NOC2L

protein-coding

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

Gene summary

Histone modification by histone acetyltransferases (HAT) and histone deacetylases (HDAC) can control major aspects of transcriptional regulation. NOC2L represents a novel HDAC-independent inhibitor of histone acetyltransferase (INHAT) (Hublitz et al., 2005 [PubMed 16322561]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_015658.4

Inheritance

—

ClinVar variants

U:163B:22

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.03

Max pathogenic AF

—

Genomic locus

chr1:944,203-959,309

External References & Databases

Ensembl (ENSG00000188976)

Transcript & Mutation Effects

hg38 • Region Span ~15.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NOC2L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 163

not providedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015658.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	6 clinvar	5 clinvar	13
missense			157 clinvar	11 clinvar		168
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	163	17	5	185

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 151 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015658.4	RefSeq	NP_056473.3	19	MANE Select
ENST00000327044.7	Ensembl	ENSP00000317992.6	19	MANE Select
ENST00000870725.1	Ensembl	ENSP00000540784.1	19	Standard
ENST00000870725.2	Ensembl	ENSP00000540784.1	19	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
noc2l	Danio rerio	Structure: anatomical system Quality: quality abnormal

Gene / Model

Organism

Observed Phenotype

noc2l

Danio rerio

Structure: anatomical system

Quality: quality

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription
Validated transcriptional targets of TAp63 isoforms
Regulation of TP53 Activity through Phosphorylation

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

Molecular Function

chromatin binding
transcription corepressor activity
RNA binding
protein binding
nucleosome binding

Cellular Component

nucleus
nucleoplasm
nucleolus
cytosol
Noc1p-Noc2p complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000327044
Coding exons: 19
Length: 15106
Individuals with no LoFs: 125546
Homozygous LoFs: 0
Heterozygous LoFs: 201
Defined: 125747
p: 0.000800

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.90	577	462	1.25	0.0000293	4856
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00068	0.00068	rare
Latino/Admixed American	0.00043	0.00043	rare
Ashkenazi Jewish	0.0043	0.0043	notable
East Asian	0.00093	0.00092	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00083	0.00080	rare
South Asian	0.00050	0.00049	rare
Other	0.0013	0.0013	notable

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.139

Intolerance Scores

LoFtool: 0.887
RVIS EVS: 0.04
RVIS percentile EVS: 56.27

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.946

Gene Damage Prediction

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