ERN2

endoplasmic reticulum to nucleus signaling 2

Basic information

Region (hg38): 16:23690310-23713226

Links

ENSG00000134398 ∙ NCBI:10595 ∙ OMIM:604034 ∙ HGNC:16942 ∙ Uniprot:Q76MJ5 ∙ 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 ERN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ERN2 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	7	1	10
missense			24	1	1	26
nonsense			2			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	28	8	2

Variants in ERN2

This is a list of pathogenic ClinVar variants found in the ERN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-23690904-T-A		not specified	Uncertain significance (Feb 10, 2022)
16-23690953-G-A		not specified	Uncertain significance (Dec 28, 2022)
16-23691010-G-A		not specified	Uncertain significance (Apr 27, 2019)
16-23691019-C-T		not specified	Uncertain significance (Jan 23, 2023)
16-23691028-C-T		not specified	Uncertain significance (May 28, 2024)
16-23691187-T-G		not specified	Uncertain significance (May 09, 2023)
16-23691196-T-G		not specified	Uncertain significance (Oct 06, 2021)
16-23691422-C-T		not specified	Uncertain significance (Jan 10, 2023)
16-23692061-C-T		not specified	Uncertain significance (Aug 16, 2021)
16-23692225-G-A		not specified	Uncertain significance (Jun 22, 2021)
16-23694775-C-G		not specified	Uncertain significance (Apr 22, 2024)
16-23694785-G-T			Likely benign (Feb 26, 2018)
16-23694798-T-C		not specified	Uncertain significance (Sep 16, 2021)
16-23694871-G-A		not specified	Uncertain significance (Nov 29, 2023)
16-23695061-G-A		not specified	Uncertain significance (May 13, 2022)
16-23695116-G-A			Likely benign (Oct 01, 2022)
16-23695273-C-T		not specified	Uncertain significance (Aug 11, 2022)
16-23695947-G-A			Likely benign (Feb 12, 2018)
16-23695960-A-T		not specified	Uncertain significance (Dec 15, 2023)
16-23695973-G-T		not specified	Uncertain significance (Apr 08, 2024)
16-23700648-A-G			Benign (Feb 26, 2018)
16-23700679-T-C		not specified	Uncertain significance (Feb 07, 2023)
16-23701033-C-T		not specified	Uncertain significance (Dec 05, 2022)
16-23701084-C-T		not specified	Uncertain significance (Oct 25, 2022)
16-23702171-G-A		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ERN2	protein_coding	protein_coding	ENST00000256797	22	23175

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.18e-24	0.0407	125457	1	290	125748	0.00116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.295	587	567	1.03	0.0000332	6177
Missense in Polyphen		218	229.23	0.95103		2461
Synonymous	0.0807	242	244	0.993	0.0000144	2098
Loss of Function	1.38	42	52.8	0.795	0.00000305	526

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00161	0.00161
Ashkenazi Jewish	0.00	0.00
East Asian	0.00136	0.00136
Finnish	0.000232	0.000231
European (Non-Finnish)	0.00114	0.00111
Middle Eastern	0.00136	0.00136
South Asian	0.00262	0.00258
Other	0.00214	0.00212

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Induces translational repression through 28S ribosomal RNA cleavage in response to ER stress. Pro-apoptotic. Appears to play no role in the unfolded-protein response, unlike closely related proteins. {ECO:0000269|PubMed:11175748}.

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.989
• rvis_EVS: -1.7
• rvis_percentile_EVS: 2.58

Haploinsufficiency Scores

• pHI: 0.373
• hipred: N
• hipred_score: 0.266
• ghis: 0.497

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.140

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ern2
• Phenotype: immune system phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: mRNA processing;protein phosphorylation;cell cycle arrest;activation of JUN kinase activity;rRNA catabolic process;apoptotic chromosome condensation;endoplasmic reticulum unfolded protein response;response to endoplasmic reticulum stress;IRE1-mediated unfolded protein response;negative regulation of transcription, DNA-templated;intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress;RNA phosphodiester bond hydrolysis
• Cellular component: endoplasmic reticulum membrane;integral component of membrane;IRE1-TRAF2-ASK1 complex
• Molecular function: magnesium ion binding;endonuclease activity;endoribonuclease activity;ribonuclease activity;protein kinase activity;protein serine/threonine kinase activity;ATP binding;unfolded protein binding