PRRC1
protein-codingproline rich coiled-coil 1
Gene summary
Predicted to enable protein kinase A regulatory subunit binding activity. Predicted to be involved in epithelial structure maintenance. Predicted to be located in Golgi apparatus. Predicted to be active in cytoplasm. [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 ~37.5 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 PRRC1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_130809.5. 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 | 2 | 1 | 3 | |||
| missense | 82 | 4 | 86 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 85 | 5 | 0 | 90 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_570721.1 | 8 | MANE Select | |
| Ensembl | ENSP00000296666.9 | 8 | MANE Select | |
| RefSeq | NP_001273737.1 | 9 | Standard | |
| Ensembl | ENSP00000392873.2 | 7 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| prrc1 | Danio rerio | Structure: cell Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- activation of protein kinase A activity
Molecular Function
- protein binding
- protein kinase A regulatory subunit binding
Cellular Component
- cytoplasm
- Golgi apparatus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000296666
- Coding exons
- 8
- Length
- 37481
- Individuals with no LoFs
- 125629
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 119
- Defined
- 125748
- p
- 0.000473
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0175 | 246 | 247 | 0.997 | 0.0000124 | 2821 |
| Missense (PolyPhen) | 60 | 76.214 | 0.78726 | 901 | ||
| Synonymous | 0.795 | 77 | 86.4 | 0.891 | 0.00000417 | 997 |
| Loss of Function | 0.0105 | 18 | 18.0 | 0.997 | 9.16e-7 | 212 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0011 | 0.0011 | notable |
| Latino/Admixed American | 0.00099 | 0.00098 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00047 | 0.00047 | rare |
| South Asian | 0.00023 | 0.00023 | rare |
| Other | 0.00099 | 0.00098 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0856
Intolerance Scores
- LoFtool
- 0.256
- RVIS EVS
- -0.91
- RVIS percentile EVS
- 9.96
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.501
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |