NSA2

gene
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Also known as HUSSY-29HCLG1FLJ94393TINP1

Summary

NSA2 (NSA2 ribosome biogenesis factor, HGNC:30728) is a protein-coding gene on chromosome 5q13.3, encoding Ribosome biogenesis protein NSA2 homolog (O95478). Involved in the biogenesis of the 60S ribosomal subunit. It is a common-essential gene (DepMap: required in 99.8% of cancer cell lines).

This gene encodes a nucleolar protein involved in cell cycle regulation and proliferation. This gene was identified based on sequence similarity to a highly conserved Saccharomyces cerevisiae gene encoding a pre-ribosomal protein, which is involved in large ribosomal subunit biogenesis. The encoded protein is found at elevated levels in diabetic nephropathy. Alternative splicing results in multiple transcript variants. Several related pseudogenes have been identified.

Source: NCBI Gene 10412 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 33 total
  • Cancer dependency (DepMap): dependent in 99.8% of screened cell lines (common-essential)
  • MANE Select transcript: NM_014886

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30728
Approved symbolNSA2
NameNSA2 ribosome biogenesis factor
Location5q13.3
Locus typegene with protein product
StatusApproved
AliasesHUSSY-29, HCLG1, FLJ94393, TINP1
Ensembl geneENSG00000164346
Ensembl biotypeprotein_coding
OMIM612497
Entrez10412

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000296802, ENST00000513356, ENST00000514918, ENST00000515524, ENST00000610426, ENST00000854645, ENST00000921903

RefSeq mRNA: 3 — MANE Select: NM_014886 NM_001271665, NM_001364506, NM_014886

CCDS: CCDS4025, CCDS75260

Canonical transcript exons

ENST00000610426 — 6 exons

ExonStartEnd
ENSE000010837157477386874774060
ENSE000010837167476724974767363
ENSE000035097217477063174770810
ENSE000035948777476893174769118
ENSE000036543777476921474769364
ENSE000037134217477660474780113

Expression profiles

Bgee: expression breadth ubiquitous, 300 present calls, max score 99.21.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 57.5079 / max 2238.1394, expressed in 1804 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
5706855.96051804
570691.4463770
570670.10124

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370199.21gold quality
parotid glandUBERON:000183199.18gold quality
upper leg skinUBERON:000426299.03gold quality
skin of hipUBERON:000155498.96gold quality
hair follicleUBERON:000207398.85gold quality
cervix squamous epitheliumUBERON:000692298.85gold quality
tendonUBERON:000004398.83gold quality
gluteal muscleUBERON:000200098.80gold quality
germinal epithelium of ovaryUBERON:000130498.73gold quality
parietal pleuraUBERON:000240098.72gold quality
cauda epididymisUBERON:000436098.61gold quality
left ovaryUBERON:000211998.60gold quality
seminal vesicleUBERON:000099898.59gold quality
superficial temporal arteryUBERON:000161498.55gold quality
type B pancreatic cellCL:000016998.54gold quality
mucosa of sigmoid colonUBERON:000499398.51gold quality
ovaryUBERON:000099298.47gold quality
pleuraUBERON:000097798.45gold quality
corpus epididymisUBERON:000435998.42gold quality
tendon of biceps brachiiUBERON:000818898.39gold quality
epithelium of nasopharynxUBERON:000195198.38gold quality
nasopharynxUBERON:000172898.36gold quality
caput epididymisUBERON:000435898.33gold quality
cortical plateUBERON:000534398.33gold quality
ganglionic eminenceUBERON:000402398.29gold quality
biceps brachiiUBERON:000150798.27gold quality
cartilage tissueUBERON:000241898.27gold quality
lymph nodeUBERON:000002998.25gold quality
colonic mucosaUBERON:000031798.25gold quality
palpebral conjunctivaUBERON:000181298.25gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes10.31

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

26 targeting NSA2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-6515-3P99.8268.191933
HSA-MIR-6875-3P99.8270.262983
HSA-MIR-4659A-3P99.8072.624248
HSA-MIR-4659B-3P99.8072.624248
HSA-MIR-6885-3P99.7570.363187
HSA-MIR-33A-3P99.7070.273362
HSA-MIR-7161-5P99.6868.921592
HSA-MIR-432899.5771.064094
HSA-MIR-4687-3P99.4866.41968
HSA-MIR-889-5P99.4168.751025
HSA-MIR-3678-3P99.3167.101432
HSA-MIR-1273H-3P99.2967.55980
HSA-MIR-499A-3P99.1869.201392
HSA-MIR-499B-3P99.1869.271391
HSA-MIR-892C-5P99.1670.562116
HSA-MIR-382-3P98.8367.101074
HSA-MIR-615-5P98.1063.76591
HSA-MIR-1912-5P97.9467.98832
HSA-MIR-365097.8864.89693
HSA-MIR-6502-3P97.8665.43569
HSA-MIR-365496.4366.55646
HSA-MIR-770495.3062.35115

Functional genomics

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

Literature-anchored findings (GeneRIF, showing 6)

  • The yeast ortholog, Nsa2, is a pre-ribosomal factor that is essential for biogenesis of the large ribosomal subunit. (PMID:16861225)
  • these results demonstrated that NSA2 is a nucleolar protein involved in cell proliferation and cell cycle regulation. (PMID:19932687)
  • Data suggest that circulating NSA2 is elevated in diabetic nephropathy patients with albuminuria, and that renal and circulating NSA2 levels are increased in hyperglycemia in experimental models of diabetes. (PMID:22095236)
  • NSA2, which increases in diabetic nephropathy, may be involved in the actions of TGFbeta1 and contribute to the development of diabetic nephropathy. (PMID:23220173)
  • TINP1 promotes cell proliferation and significantly reduces p53 and p21 expression. (PMID:23912275)
  • Findings indicate a function of Nop-7-associated 2 (NSA2) in the regulation of ribosome biogenesis. (PMID:30243719)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerionsa2ENSDARG00000007708
mus_musculusNsa2ENSMUSG00000060739
rattus_norvegicusNsa2ENSRNOG00000016530
drosophila_melanogasterIp259FBGN0025366
caenorhabditis_elegansW09C5.1WBGENE00012351

Protein

Protein identifiers

Ribosome biogenesis protein NSA2 homologO95478 (reviewed: O95478)

Alternative names: Hairy cell leukemia protein 1, TGF-beta-inducible nuclear protein 1

All UniProt accessions (4): A0A0A0MQZ6, O95478, H0YAI9, Q5J7U2

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the biogenesis of the 60S ribosomal subunit. May play a part in the quality control of pre-60S particles.

Subunit / interactions. Component of the pre-66S ribosomal particle.

Subcellular location. Nucleus. Nucleolus.

Similarity. Belongs to the eukaryotic ribosomal protein eS8 family. Ribosome biogenesis protein NSA2 subfamily.

RefSeq proteins (3): NP_001258594, NP_001351435, NP_055701* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR022309Ribosomal_Se8/biogenesis_NSA2Family
IPR039411NSA2_famFamily

Pfam: PF01201

UniProt features (7 total): chain 1, region of interest 1, short sequence motif 1, compositionally biased region 1, modified residue 1, cross-link 1, sequence variant 1

Structure

Experimental structures (PDB)

28 structures.

PDBMethodResolution (Å)
8FKVELECTRON MICROSCOPY2.47
8FKWELECTRON MICROSCOPY2.5
8FL3ELECTRON MICROSCOPY2.53
8FL7ELECTRON MICROSCOPY2.55
8FKXELECTRON MICROSCOPY2.59
8FL6ELECTRON MICROSCOPY2.62
8FKYELECTRON MICROSCOPY2.67
8FL2ELECTRON MICROSCOPY2.67
8FL9ELECTRON MICROSCOPY2.75
8FKTELECTRON MICROSCOPY2.81
8FKUELECTRON MICROSCOPY2.82
8RL2ELECTRON MICROSCOPY2.84
8FKSELECTRON MICROSCOPY2.88
8FKRELECTRON MICROSCOPY2.89
8FL4ELECTRON MICROSCOPY2.89
8FL0ELECTRON MICROSCOPY2.91
8IDYELECTRON MICROSCOPY3
8INFELECTRON MICROSCOPY3
8FKZELECTRON MICROSCOPY3.04
9QIWELECTRON MICROSCOPY3.04
8INEELECTRON MICROSCOPY3.2
8INKELECTRON MICROSCOPY3.2
8IPDELECTRON MICROSCOPY3.2
8IPYELECTRON MICROSCOPY3.2
8IE3ELECTRON MICROSCOPY3.3
8IR1ELECTRON MICROSCOPY3.3
8IR3ELECTRON MICROSCOPY3.5
8IPXELECTRON MICROSCOPY4.3

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O95478-F187.850.72

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 (2): 81, 80

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 178 (showing top): GOBP_RIBOSOME_BIOGENESIS, MODULE_151, PUJANA_CHEK2_PCC_NETWORK, GOBP_MATURATION_OF_LSU_RRNA, GNF2_FBL, SCHLOSSER_SERUM_RESPONSE_DN, GNF2_ST13, GOBP_MATURATION_OF_5_8S_RRNA, BURTON_ADIPOGENESIS_8, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS, MODULE_114, GOCC_PRERIBOSOME, GOCC_PRERIBOSOME_LARGE_SUBUNIT_PRECURSOR, GOCC_NUCLEOLUS

GO Biological Process (5): maturation of 5.8S rRNA (GO:0000460), maturation of LSU-rRNA (GO:0000470), rRNA processing (GO:0006364), ribosome biogenesis (GO:0042254), ribosomal large subunit biogenesis (GO:0042273)

GO Molecular Function (1): RNA binding (GO:0003723)

GO Cellular Component (5): nucleolus (GO:0005730), preribosome, large subunit precursor (GO:0030687), nucleus (GO:0005634), preribosome (GO:0030684), ribonucleoprotein complex (GO:1990904)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
rRNA processing2
ribosome biogenesis2
ribonucleoprotein complex biogenesis2
ribosomal large subunit biogenesis1
RNA processing1
rRNA metabolic process1
nucleic acid binding1
nuclear lumen1
intracellular membraneless organelle1
preribosome1
intracellular membrane-bounded organelle1
ribonucleoprotein complex1
protein-containing complex1

Protein interactions and networks

STRING

2576 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NSA2MRTO4Q9UKD2928
NSA2RSL24D1Q9UHA3904
NSA2GNL2Q13823904
NSA2RPF2Q9H7B2900
NSA2GTPBP4Q9BZE4892
NSA2NMD3Q96D46840
NSA2NUPR1O60356828
NSA2WDR74Q6RFH5774
NSA2WDR12Q9GZL7770
NSA2MDN1Q9NU22769
NSA2NIP7Q9Y221744
NSA2PAK1IP1Q9NWT1744
NSA2NOP53Q9NZM5719
NSA2LSG1Q9H089706
NSA2NOP2P46087691

IntAct

160 interactions, top by confidence:

ABTypeScore
SART3PRPF4psi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
RBM34RRP8psi-mi:“MI:0914”(association)0.640
NSA2GNL2psi-mi:“MI:0914”(association)0.640
RPL28MAGEB2psi-mi:“MI:0914”(association)0.560
NSA2TYW5psi-mi:“MI:0914”(association)0.530
FGF3GTPBP10psi-mi:“MI:0914”(association)0.530
RPL37AMPHOSPH10psi-mi:“MI:0914”(association)0.530
RPL18NOP56psi-mi:“MI:0914”(association)0.530
MACROH2A2PPM1Gpsi-mi:“MI:0914”(association)0.530
PRR11NVLpsi-mi:“MI:0914”(association)0.530
MAK16NVLpsi-mi:“MI:0914”(association)0.530
ZBTB48ZBTB24psi-mi:“MI:0914”(association)0.530
E4F1ZBTB24psi-mi:“MI:0914”(association)0.530
PDGFBDKC1psi-mi:“MI:0914”(association)0.530
ZCRB1DKC1psi-mi:“MI:0914”(association)0.530
NNOP56psi-mi:“MI:0914”(association)0.530
ATP6V1B2ATP6V1G1psi-mi:“MI:0914”(association)0.530
SART3NSA2psi-mi:“MI:0914”(association)0.530
RPS2MPHOSPH10psi-mi:“MI:0914”(association)0.530
KRR1MPHOSPH10psi-mi:“MI:0914”(association)0.530
NHSL3NCK2psi-mi:“MI:0914”(association)0.530
ABT1ZNF316psi-mi:“MI:0914”(association)0.530
RPL7ANVLpsi-mi:“MI:0914”(association)0.530

BioGRID (301): NSA2 (Affinity Capture-MS), NSA2 (Affinity Capture-MS), NSA2 (Affinity Capture-MS), NSA2 (Affinity Capture-MS), RPL26L1 (Affinity Capture-MS), NPM1 (Affinity Capture-MS), RRS1 (Affinity Capture-MS), PTCD3 (Affinity Capture-MS), PABPC4 (Affinity Capture-MS), MAGEA9B (Affinity Capture-MS), GNL2 (Affinity Capture-MS), GTPBP4 (Affinity Capture-MS), MRPS9 (Affinity Capture-MS), CCDC86 (Affinity Capture-MS), MRTO4 (Affinity Capture-MS)

ESM2 similar proteins: A9L994, B2XWK3, D0VWQ3, G1SKF7, G1TFE0, G1U7L1, O95478, P02412, P12001, P17702, P21533, P35980, P40590, P41098, P41105, P46779, P47911, P49205, P69090, P69091, Q02878, Q07020, Q08200, Q27S52, Q2MIA2, Q2MII9, Q2YGT9, Q3SX11, Q3T0L7, Q42351, Q4R5H8, Q4VZN5, Q58DQ3, Q5E973, Q6B860, Q6P1L8, Q6QMZ4, Q70Y05, Q7ZV96, Q7ZWJ7

Diamond homologs: A1CJS8, A1D7P0, A2BK08, A2STM4, A3CSQ2, A3LQ06, A5DCN7, A5DZE1, A6R3Q6, A6S4J2, A6ZR80, A7TIZ1, A8AAJ7, C5A4I6, O28130, O95478, P0CQ60, P0CQ61, P0CU36, P40078, P54055, P61301, Q0UV95, Q0W1L5, Q12UA1, Q1DQ27, Q3SX11, Q465V4, Q4JAP5, Q4P3S7, Q4WX36, Q54GN8, Q5A2Y7, Q5B954, Q6BU14, Q6C6D1, Q6CNC5, Q6FN72, Q6L0D3, Q75CG9

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 180 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:

PathwayPartnersFoldFDR
Peptide chain elongation1720.2×8e-16
Viral mRNA Translation1720.2×8e-16
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA1719.9×8e-16
Selenocysteine synthesis1719.1×1e-15
Eukaryotic Translation Termination1719.1×1e-15
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)1718.7×1e-15
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA1718.7×1e-15
Formation of a pool of free 40S subunits1717.8×2e-15

GO biological processes:

GO termPartnersFoldFDR
ribosomal large subunit biogenesis821.6×5e-07
cytoplasmic translation1820.3×5e-16
negative regulation of viral genome replication716.0×3e-05
rRNA processing1714.7×6e-13
translation1911.9×6e-13
ribosomal small subunit biogenesis811.1×7e-05
regulation of alternative mRNA splicing, via spliceosome68.9×4e-03
RNA processing68.0×6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance24
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1147 predictions. Top by Δscore:

VariantEffectΔscore
5:74768921:A:AGacceptor_gain1.0000
5:74768922:T:Gacceptor_gain1.0000
5:74768924:A:AGacceptor_gain1.0000
5:74768925:T:Gacceptor_gain1.0000
5:74768927:A:AGacceptor_gain1.0000
5:74768928:T:Gacceptor_gain1.0000
5:74768929:A:AGacceptor_gain1.0000
5:74768930:G:GTacceptor_gain1.0000
5:74768930:GC:Gacceptor_gain1.0000
5:74768930:GCC:Gacceptor_gain1.0000
5:74768930:GCCA:Gacceptor_gain1.0000
5:74768930:GCCAC:Gacceptor_gain1.0000
5:74769066:GC:Gdonor_gain1.0000
5:74769114:AAGAC:Adonor_gain1.0000
5:74769115:AGAC:Adonor_gain1.0000
5:74769116:GAC:Gdonor_gain1.0000
5:74769116:GACG:Gdonor_gain1.0000
5:74769117:AC:Adonor_gain1.0000
5:74769117:ACGT:Adonor_loss1.0000
5:74769119:G:GGdonor_gain1.0000
5:74769208:T:TAacceptor_gain1.0000
5:74769209:G:Aacceptor_gain1.0000
5:74769211:TAGT:Tacceptor_loss1.0000
5:74769212:A:AGacceptor_gain1.0000
5:74769213:G:GAacceptor_gain1.0000
5:74769213:GT:Gacceptor_gain1.0000
5:74769213:GTA:Gacceptor_gain1.0000
5:74769213:GTAT:Gacceptor_gain1.0000
5:74769213:GTATC:Gacceptor_gain1.0000
5:74769318:C:Gdonor_gain1.0000

AlphaMissense

1693 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:74770637:T:AW117R1.000
5:74770637:T:CW117R1.000
5:74770639:G:CW117C1.000
5:74770639:G:TW117C1.000
5:74770724:T:AW146R1.000
5:74770724:T:CW146R1.000
5:74770732:A:CR148S1.000
5:74770732:A:TR148S1.000
5:74770750:C:GC154W1.000
5:74770766:T:CF160L1.000
5:74770768:T:AF160L1.000
5:74770768:T:GF160L1.000
5:74770773:G:CR162T1.000
5:74770774:A:CR162S1.000
5:74770774:A:TR162S1.000
5:74770803:G:CR172T1.000
5:74770803:G:TR172M1.000
5:74770804:G:CR172S1.000
5:74770804:G:TR172S1.000
5:74773893:T:AV183E1.000
5:74773908:T:CL188P1.000
5:74773951:T:AN202K1.000
5:74773951:T:GN202K1.000
5:74773979:G:CG212R1.000
5:74773994:G:CG217R1.000
5:74774001:T:AV219D1.000
5:74774027:G:CG228R1.000
5:74774057:T:AW238R1.000
5:74774057:T:CW238R1.000
5:74776613:C:AA242D1.000

dbSNP variants (sampled 300 via entrez): RS1000131685 (5:74776343 C>G,T), RS1000271888 (5:74770026 T>G), RS1000289844 (5:74770500 G>A), RS1000466285 (5:74776662 A>C), RS1000881640 (5:74779683 T>C), RS1001308169 (5:74776768 C>G), RS1001505663 (5:74779481 A>G), RS1001639739 (5:74777202 T>A), RS1002176320 (5:74776688 A>C,T), RS1002290871 (5:74778291 T>G), RS1002306825 (5:74769611 C>G,T), RS1002435323 (5:74772734 T>C), RS1002932186 (5:74778441 C>T), RS1002968590 (5:74775605 A>G), RS1003020113 (5:74772354 C>T)

Disease associations

OMIM: gene MIM:612497 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

ChemicalActions (top 5)PubMed papers
dicrotophosdecreases expression1
deoxynivalenolincreases expression1
sodium arsenitedecreases expression1
nivalenolincreases expression1
chloropicrinaffects expression1
K 7174increases expression1
ICG 001decreases expression1
picoxystrobindecreases expression1
Arsenic Trioxideincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Benzo(a)pyrenedecreases methylation1
Caffeinedecreases phosphorylation1
Hydrogen Peroxideaffects expression1
Ribonucleotidesaffects binding1
Rotenonedecreases expression1
Aflatoxin B1affects cotreatment, decreases expression1
Gold Compoundsdecreases expression1
Antirheumatic Agentsincreases expression1
beta-Naphthoflavoneaffects cotreatment, decreases expression, increases expression1
Acrylamideincreases expression1
Particulate Matterdecreases expression, increases abundance1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.