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

• spondyloepimetaphyseal dysplasia, Guo-Campeau type (Moderate), mode of inheritance: AR
• Hoxha-Aliu syndrome (Moderate), mode of inheritance: AR

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.

• not_specified (66 variants)
• not_provided (14 variants)
• ERI1-related_disorder (12 variants)
• Spondyloepimetaphyseal_dysplasia,_Guo-Campeau_type (7 variants)
• Hoxha-Aliu_syndrome (4 variants)
• See_cases (2 variants)
• Coarse_facial_features (1 variants)
• ERI1-associated_disorder (1 variants)
• Global_developmental_delay (1 variants)
• Unilateral_renal_agenesis (1 variants)
• Abnormal_finger_morphology (1 variants)

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. These statistics are base on transcript: NM_000153332.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				7	1	8
missense	1	5	67	3		76
nonsense		4	1			5
start loss						0
frameshift	1	1				2
splice donor/acceptor (+/-2bp)	1					1
Total	3	10	68	10	1

Highest pathogenic variant AF is 0.000016143895

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