DENR

density regulated re-initiation and release factor

Basic information

Region (hg38): 12:122752824-122771064

Links

ENSG00000139726 ∙ NCBI:8562 ∙ OMIM:604550 ∙ HGNC:2769 ∙ Uniprot:O43583 ∙ 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 DENR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DENR 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				2		2
missense			6	2		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				2		2
Total	0	0	6	6	0

Variants in DENR

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

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

Position	Type	Phenotype	Significance	ClinVar
12-122753700-A-C		DENR-related disorder	Likely benign (Mar 01, 2019)
12-122753750-C-T		not specified	Likely benign (Dec 16, 2022)
12-122753763-C-T		not specified	Uncertain significance (May 10, 2022)
12-122753766-A-C		DENR-related disorder	Likely benign (Dec 28, 2022)
12-122753777-G-T		not specified	Uncertain significance (Oct 12, 2021)
12-122753796-T-C		not specified	Uncertain significance (Feb 10, 2023)
12-122762178-C-T			Likely benign (Dec 26, 2018)
12-122762920-C-T		not specified	Uncertain significance (Sep 27, 2021)
12-122765356-G-A		DENR-related disorder	Likely benign (Jan 06, 2020)
12-122765359-A-C		not specified	Uncertain significance (Mar 31, 2023)
12-122765393-A-T		DENR-related disorder	Likely benign (May 21, 2019)
12-122767522-C-G		DENR-related disorder	Likely benign (Dec 28, 2022)
12-122767523-G-A		not specified	Uncertain significance (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DENR	protein_coding	protein_coding	ENST00000280557	7	18291

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.875	0.125	124386	0	3	124389	0.0000121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	48	90.3	0.532	0.00000416	1300
Missense in Polyphen		12	23.551	0.50952		378
Synonymous	0.549	25	28.7	0.870	0.00000143	334
Loss of Function	2.82	1	11.2	0.0895	5.38e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000654	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000179	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the translation of target mRNAs by scanning and recognition of the initiation codon. Involved in translation initiation; promotes recruitmnet of aminoacetyled initiator tRNA to P site of 40S ribosomes. Can promote release of deacylated tRNA and mRNA from recycled 40S subunits following ABCE1-mediated dissociation of post-termination ribosomal complexes into subunits. Plays a role in the modulation of the translational profile of a subset of cancer-related mRNAs when recruited to the translational initiation complex by the oncogene MCTS1. {ECO:0000269|PubMed:16982740, ECO:0000269|PubMed:17878526, ECO:0000269|PubMed:20713520}.

Recessive Scores

• pRec: 0.0910

Intolerance Scores

• loftool: 0.589
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.72

Haploinsufficiency Scores

• pHI: 0.0990
• hipred: Y
• hipred_score: 0.783
• ghis: 0.564

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Denr
• Phenotype: immune system phenotype; skeleton 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)

Gene ontology

• Biological process: formation of translation preinitiation complex;translation reinitiation;ribosome disassembly;IRES-dependent viral translational initiation
• Cellular component: cellular_component
• Molecular function: molecular_function;mRNA binding;translation initiation factor activity;protein binding