NOCT

nocturnin

Basic information

Region (hg38): 4:139015780-139045939

Previous symbols: [ "CCRN4L" ]

Links

ENSG00000151014 ∙ NCBI:25819 ∙ OMIM:608468 ∙ HGNC:14254 ∙ Uniprot:Q9UK39 ∙ 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 NOCT gene.

• Inborn genetic diseases (9 variants)
• not provided (2 variants)

Variants pathogenicity by type

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

Variants in NOCT

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

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

Position	Type	Phenotype	Significance	ClinVar
4-139016013-C-T		not specified	Uncertain significance (Jul 06, 2021)
4-139016061-G-A		not specified	Uncertain significance (Jul 16, 2021)
4-139016156-T-G		not specified	Uncertain significance (Jan 03, 2022)
4-139016166-G-C		not specified	Uncertain significance (Sep 17, 2021)
4-139043197-T-C		not specified	Uncertain significance (Dec 28, 2022)
4-139043230-C-T		not specified	Uncertain significance (Dec 01, 2022)
4-139043286-G-C		not specified	Uncertain significance (Nov 10, 2022)
4-139043288-T-C			Benign (May 29, 2018)
4-139044674-C-T		not specified	Uncertain significance (Jun 02, 2023)
4-139044725-A-G		not specified	Uncertain significance (Jan 03, 2024)
4-139044899-C-T		not specified	Uncertain significance (Jun 29, 2023)
4-139044907-C-T			Likely benign (Apr 04, 2018)
4-139044947-G-A		not specified	Uncertain significance (May 09, 2023)
4-139045020-G-T		not specified	Uncertain significance (Feb 27, 2024)
4-139045025-G-A		not specified	Uncertain significance (Oct 12, 2021)
4-139045281-C-T		not specified	Uncertain significance (Oct 17, 2023)
4-139045297-G-T		not specified	Uncertain significance (Oct 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOCT	protein_coding	protein_coding	ENST00000280614	3	29964

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0421	0.952	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.896	170	206	0.824	0.0000107	2766
Missense in Polyphen		41	66.731	0.6144		815
Synonymous	-1.40	100	83.7	1.19	0.00000433	911
Loss of Function	2.43	5	15.3	0.328	9.89e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000706	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Circadian deadenylase which plays an important role in post-transcriptional regulation of metabolic genes under circadian control. Degrades poly(A) tails of specific target mRNAs leading to their degradation and suppression of translation. Exerts a rhythmic post-transcriptional control of genes necessary for metabolic functions including nutrient absorption, glucose/insulin sensitivity, lipid metabolism, adipogenesis, inflammation and osteogenesis. Plays an important role in favoring adipogenesis over osteoblastogenesis and acts as a key regulator of the adipogenesis/osteogenesis balance. Promotes adipogenesis by activating PPARG transcriptional activity in a deadenylase- independent manner by facilitating its nuclear translocation. Regulates circadian expression of NOS2 in the liver and negatively regulates the circadian expression of IGF1 in the bone. Critical for proper development of early embryos (By similarity). {ECO:0000250}.
• Pathway: BMAL1-CLOCK,NPAS2 activates circadian gene expression;Circadian Clock;BMAL1:CLOCK,NPAS2 activates circadian gene expression (Consensus)

Recessive Scores

• pRec: 0.172

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• pHI: 0.271
• hipred: Y
• hipred_score: 0.518
• ghis: 0.422

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Noct
• Phenotype: liver/biliary system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: deadenylation-dependent decapping of nuclear-transcribed mRNA;regulation of transcription, DNA-templated;transcription by RNA polymerase II;mRNA processing;circadian rhythm;response to extracellular stimulus;negative regulation of gene expression;response to lipopolysaccharide;circadian regulation of gene expression;cytoplasmic mRNA processing body assembly;regulation of circadian rhythm;positive regulation of fat cell differentiation;negative regulation of osteoblast differentiation;regulation of embryonic development;mRNA stabilization;RNA phosphodiester bond hydrolysis, exonucleolytic
• Cellular component: P-body;nucleus;nucleoplasm;cytoplasm;perinuclear region of cytoplasm
• Molecular function: DNA-binding transcription factor activity;mRNA binding;poly(A)-specific ribonuclease activity;metal ion binding