ERI1

exoribonuclease 1, the group of Exonucleases|MicroRNA protein coding host genes

Basic information

Region (hg38): 8:9002147-9116746

Previous symbols: [ "THEX1" ]

Links

ENSG00000104626 ∙ NCBI:90459 ∙ OMIM:608739 ∙ HGNC:23994 ∙ Uniprot:Q8IV48 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spondyloepimetaphyseal dysplasia, Guo-Salian type	AR	Cardiovascular; Renal	Among other features, the condition can include cardiovascular anomalies and hydronephrosis with vesicoureteral reflux, and awareness may allow early diagnosis and management	Cardiovascular; Craniofacial; Musculoskeletal; Neurologic; Renal	36208065; 37352860

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ERI1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ERI1 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				5	2	7
missense		2	32	2	1	37
nonsense		2				2
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				4		4
non coding				3		3
Total	0	5	32	10	3

Variants in ERI1

This is a list of pathogenic ClinVar variants found in the ERI1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-9003073-C-T		not specified	Uncertain significance (Dec 07, 2021)
8-9003085-G-C		not specified	Likely benign (Dec 15, 2022)
8-9003091-G-T		not specified	Uncertain significance (May 23, 2023)
8-9003101-C-A		not specified	Uncertain significance (Sep 22, 2022)
8-9003110-T-C		ERI1-related disorder	Benign (Oct 16, 2019)
8-9003112-G-T		not specified	Uncertain significance (Aug 28, 2023)
8-9003113-C-A		not specified	Uncertain significance (Jul 25, 2023)
8-9003134-C-G		ERI1-related disorder	Likely benign (May 01, 2019)
8-9003168-C-G			Likely benign (Apr 01, 2022)
8-9007935-CTTTTTT-C		ERI1-related disorder	Likely benign (Mar 20, 2019)
8-9007935-CTTTTTTTTTTTTT-C		ERI1-related disorder	Likely benign (Aug 14, 2019)
8-9007961-T-G		ERI1-related disorder	Likely benign (Aug 20, 2018)
8-9007961-T-TTG			Likely benign (Dec 28, 2017)
8-9007980-A-C		not specified	Uncertain significance (Dec 19, 2022)
8-9008027-T-C		not specified • ERI1-related disorder	Uncertain significance (Aug 12, 2021)
8-9008034-C-A		not specified	Uncertain significance (Jun 28, 2023)
8-9008051-C-T		not specified	Uncertain significance (Mar 14, 2023)
8-9008052-C-A		not specified	Uncertain significance (Aug 04, 2023)
8-9008052-C-T		not specified	Uncertain significance (Mar 28, 2024)
8-9008076-C-T		not specified	Uncertain significance (Oct 26, 2022)
8-9008126-T-G		not specified	Uncertain significance (Dec 01, 2022)
8-9011581-T-C		ERI1-related disorder	Likely benign (Aug 06, 2019)
8-9011582-T-C		not specified	Uncertain significance (Aug 26, 2024)
8-9011583-A-G		not specified	Uncertain significance (Oct 06, 2022)
8-9011616-A-G			Likely benign (Nov 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ERI1	protein_coding	protein_coding	ENST00000523898	7	114600

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000119	0.833	125714	0	33	125747	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.38	217	167	1.30	0.00000815	2300
Missense in Polyphen		45	55.085	0.81692		700
Synonymous	-3.23	92	60.1	1.53	0.00000322	613
Loss of Function	1.35	10	15.8	0.633	7.63e-7	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000299	0.000299
Ashkenazi Jewish	0.000108	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000235	0.000231
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.000106	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA exonuclease that binds to the 3'-end of histone mRNAs and degrades them, suggesting that it plays an essential role in histone mRNA decay after replication. A 2' and 3'-hydroxyl groups at the last nucleotide of the histone 3'-end is required for efficient degradation of RNA substrates. Also able to degrade the 3'-overhangs of short interfering RNAs (siRNAs) in vitro, suggesting a possible role as regulator of RNA interference (RNAi). Requires for binding the 5'-ACCCA-3' sequence present in stem-loop structure. Able to bind other mRNAs. Required for 5.8S rRNA 3'-end processing. Also binds to 5.8s ribosomal RNA. Binds with high affinity to the stem-loop structure of replication- dependent histone pre-mRNAs. {ECO:0000269|PubMed:14536070, ECO:0000269|PubMed:16912046}.
• Pathway: RNA interference (Consensus)

Recessive Scores

• pRec: 0.0822

Intolerance Scores

• loftool: 0.806
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.197
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.705

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eri1
• 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); growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);DNA catabolic process, exonucleolytic;rRNA processing;gene silencing by RNA;rRNA 3'-end processing;histone mRNA catabolic process
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;histone pre-mRNA 3'end processing complex
• Molecular function: 3'-5'-exoribonuclease activity;protein binding;3'-5' exonuclease activity;rRNA binding;ribosome binding;metal ion binding;histone pre-mRNA stem-loop binding