:41342454:GGTG:G	donor_loss	1.0000
15:41342455:G:GG	donor_gain	1.0000
15:41342455:GTGA:G	donor_loss	1.0000
15:41342456:T:A	donor_loss	1.0000
15:41349239:CAGGT:C	donor_loss	1.0000
15:41349240:AGGTG:A	donor_loss	1.0000
15:41349241:GG:G	donor_loss	1.0000
15:41349242:G:GA	donor_loss	1.0000
15:41356140:AG:A	donor_loss	1.0000
15:41356141:G:GG	donor_gain	1.0000
15:41356141:GTAAG:G	donor_loss	1.0000
15:41356142:TAA:T	donor_loss	1.0000
15:41358125:A:AG	acceptor_gain	1.0000
15:41358132:A:AG	acceptor_gain	1.0000
15:41358132:ATATT:A	acceptor_gain	1.0000
15:41358133:T:G	acceptor_gain	1.0000
15:41358134:A:AG	acceptor_gain	1.0000
15:41358134:ATT:A	acceptor_gain	1.0000

AlphaMissense

2886 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:41375777:T:C	F358L	0.992
15:41375779:T:A	F358L	0.992
15:41375779:T:G	F358L	0.992
15:41333019:C:A	A21D	0.987
15:41358151:T:C	F185L	0.987
15:41358153:T:A	F185L	0.987
15:41358153:T:G	F185L	0.987
15:41375792:A:C	S363R	0.986
15:41375794:T:A	S363R	0.986
15:41375794:T:G	S363R	0.986
15:41342396:T:C	L35S	0.984
15:41333007:T:C	L17P	0.983
15:41358163:C:G	H189D	0.983
15:41358175:T:C	F193L	0.983
15:41358177:T:A	F193L	0.983
15:41358177:T:G	F193L	0.983
15:41358169:G:C	A191P	0.979
15:41375796:T:C	L364S	0.978
15:41358176:T:C	F193S	0.977
15:41375784:T:C	L360P	0.975
15:41375784:T:A	L360H	0.973
15:41375822:C:G	H373D	0.971
15:41371528:T:C	F284L	0.969
15:41371530:T:A	F284L	0.969
15:41371530:T:G	F284L	0.969
15:41358203:A:C	Y202S	0.968
15:41342408:T:C	L39S	0.966
15:41358152:T:C	F185S	0.966
15:41333018:G:C	A21P	0.964
15:41333011:G:C	Q18H	0.961

dbSNP variants (sampled 300 via entrez): RS1000030820 (15:41332748 T>A,C), RS1000054809 (15:41370924 G>GA), RS1000080188 (15:41336210 G>A), RS1000135132 (15:41377102 G>A,T), RS1000135518 (15:41333171 G>C,T), RS1000219725 (15:41362913 C>T), RS1000272026 (15:41363259 C>A), RS1000290473 (15:41341909 C>G,T), RS1000333354 (15:41331122 C>T), RS1000345897 (15:41348249 T>C), RS1000416917 (15:41345143 C>A), RS1000479008 (15:41340460 T>A), RS1000522041 (15:41380164 G>A), RS1000599972 (15:41342258 T>G), RS1000631579 (15:41333936 A>C)

Disease associations

OMIM: gene MIM:612818 | disease phenotypes: MIM:613402

GenCC curated gene-disease

Mondo (1): microcephaly, seizures, and developmental delay (MONDO:0013254)

Orphanet (2): Early infantile developmental and epileptic encephalopathy (Orphanet:1934), OBSOLETE: Microcephaly-seizures-developmental delay syndrome (Orphanet:228418)

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001728_13	Ulcerative colitis	2.000000e-08
GCST004133_26	Ulcerative colitis	3.000000e-07
GCST007563_20	Allergic disease (asthma, hay fever or eczema)	4.000000e-08

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	decreases expression	4
sodium arsenite	increases abundance, increases expression, decreases expression	3
Air Pollutants	decreases expression, affects cotreatment, increases abundance, increases expression, increases oxidation	3
Benzo(a)pyrene	decreases expression	3
Doxorubicin	decreases expression, affects response to substance	3
Estradiol	decreases expression, increases expression	3
Tretinoin	decreases expression	3
bisphenol A	affects expression, decreases expression	2
methacrylaldehyde	affects cotreatment, increases expression, increases oxidation, increases abundance	2
Acrolein	affects cotreatment, increases expression, increases oxidation, increases abundance	2
Cadmium	decreases expression	2
Coumestrol	affects cotreatment, increases expression, affects reaction	2
Ozone	increases oxidation, increases abundance, affects cotreatment, increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Progesterone	decreases expression, increases expression	2
Tetrachlorodibenzodioxin	affects expression, decreases expression	2
Valproic Acid	decreases expression, affects expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
Aflatoxin B1	decreases expression, affects expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
dicrotophos	decreases expression	1
alpha-pinene	increases expression, increases oxidation, increases abundance, affects cotreatment	1
propionaldehyde	decreases expression	1
deoxynivalenol	increases expression	1
geraniol	decreases expression	1
3,4-dichloroaniline	decreases expression	1
cobaltous chloride	decreases expression	1
zinc chromate	decreases expression, increases abundance	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, increases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_TB51	HAP1 NUSAP1 (-) 1	Cancer cell line	Male
CVCL_TB52	HAP1 NUSAP1 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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