PUS7L
protein-codingpseudouridine synthase 7 like, the group of Pseudouridine synthases
Gene summary
Enables pseudouridine synthase activity. Involved in mRNA pseudouridine synthesis. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~39.8 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 PUS7L variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_031292.5. 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 | 0 | |||||
| missense | 86 | 3 | 89 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 90 | 3 | 0 | 93 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_112582.3 | 8 | MANE Select | |
| Ensembl | ENSP00000343081.5 | 8 | MANE Select | |
| RefSeq | NP_001092084.1 | 8 | Standard | |
| RefSeq | NP_001092085.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- pseudouridine synthesis
Molecular Function
- RNA binding
- protein binding
- pseudouridine synthase activity
Cellular Component
- nucleus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000416848
- Coding exons
- 8
- Length
- 30211
- Individuals with no LoFs
- 125588
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 160
- Defined
- 125748
- p
- 0.000636
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.201 | 367 | 356 | 1.03 | 0.0000172 | 4685 |
| Missense (PolyPhen) | 88 | 98.014 | 0.89783 | 1276 | ||
| Synonymous | 0.896 | 113 | 126 | 0.898 | 0.00000639 | 1255 |
| Loss of Function | 2.16 | 13 | 24.5 | 0.530 | 0.00000111 | 372 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0028 | 0.0026 | notable |
| Latino/Admixed American | 0.00027 | 0.00023 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0035 | 0.0033 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00017 | 0.00017 | rare |
| South Asian | 0.0010 | 0.00098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Pseudouridylate synthase that catalyzes pseudouridylation of RNAs. {ECO:0000250|UniProtKB:Q96PZ0}.;
Intolerance Scores
- LoFtool
- 0.991
- RVIS EVS
- 0.65
- RVIS percentile EVS
- 84.12
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0678
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |