NOC2L

NOC2 like nucleolar associated transcriptional repressor, the group of Armadillo like helical domain containing|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 1:944203-959309

Links

ENSG00000188976 ∙ NCBI:26155 ∙ OMIM:610770 ∙ HGNC:24517 ∙ Uniprot:Q9Y3T9 ∙ 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 NOC2L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOC2L 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				4	5	9
missense			75	7		82
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	75	11	6

Variants in NOC2L

This is a list of pathogenic ClinVar variants found in the NOC2L region.

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

Position	Type	Phenotype	Significance	ClinVar
1-944710-A-C		not specified	Uncertain significance (Aug 27, 2024)
1-944711-G-T		not specified	Uncertain significance (Feb 28, 2024)
1-944729-C-G		not specified	Uncertain significance (Jan 31, 2025)
1-944732-C-T		not specified	Uncertain significance (Sep 27, 2024)
1-944779-G-C		not specified	Uncertain significance (Mar 03, 2022)
1-944781-C-G		not specified	Uncertain significance (Feb 08, 2025)
1-944786-C-T		not specified	Likely benign (Jan 19, 2022)
1-944788-T-A		not specified	Uncertain significance (Dec 01, 2023)
1-945072-T-C		not specified	Uncertain significance (Mar 02, 2023)
1-945076-C-G		not specified	Likely benign (Jan 19, 2024)
1-945094-G-C		not specified	Likely benign (Jan 03, 2025)
1-945099-C-T		not specified	Uncertain significance (Jan 22, 2025)
1-945103-A-G			Likely benign (Jul 01, 2022)
1-945123-G-A		not specified	Likely benign (Sep 28, 2022)
1-945536-C-T		not specified	Uncertain significance (May 03, 2023)
1-945540-G-A			Likely benign (Jul 01, 2022)
1-945564-G-A			Benign (Dec 31, 2019)
1-945572-G-A		not specified	Uncertain significance (Jan 15, 2025)
1-945587-T-C		not specified	Uncertain significance (Nov 08, 2022)
1-945611-C-T		not specified	Uncertain significance (Apr 07, 2023)
1-945625-T-C		not specified	Uncertain significance (Feb 06, 2024)
1-945633-A-C			Likely benign (Apr 01, 2023)
1-946207-C-T		not specified	Uncertain significance (Jan 04, 2025)
1-946213-C-T		not specified	Uncertain significance (Jan 03, 2024)
1-946238-A-T		not specified	Uncertain significance (Feb 22, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOC2L	protein_coding	protein_coding	ENST00000327044	19	15106

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.89e-29	0.0000528	125546	0	201	125747	0.000800

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.90	577	462	1.25	0.0000293	4856
Missense in Polyphen		140	135.62	1.0323		1490
Synonymous	-6.71	320	199	1.60	0.0000137	1471
Loss of Function	-0.174	43	41.8	1.03	0.00000215	447

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00112	0.00111
Ashkenazi Jewish	0.00428	0.00428
East Asian	0.000931	0.000925
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000830	0.000800
Middle Eastern	0.000931	0.000925
South Asian	0.000500	0.000490
Other	0.00133	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as an inhibitor of histone acetyltransferase activity; prevents acetylation of all core histones by the EP300/p300 histone acetyltransferase at p53/TP53-regulated target promoters in a histone deacetylases (HDAC)-independent manner. Acts as a transcription corepressor of p53/TP53- and TP63-mediated transactivation of the p21/CDKN1A promoter. Involved in the regulation of p53/TP53-dependent apoptosis. Associates together with TP63 isoform TA*-gamma to the p21/CDKN1A promoter. {ECO:0000269|PubMed:16322561, ECO:0000269|PubMed:20123734, ECO:0000269|PubMed:20959462}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Validated transcriptional targets of TAp63 isoforms;Regulation of TP53 Activity through Phosphorylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.887
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.27

Haploinsufficiency Scores

• pHI: 0.240
• hipred: Y
• hipred_score: 0.519
• ghis: 0.526

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.946

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Noc2l
• Phenotype: endocrine/exocrine gland phenotype; cellular 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); hematopoietic system phenotype; immune system phenotype

Zebrafish Information Network

• Gene name: noc2l
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;negative regulation of B cell apoptotic process;apoptotic process;chromatin assembly;cellular response to UV;negative regulation of histone acetylation;ribosomal large subunit biogenesis;regulation of signal transduction by p53 class mediator;negative regulation of intrinsic apoptotic signaling pathway
• Cellular component: nucleus;nucleoplasm;nucleolus;cytosol;Noc1p-Noc2p complex;Noc2p-Noc3p complex
• Molecular function: chromatin binding;transcription corepressor activity;RNA binding;protein binding;nucleosome binding;histone binding;repressing transcription factor binding