GeneBe

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.

  • not_specified (147 variants)
  • not_provided (12 variants)

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. These statistics are base on transcript: NM_000015658.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
6
clinvar
5
clinvar
 11
missense
136
clinvar
11
clinvar
 147
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 136 17 5
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NOC2Lprotein_codingprotein_codingENST00000327044 1915106
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
2.89e-290.000052812554602011257470.000800
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.905774621.250.00002934856
Missense in Polyphen140135.621.03231490
Synonymous-6.713201991.600.00001371471
Loss of Function-0.1744341.81.030.00000215447

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001120.00111
Ashkenazi Jewish0.004280.00428
East Asian0.0009310.000925
Finnish0.00004620.0000462
European (Non-Finnish)0.0008300.000800
Middle Eastern0.0009310.000925
South Asian0.0005000.000490
Other0.001330.00130

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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