NOP53

NOP53 ribosome biogenesis factor, the group of Ribosomal biogenesis factors

Basic information

Region (hg38): 19:47745546-47757058

Previous symbols: [ "GLTSCR2" ]

Links

ENSG00000105373 ∙ NCBI:29997 ∙ OMIM:605691 ∙ HGNC:4333 ∙ Uniprot:Q9NZM5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NOP53 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOP53 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					3	3
missense			71	2		73
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	71	2	3

Variants in NOP53

This is a list of pathogenic ClinVar variants found in the NOP53 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-47745564-C-T		not specified	Uncertain significance (Apr 26, 2023)
19-47745566-G-A		not specified	Uncertain significance (Apr 18, 2023)
19-47745570-G-A		not specified	Uncertain significance (Dec 12, 2024)
19-47745592-G-T		not specified	Uncertain significance (Jan 02, 2024)
19-47745596-A-C		not specified	Uncertain significance (Dec 05, 2024)
19-47745671-C-G		not specified	Uncertain significance (Nov 24, 2024)
19-47745675-G-C		not specified	Uncertain significance (Apr 07, 2022)
19-47745677-G-A		not specified	Uncertain significance (Sep 10, 2024)
19-47745691-G-C		not specified	Uncertain significance (Sep 14, 2023)
19-47745726-T-C		not specified	Uncertain significance (Jun 07, 2024)
19-47745731-C-G		not specified	Uncertain significance (Jun 07, 2024)
19-47745746-T-C		not specified	Uncertain significance (Aug 04, 2023)
19-47746986-C-G		not specified	Uncertain significance (Mar 06, 2023)
19-47746989-A-C		not specified	Uncertain significance (Jan 27, 2025)
19-47746989-A-G		not specified	Likely benign (Oct 25, 2024)
19-47747020-C-G		not specified	Uncertain significance (Jun 07, 2023)
19-47750183-A-G		not specified	Uncertain significance (Jun 19, 2024)
19-47750197-C-G			Benign (Jan 25, 2018)
19-47750238-G-A		not specified	Uncertain significance (Jul 31, 2024)
19-47750247-T-C		not specified	Uncertain significance (Dec 27, 2023)
19-47750264-T-C		not specified	Uncertain significance (Oct 24, 2024)
19-47750276-G-T		not specified	Uncertain significance (Jan 16, 2025)
19-47750277-C-T		not specified	Uncertain significance (Sep 14, 2023)
19-47750915-G-A		not specified	Uncertain significance (Jul 07, 2024)
19-47750915-G-T		not specified	Uncertain significance (Mar 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOP53	protein_coding	protein_coding	ENST00000246802	13	11537

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.181	0.818	125727	0	17	125744	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.647	306	276	1.11	0.0000182	2932
Missense in Polyphen		84	82.507	1.0181		857
Synonymous	-1.99	152	124	1.23	0.00000827	997
Loss of Function	3.40	6	24.0	0.250	0.00000115	294

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000246	0.000246
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.0000792	0.0000791
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Nucleolar protein which is involved in the integration of the 5S RNP into the ribosomal large subunit during ribosome biogenesis (PubMed:24120868). In ribosome biogenesis, may also play a role in rRNA transcription (PubMed:27729611). Also functions as a nucleolar sensor that regulates the activation of p53/TP53 in response to ribosome biogenesis perturbation, DNA damage and other stress conditions (PubMed:21741933, PubMed:24120868, PubMed:27829214). DNA damage or perturbation of ribosome biogenesis disrupt the interaction between NOP53 and RPL11 allowing RPL11 transport to the nucleoplasm where it can inhibit MDM2 and allow p53/TP53 activation (PubMed:24120868, PubMed:27829214). It may also positively regulate the function of p53/TP53 in cell cycle arrest and apoptosis through direct interaction, preventing its MDM2-dependent ubiquitin-mediated proteasomal degradation (PubMed:22522597). Originally identified as a tumor suppressor, it may also play a role in cell proliferation and apoptosis by positively regulating the stability of PTEN, thereby antagonizing the PI3K-AKT/PKB signaling pathway (PubMed:15355975, PubMed:16971513, PubMed:27729611). May also inhibit cell proliferation and increase apoptosis through its interaction with NF2 (PubMed:21167305). May negatively regulate NPM1 by regulating its nucleoplasmic localization, oligomerization and ubiquitin-mediated proteasomal degradation (PubMed:25818168). Thereby, may prevent NPM1 interaction with MYC and negatively regulate transcription mediated by the MYC-NPM1 complex (PubMed:25956029). May also regulate cellular aerobic respiration (PubMed:24556985). In the cellular response to viral infection, may play a role in the attenuation of interferon-beta through the inhibition of DDX58/RIG-1 (PubMed:27824081). {ECO:0000269|PubMed:15355975, ECO:0000269|PubMed:16971513, ECO:0000269|PubMed:21167305, ECO:0000269|PubMed:21741933, ECO:0000269|PubMed:22522597, ECO:0000269|PubMed:24120868, ECO:0000269|PubMed:24556985, ECO:0000269|PubMed:25818168, ECO:0000269|PubMed:25956029, ECO:0000269|PubMed:27729611, ECO:0000269|PubMed:27824081, ECO:0000269|PubMed:27829214}.
• Pathway: Herpes simplex infection - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.181

Intolerance Scores

• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.41

Haploinsufficiency Scores

• pHI: 0.622
• hipred: Y
• hipred_score: 0.736
• ghis: 0.505

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Nop53
• Phenotype: immune system phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: ribosomal large subunit assembly;negative regulation of transcription by RNA polymerase II;regulation of protein phosphorylation;DNA repair;rRNA processing;cellular response to DNA damage stimulus;mitotic G2 DNA damage checkpoint;negative regulation of phosphatidylinositol 3-kinase signaling;negative regulation of protein complex assembly;negative regulation of proteasomal ubiquitin-dependent protein catabolic process;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;regulation of RIG-I signaling pathway;regulation of apoptotic process;protein stabilization;regulation of cell cycle;negative regulation of protein kinase B signaling;cellular response to hypoxia;regulation of signal transduction by p53 class mediator;negative regulation of signal transduction by p53 class mediator;negative regulation of transcription of nucleolar large rRNA by RNA polymerase I;protein localization to nucleolus;positive regulation of protein K63-linked deubiquitination;regulation of aerobic respiration;protein localization to nucleoplasm
• Cellular component: fibrillar center;nucleoplasm;nucleolus;cytosol;rDNA heterochromatin;intracellular membrane-bounded organelle
• Molecular function: p53 binding;RNA binding;protein binding;5S rRNA binding;identical protein binding