ERI1
protein-codingexoribonuclease 1, the group of Exonucleases|MicroRNA protein coding host genes
Gene summary
Enables 3'-5' exonuclease activity. Involved in maturation of 5.8S rRNA. Located in cytoplasm and nucleolus. [provided by Alliance of Genome Resources, Jul 2025]
- THEX1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~114.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0958006
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0958005
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0958006
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0958005
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Craniofacial; Musculoskeletal; Neurologic; Renal
Intervention: Cardiovascular; Renal
Rationale: Among other features, the condition can include cardiovascular anomalies and hydronephrosis with vesicoureteral reflux, and awareness may allow early diagnosis and management
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ERI1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_153332.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 10 | 1 | 11 | |||
| missense | 1 | 5 | 77 | 3 | 86 | |
| nonsense | 5 | 1 | 6 | |||
| start loss | 0 | |||||
| frameshift | 1 | 1 | 2 | |||
| splice donor/acceptor (+/-2bp) | 1 | 3 | 4 | |||
| Total | 3 | 11 | 81 | 13 | 1 | 109 |
Highest pathogenic variant AF is 0.000016143895
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_699163.2 | 7 | MANE Select | |
| Ensembl | ENSP00000250263.7 | 7 | MANE Select | |
| RefSeq | NP_001341564.1 | 6 | Standard | |
| RefSeq | NP_001341565.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- RNA interference
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
Molecular Function
- 3'-5'-exoribonuclease activity
- protein binding
- 3'-5' exonuclease activity
- rRNA binding
- ribosome binding
Cellular Component
- nucleus
- nucleoplasm
- nucleolus
- cytoplasm
- histone pre-mRNA 3'end processing complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000523898
- Coding exons
- 7
- Length
- 114600
- Individuals with no LoFs
- 125714
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 33
- Defined
- 125747
- p
- 0.000131
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.38 | 217 | 167 | 1.30 | 0.00000815 | 2300 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00018 | 0.00017 | rare |
| Ashkenazi Jewish | 0.00011 | 0.000099 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.00023 | 0.00023 | rare |
| European (Non-Finnish) | 0.00012 | 0.00012 | rare |
| South Asian | 0.00011 | 0.000098 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.0822
Intolerance Scores
- LoFtool
- 0.806
- RVIS EVS
- -0.16
- RVIS percentile EVS
- 41.91
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.705
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |