PAN3
protein-codingpoly(A) specific ribonuclease subunit PAN3
Gene summary
Contributes to poly(A)-specific ribonuclease activity. Involved in nuclear-transcribed mRNA poly(A) tail shortening. Part of PAN complex. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~156.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PAN3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_175854.8. 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 | 1 | 1 | ||||
| missense | 94 | 1 | 95 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 8 | 8 | ||||
| Total | 0 | 0 | 105 | 1 | 0 | 106 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_787050.6 | 19 | MANE Select | |
| Ensembl | ENSP00000370345.3 | 19 | MANE Select | |
| Ensembl | ENSP00000382522.1 | 17 | Standard | |
| Ensembl | ENSP00000583253.1 | 18 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- RNA degradation - Homo sapiens (human)
- Metabolism of RNA
- Deadenylation of mRNA
- Deadenylation-dependent mRNA decay
Biological Process
- nuclear-transcribed mRNA poly(A) tail shortening
- deadenylation-dependent decapping of nuclear-transcribed mRNA
- mRNA processing
- protein phosphorylation
- protein targeting
Molecular Function
- RNA binding
- poly(A)-specific ribonuclease activity
- protein kinase activity
- protein binding
- ATP binding
Cellular Component
- P-body
- cytosol
- PAN complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000380958
- Coding exons
- 19
- Length
- 156833
- Individuals with no LoFs
- 125507
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 125510
- p
- 0.0000120
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.52 | 285 | 432 | 0.659 | 0.0000214 | 5734 |
| Missense (PolyPhen) | 73 | 171.13 | 0.42657 | 2176 | ||
| Synonymous | 0.310 | 145 | 150 | 0.968 | 0.00000740 | 1783 |
| Loss of Function | 5.72 | 2 | 42.0 | 0.0477 | 0.00000243 | 507 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Regulatory subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in general and miRNA-mediated mRNA turnover. PAN specifically shortens poly(A) tails of RNA and the activity is stimulated by poly(A)-binding protein (PABP). PAN deadenylation is followed by rapid degradation of the shortened mRNA tails by the CCR4-NOT complex. Deadenylated mRNAs are then degraded by two alternative mechanisms, namely exosome-mediated 3'-5' exonucleolytic degradation, or deadenlyation-dependent mRNA decaping and subsequent 5'-3' exonucleolytic degradation by XRN1. PAN3 acts as a positive regulator for PAN activity, recruiting the catalytic subunit PAN2 to mRNA via its interaction with RNA and PABP, and to miRNA targets via its interaction with GW182 family proteins. {ECO:0000255|HAMAP-Rule:MF_03181, ECO:0000269|PubMed:14583602, ECO:0000269|PubMed:23932717}.;
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- RVIS EVS
- -0.49
- RVIS percentile EVS
- 22.65
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- H
- Indispensability pred.
- E
- Indispensability score
- 0.831
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |